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Cabral G, Moss WJ, Brown KM. Proteomic approaches for protein kinase substrate identification in Apicomplexa. Mol Biochem Parasitol 2024; 259:111633. [PMID: 38821187 PMCID: PMC11194964 DOI: 10.1016/j.molbiopara.2024.111633] [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: 03/30/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Apicomplexa is a phylum of protist parasites, notable for causing life-threatening diseases including malaria, toxoplasmosis, cryptosporidiosis, and babesiosis. Apicomplexan pathogenesis is generally a function of lytic replication, dissemination, persistence, host cell modification, and immune subversion. Decades of research have revealed essential roles for apicomplexan protein kinases in establishing infections and promoting pathogenesis. Protein kinases modify their substrates by phosphorylating serine, threonine, tyrosine, or other residues, resulting in rapid functional changes in the target protein. Post-translational modification by phosphorylation can activate or inhibit a substrate, alter its localization, or promote interactions with other proteins or ligands. Deciphering direct kinase substrates is crucial to understand mechanisms of kinase signaling, yet can be challenging due to the transient nature of kinase phosphorylation and potential for downstream indirect phosphorylation events. However, with recent advances in proteomic approaches, our understanding of kinase function in Apicomplexa has improved dramatically. Here, we discuss methods that have been used to identify kinase substrates in apicomplexan parasites, classifying them into three main categories: i) kinase interactome, ii) indirect phosphoproteomics and iii) direct labeling. We briefly discuss each approach, including their advantages and limitations, and highlight representative examples from the Apicomplexa literature. Finally, we conclude each main category by introducing prospective approaches from other fields that would benefit kinase substrate identification in Apicomplexa.
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Affiliation(s)
- Gabriel Cabral
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - William J Moss
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin M Brown
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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2
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Zibrova D, Ernst T, Hochhaus A, Heller R. The BCR::ABL1 tyrosine kinase inhibitors ponatinib and nilotinib differentially affect endothelial angiogenesis and signalling. Mol Cell Biochem 2024:10.1007/s11010-024-05070-5. [PMID: 39009935 DOI: 10.1007/s11010-024-05070-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024]
Abstract
BCR::ABL1 inhibitors, the treatment of choice for the majority of patients with chronic myeloid leukaemia (CML), can cause vascular side effects that vary between agents. The exact underlying mechanisms are still poorly understood, but the vascular endothelium has been proposed as a site of origin. The present study investigates the effects of three BCR::ABL1 inhibitors, ponatinib, nilotinib and imatinib, on angiogenesis and signalling in human endothelial cells in response to vascular endothelial growth factor (VEGF). The experiments were performed in endothelial cells isolated from human umbilical veins. After exposure to imatinib, ponatinib and nilotinib, the angiogenic capacity of endothelial cells was assessed in spheroid assays. VEGF-induced signalling pathways were examined in Western blotting experiments using different specific antibodies. RNAi technology was used to downregulate proteins of interest. Intracellular cGMP levels were measured by ELISA. Imatinib had no effect on endothelial function. Ponatinib inhibited VEGF-induced sprouting, while nilotinib increased spontaneous and VEGF-stimulated angiogenesis. These effects did not involve wild-type ABL1 or ABL2, as siRNA-mediated knockdown of these kinases did not affect angiogenesis and VEGF signalling. Consistent with their effects on sprouting, ponatinib and nilotinib affected angiogenic pathways in opposite directions. While ponatinib inhibited VEGF-induced signalling and cGMP formation, nilotinib activated angiogenic signalling, in particular phosphorylation of extracellular signal-regulated kinase 1/2 (Erk1/2). The latter occurred in an epidermal growth factor receptor (EGFR)-dependent manner possibly via suppressing Fyn-related kinase (FRK), a negative regulator of EGFR signalling. Both, pharmacological inhibition of Erk1/2 or EGFR suppressed nilotinib-induced angiogenic sprouting. These results support the notion that the vascular endothelium is a site of action of BCR::ABL1 inhibitors from which side effects may arise, and that the different vascular toxicity profiles of BCR::ABL1 inhibitors may be due to their different actions at the molecular level. In addition, the as yet unknown pro-angiogenic effect of nilotinib should be considered in the treatment of patients with comorbidities associated with pathological angiogenesis, such as ocular disease, arthritis or obesity.
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Affiliation(s)
- Darya Zibrova
- Center for Molecular Biomedicine, Institute of Molecular Cell Biology, Jena University Hospital, Hans-Knöll-Straße 2, 07745, Jena, Germany
| | - Thomas Ernst
- Department of Hematology and Oncology, Jena University Hospital, Jena, Germany
| | - Andreas Hochhaus
- Department of Hematology and Oncology, Jena University Hospital, Jena, Germany
| | - Regine Heller
- Center for Molecular Biomedicine, Institute of Molecular Cell Biology, Jena University Hospital, Hans-Knöll-Straße 2, 07745, Jena, Germany.
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3
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Ribeuz HL, Willer ASM, Chevalier B, Sancho M, Masson B, Eyries M, Jung V, Guerrera IC, Dutheil M, Jekmek KE, Laubry L, Carpentier G, Perez-Vizcaino F, Tu L, Guignabert C, Chaumais MC, Péchoux C, Humbert M, Hinzpeter A, Mercier O, Capuano V, Montani D, Antigny F. Role of KCNK3 Dysfunction in Dasatinib-associated Pulmonary Arterial Hypertension and Endothelial Cell Dysfunction. Am J Respir Cell Mol Biol 2024; 71:95-109. [PMID: 38546978 DOI: 10.1165/rcmb.2023-0185oc] [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: 05/23/2023] [Accepted: 03/27/2024] [Indexed: 07/02/2024] Open
Abstract
Pulmonary arterial (PA) hypertension (PAH) is a severe cardiopulmonary disease that may be triggered by exposure to drugs such as dasatinib or facilitated by genetic predispositions. The incidence of dasatinib-associated PAH is estimated at 0.45%, suggesting individual predispositions. The mechanisms of dasatinib-associated PAH are still incomplete. We discovered a KCNK3 gene (Potassium channel subfamily K member 3; coding for outward K+ channel) variant in a patient with dasatinib-associated PAH and investigated the impact of this variant on KCNK3 function. Additionally, we assessed the effects of dasatinib exposure on KCNK3 expression. In control human PA smooth muscle cells (hPASMCs) and human pulmonary endothelial cells (hPECs), we evaluated the consequences of KCNK3 knockdown on cell migration, mitochondrial membrane potential, ATP production, and in vitro tube formation. Using mass spectrometry, we determined the KCNK3 interactome. Patch-clamp experiments revealed that the KCNK3 variant represents a loss-of-function variant. Dasatinib contributed to PA constriction by decreasing KCNK3 function and expression. In control hPASMCs, KCNK3 knockdown promotes mitochondrial membrane depolarization and glycolytic shift. Dasatinib exposure or KCNK3 knockdown reduced the number of caveolae in hPECs. Moreover, KCNK3 knockdown in control hPECs reduced migration, proliferation, and in vitro tubulogenesis. Using proximity labeling and mass spectrometry, we identified the KCNK3 interactome, revealing that KCNK3 interacts with various proteins across different cellular compartments. We identified a novel pathogenic variant in KCNK3 and showed that dasatinib downregulates KCNK3, emphasizing the relationship between dasatinib-associated PAH and KCNK3 dysfunction. We demonstrated that a loss of KCNK3-dependent signaling contributes to endothelial dysfunction in PAH and glycolytic switch of hPASMCs.
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Affiliation(s)
- Hélène Le Ribeuz
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Anaïs Saint-Martin Willer
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Benoit Chevalier
- Paris Cité University, CNRS, INSERM, Institut Necker Enfants Malades-INEM, Paris, France
| | - Maria Sancho
- Department of Physiology and
- Department of Pharmacology, University of Vermont, Burlington, Vermont
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Bastien Masson
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Mélanie Eyries
- Genetics Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Vincent Jung
- INSERM US24/CNRS UAR3633, Proteomic Platform Necker, Université Paris Cité-Federative Research Structure Necker, Paris, France
| | - Ida Chiara Guerrera
- INSERM US24/CNRS UAR3633, Proteomic Platform Necker, Université Paris Cité-Federative Research Structure Necker, Paris, France
| | - Mary Dutheil
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Kristelle El Jekmek
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Loann Laubry
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Gilles Carpentier
- Gly-CRRET Research Unit 4397, Paris-Est Créteil University, Créteil, France
| | - Francisco Perez-Vizcaino
- Department of Pharmacology and Toxicology, Faculty of Medicine, University Complutense of Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Ciber Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ly Tu
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Christophe Guignabert
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Marie-Camille Chaumais
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
- Paris-Saclay University, Faculty of Pharmacy, Orsay, France
- Department of Respiratory and Intensive Care Medicine, Pulmonary Hypertension National Referral Center, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Christine Péchoux
- Paris-Saclay University, INRAE, AgroparisTech, GABI, Jouy-en-Josas, France
| | - Marc Humbert
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
- Department of Respiratory and Intensive Care Medicine, Pulmonary Hypertension National Referral Center, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Alexandre Hinzpeter
- Paris Cité University, CNRS, INSERM, Institut Necker Enfants Malades-INEM, Paris, France
| | - Olaf Mercier
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
- Department of Thoracic and Vascular Surgery and Heart-Lung Transplantation, Groupe Hospitalier Paris Saint-Joseph-Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - Véronique Capuano
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
| | - David Montani
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
- Department of Respiratory and Intensive Care Medicine, Pulmonary Hypertension National Referral Center, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Fabrice Antigny
- Paris-Saclay University, Faculty of Medecine, Le Kremlin-Bicêtre, France
- INSERM UMR_S 999 Pulmonary Hypertension: Pathophysiology and Novel Therapies, Marie Lannelongue Hospital, Le Plessis-Robinson, France
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4
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Adebayo AK, Bhat-Nakshatri P, Davis C, Angus SP, Erdogan C, Gao H, Green N, Kumar B, Liu Y, Nakshatri H. Oxygen tension-dependent variability in the cancer cell kinome impacts signaling pathways and response to targeted therapies. iScience 2024; 27:110068. [PMID: 38872973 PMCID: PMC11170190 DOI: 10.1016/j.isci.2024.110068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/05/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Most cells in solid tumors are exposed to oxygen levels between 0.5% and 5%. We developed an approach that allows collection, processing, and evaluation of cancer and non-cancer cells under physioxia, while preventing exposure to ambient air. This aided comparison of baseline and drug-induced changes in signaling pathways under physioxia and ambient oxygen. Using tumor cells from transgenic models of breast cancer and cells from breast tissues of clinically breast cancer-free women, we demonstrate oxygen-dependent differences in cell preference for epidermal growth factor receptor (EGFR) or platelet-derived growth factor receptor beta (PDGFRβ) signaling. Physioxia caused PDGFRβ-mediated activation of AKT and extracellular regulated kinase (ERK) that reduced sensitivity to EGFR and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) inhibition and maintained PDGFRβ+ epithelial-mesenchymal hybrid cells with potential cancer stem cell (CSC) properties. Cells in ambient air displayed differential EGFR activation and were more sensitive to targeted therapies. Our data emphasize the importance of oxygen considerations in preclinical cancer research to identify effective drug targets and develop combination therapy regimens.
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Affiliation(s)
- Adedeji K. Adebayo
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Christopher Davis
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Steven P. Angus
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Cihat Erdogan
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nick Green
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brijesh Kumar
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Roudebush VA Medical Center, Indianapolis, IN 46202, USA
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5
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Gualdrini F, Rizzieri S, Polletti S, Pileri F, Zhan Y, Cuomo A, Natoli G. An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors. Mol Syst Biol 2024; 20:626-650. [PMID: 38724853 PMCID: PMC11148061 DOI: 10.1038/s44320-024-00040-x] [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: 10/28/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 06/05/2024] Open
Abstract
More than 500 kinases are implicated in the control of most cellular process in mammals, and deregulation of their activity is linked to cancer and inflammatory disorders. 80 clinical kinase inhibitors (CKIs) have been approved for clinical use and hundreds are in various stages of development. However, CKIs inhibit other kinases in addition to the intended target(s), causing both enhanced clinical effects and undesired side effects that are only partially predictable based on in vitro selectivity profiling. Here, we report an integrative approach grounded on the use of chromatin modifications as unbiased, information-rich readouts of the functional effects of CKIs on macrophage activation. This approach exceeded the performance of transcriptome-based approaches and allowed us to identify similarities and differences among CKIs with identical intended targets, to recognize novel CKI specificities and to pinpoint CKIs that may be repurposed to control inflammation, thus supporting the utility of this strategy to improve selection and use of CKIs in clinical settings.
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Affiliation(s)
- Francesco Gualdrini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy.
| | - Stefano Rizzieri
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Francesco Pileri
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy.
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6
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van Outersterp I, Tasian SK, Reichert CEJ, Boeree A, de Groot-Kruseman HA, Escherich G, Boer JM, den Boer ML. Tyrosine kinase inhibitor response of ABL-class acute lymphoblastic leukemia: the role of kinase type and SH3 domain. Blood 2024; 143:2178-2189. [PMID: 38394665 PMCID: PMC11143520 DOI: 10.1182/blood.2023023120] [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: 11/01/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
ABSTRACT Acute lymphoblastic leukemia (ALL) with fusions of ABL-class tyrosine kinase genes other than BCR::ABL1 occurs in ∼3% of children with ALL. The tyrosine kinase genes involved in this BCR::ABL1-like (Ph-like) subtype include ABL1, PDGFRB, ABL2, and CSF1R, each of which has up to 10 described partner genes. ABL-class ALL resembles BCR::ABL1-positive ALL with a similar gene expression profile, poor response to chemotherapy, and sensitivity to tyrosine kinase inhibitors (TKIs). There is a lack of comprehensive data regarding TKI sensitivity in the heterogeneous group of ABL-class ALL. We observed variability in TKI sensitivity within and among each ABL-class tyrosine kinase gene subgroup. We showed that ALL samples with fusions for any of the 4 tyrosine kinase genes were relatively sensitive to imatinib. In contrast, the PDGFRB-fused ALL samples were less sensitive to dasatinib and bosutinib. Variation in ex vivo TKI response within the subset of samples with the same ABL-class tyrosine kinase gene was not associated with the ALL immunophenotype, 5' fusion partner, presence or absence of Src-homology-2/3 domains, or deletions of IKZF1, PAX5, or CDKN2A/B. In conclusion, the tyrosine kinase gene involved in ABL-class ALL is the main determinant of TKI sensitivity and relevant for specific TKI selection.
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Affiliation(s)
| | - Sarah K Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Aurélie Boeree
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Gabriele Escherich
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology and Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
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7
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Reinecke M, Brear P, Vornholz L, Berger BT, Seefried F, Wilhelm S, Samaras P, Gyenis L, Litchfield DW, Médard G, Müller S, Ruland J, Hyvönen M, Wilhelm M, Kuster B. Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Nat Chem Biol 2024; 20:577-585. [PMID: 37904048 PMCID: PMC11062922 DOI: 10.1038/s41589-023-01459-3] [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] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/22/2023] [Indexed: 11/01/2023]
Abstract
Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Compounds targeting PKN3 were discovered and phosphoproteomics identified substrates that indicate target engagement in cells. We anticipate that this molecular resource will aid research in drug discovery and chemical biology.
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Affiliation(s)
- Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Larsen Vornholz
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Benedict-Tilmann Berger
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Florian Seefried
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David William Litchfield
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Jürgen Ruland
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
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8
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Veth TS, Nouwen LV, Zwaagstra M, Lyoo H, Wierenga KA, Westendorp B, Altelaar MAFM, Berkers C, van Kuppeveld FJM, Heck AJR. Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection. Mol Cell Proteomics 2024; 23:100757. [PMID: 38556169 PMCID: PMC11067349 DOI: 10.1016/j.mcpro.2024.100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/16/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Picornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a proteome-wide overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the kinase activity landscape during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays covering ∼40% of the human kinome. Our data show that upon infection, kinases of the MAPK pathways become activated (e.g., ERK1/2, RSK1/2, JNK1/2/3, and p38), while kinases involved in regulating the cell cycle (e.g., CDK1/2, GWL, and DYRK3) become inactivated. Additionally, we observed the activation of CHK2, an important kinase involved in the DNA damage response. Using pharmacological kinase inhibitors, we demonstrate that several of these activated kinases are essential for the replication of encephalomyocarditis virus. Altogether, the data provide a quantitative understanding of the regulation of kinome activity induced by picornavirus infection, providing a resource important for developing novel antiviral therapeutic interventions.
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Affiliation(s)
- Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Lonneke V Nouwen
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Heyrhyoung Lyoo
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Kathryn A Wierenga
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Bart Westendorp
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Celia Berkers
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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9
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Hanswillemenke A, Hofacker DT, Sorgenfrei M, Fruhner C, Franz-Wachtel M, Schwarzer D, Maček B, Stafforst T. Profiling the interactome of oligonucleotide drugs by proximity biotinylation. Nat Chem Biol 2024; 20:555-565. [PMID: 38233583 PMCID: PMC11062921 DOI: 10.1038/s41589-023-01530-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
Drug-ID is a novel method applying proximity biotinylation to identify drug-protein interactions inside living cells. The covalent conjugation of a drug with a biotin ligase enables targeted biotinylation and identification of the drug-bound proteome. We established Drug-ID for two small-molecule drugs, JQ1 and SAHA, and applied it for RNaseH-recruiting antisense oligonucleotides (ASOs). Drug-ID profiles the drug-protein interactome de novo under native conditions, directly inside living cells and at pharmacologically effective drug concentrations. It requires minimal amounts of cell material and might even become applicable in vivo. We studied the dose-dependent aggregation of ASOs and the effect of different wing chemistries (locked nucleic acid, 2'-methoxyethyl and 2'-Fluoro) and ASO lengths on the interactome. Finally, we demonstrate the detection of stress-induced, intracellular interactome changes (actinomycin D treatment) with an in situ variant of the approach, which uses a recombinant biotin ligase and does not require genetic manipulation of the target cell.
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Affiliation(s)
| | | | - Michèle Sorgenfrei
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Carolin Fruhner
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Boris Maček
- Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University of Tübingen, Tübingen, Germany.
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10
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El-Damasy AK, Kim HJ, Al-Karmalawy AA, Alnajjar R, Khalifa MM, Bang EK, Keum G. Identification of Ureidocoumarin-Based Selective Discoidin Domain Receptor 1 (DDR1) Inhibitors via Drug Repurposing Approach, Biological Evaluation, and In Silico Studies. Pharmaceuticals (Basel) 2024; 17:427. [PMID: 38675389 PMCID: PMC11054573 DOI: 10.3390/ph17040427] [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: 02/14/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Discoidin domain receptor 1 (DDR1) kinase has emerged as a promising target for cancer therapy, and selective DDR1 inhibitors have shown promise as effective therapeutic candidates. Herein, we have identified the first coumarin-based selective DDR1 inhibitors via repurposing of a recent series of carbonic anhydrase inhibitors. Among these, ureidocoumarins 3a, 3i, and 3q showed the best DDR1 inhibitory activities. The m-trifluoromethoxy phenyl member 3q potently inhibited DDR1 with an IC50 of 191 nM, while it showed less inhibitory activity against DDR2 (IC50 = 5080 nM). 3q also exhibited favorable selectivity in a screening platform with 23 common off-target kinases, including BCR-ABL. In the cellular context, 3q showed moderate antiproliferative effects, while 3i, with the third rank in DDR1 inhibition, exerted the best anticancer activity with sub-micromolar GI50 values over certain DDR1-dependent cell lines. Molecular docking and MD simulations disclosed the putative binding mode of this coumarin chemotype and provided insights for further optimization of this scaffold. The present findings collectively supported the potential improvement of ureidocoumarins 3i and 3q for cancer treatment.
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Affiliation(s)
- Ashraf K. El-Damasy
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Hyun Ji Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt;
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City 12566, Egypt
| | - Radwan Alnajjar
- CADD Unit, Faculty of Pharmacy, Libyan International Medical University, Benghazi 16063, Libya;
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi 16063, Libya
- Department of Chemistry, University of Cape Town, Rondebosch 7700, South Africa
| | - Mohamed M. Khalifa
- Department of Pharmaceutical Medicinal Chemistry & Drug Design, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Eun-Kyoung Bang
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Gyochang Keum
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
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11
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Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer MP, Rye MB, Droit A, Bruheim P, Otterlei M. SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front Microbiol 2024; 15:1373344. [PMID: 38596376 PMCID: PMC11002266 DOI: 10.3389/fmicb.2024.1373344] [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: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at the cost of mutagenesis. The SOS response first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions, and a low dose of the antibiotic ciprofloxacin was used to activate the SOS response while avoiding extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics and a sub-proteomics approach termed signalomics, we found that the temporal segregation of error-free and error-prone repair is primarily regulated after transcription, supporting the current literature. Furthermore, the heterology index (i.e., the binding affinity of LexA to the SOS box) was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed increasing pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.
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Affiliation(s)
| | - Amanda Holstad Singleton
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lisa Marie Røst
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Antoine Bodein
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Morten Beck Rye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Arnaud Droit
- Department of Molecular Medicine, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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12
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Yoshida A, Ohtsuka S, Matsumoto F, Miyagawa T, Okino R, Ikeda Y, Tada N, Gotoh A, Magari M, Hatano N, Morishita R, Satoh A, Sunatsuki Y, Nilsson UJ, Ishikawa T, Tokumitsu H. Development of a novel AAK1 inhibitor via Kinobeads-based screening. Sci Rep 2024; 14:6723. [PMID: 38509168 PMCID: PMC10954696 DOI: 10.1038/s41598-024-57051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/13/2024] [Indexed: 03/22/2024] Open
Abstract
A chemical proteomics approach using Ca2+/calmodulin-dependent protein kinase kinase (CaMKK) inhibitor-immobilized sepharose (TIM-063-Kinobeads) identified main targets such as CaMKKα/1 and β/2, and potential off-target kinases, including AP2-associated protein kinase 1 (AAK1), as TIM-063 interactants. Because TIM-063 interacted with the AAK1 catalytic domain and inhibited its enzymatic activity moderately (IC50 = 8.51 µM), we attempted to identify potential AAK1 inhibitors from TIM-063-derivatives and found a novel AAK1 inhibitor, TIM-098a (11-amino-2-hydroxy-7H-benzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one) which is more potent (IC50 = 0.24 µM) than TIM-063 without any inhibitory activity against CaMKK isoforms and a relative AAK1-selectivity among the Numb-associated kinases family. TIM-098a could inhibit AAK1 activity in transfected cultured cells (IC50 = 0.87 µM), indicating cell-membrane permeability of the compound. Overexpression of AAK1 in HeLa cells significantly reduced the number of early endosomes, which was blocked by treatment with 10 µM TIM-098a. These results indicate TIM-063-Kinobeads-based chemical proteomics is efficient for identifying off-target kinases and re-evaluating the kinase inhibitor (TIM-063), leading to the successful development of a novel inhibitory compound (TIM-098a) for AAK1, which could be a molecular probe for AAK1. TIM-098a may be a promising lead compound for a more potent, selective and therapeutically useful AAK1 inhibitor.
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Affiliation(s)
- Akari Yoshida
- Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Satomi Ohtsuka
- Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Fumiya Matsumoto
- Department of Science Education, Graduate School of Education, Okayama University, Okayama, 700-8530, Japan
| | - Tomoyuki Miyagawa
- Department of Science Education, Graduate School of Education, Okayama University, Okayama, 700-8530, Japan
| | - Rei Okino
- Department of Science Education, Graduate School of Education, Okayama University, Okayama, 700-8530, Japan
| | - Yumeya Ikeda
- Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Natsume Tada
- Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Akira Gotoh
- Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Masaki Magari
- Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Naoya Hatano
- Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Ryo Morishita
- CellFree Sciences Co. Ltd, Matsuyama, 790-8577, Japan
| | - Ayano Satoh
- Organelle Systems Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Yukinari Sunatsuki
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Ulf J Nilsson
- Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden
| | - Teruhiko Ishikawa
- Department of Science Education, Graduate School of Education, Okayama University, Okayama, 700-8530, Japan.
| | - Hiroshi Tokumitsu
- Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan.
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13
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Islam S, Gour J, Beer T, Tang HY, Cassel J, Salvino JM, Busino L. A Tandem-Affinity Purification Method for Identification of Primary Intracellular Drug-Binding Proteins. ACS Chem Biol 2024; 19:233-242. [PMID: 38271588 PMCID: PMC10878392 DOI: 10.1021/acschembio.3c00570] [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: 09/14/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
In the field of drug discovery, understanding how small molecule drugs interact with cellular components is crucial. Our study introduces a novel methodology to uncover primary drug targets using Tandem Affinity Purification for identification of Drug-Binding Proteins (TAP-DBP). Central to our approach is the generation of a FLAG-hemagglutinin (HA)-tagged chimeric protein featuring the FKBP12(F36V) adaptor protein and the TurboID enzyme. Conjugation of drug molecules with the FKBP12(F36V) ligand allows for the coordinated recruitment of drug-binding partners effectively enabling in-cell TurboID-mediated biotinylation. By employing a tandem affinity purification protocol based on FLAG-immunoprecipitation and streptavidin pulldown, alongside mass spectrometry analysis, TAP-DBP allows for the precise identification of drug-primary binding partners. Overall, this study introduces a systematic, unbiased method for identification of drug-protein interactions, contributing a clear understanding of target engagement and drug selectivity to advance the mode of action of a drug in cells.
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Affiliation(s)
- Sehbanul Islam
- University
of Pennsylvania, Perelman School
of Medicine, Department of Cancer Biology, Philadelphia, Pennsylvania 19104, United States
| | - Jitendra Gour
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Thomas Beer
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Hsin-Yao Tang
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Joel Cassel
- Molecular
Screening and Protein Expression Shared Resource, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Joseph M. Salvino
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Luca Busino
- University
of Pennsylvania, Perelman School
of Medicine, Department of Cancer Biology, Philadelphia, Pennsylvania 19104, United States
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14
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Gao Y, Ma M, Li W, Lei X. Chemoproteomics, A Broad Avenue to Target Deconvolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305608. [PMID: 38095542 PMCID: PMC10885659 DOI: 10.1002/advs.202305608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/29/2023] [Indexed: 12/22/2023]
Abstract
As a vital project of forward chemical genetic research, target deconvolution aims to identify the molecular targets of an active hit compound. Chemoproteomics, either with chemical probe-facilitated target enrichment or probe-free, provides a straightforward and effective approach to profile the target landscape and unravel the mechanisms of action. Canonical methods rely on chemical probes to enable target engagement, enrichment, and identification, whereas click chemistry and photoaffinity labeling techniques improve the efficiency, sensitivity, and spatial accuracy of target recognition. In comparison, recently developed probe-free methods detect protein-ligand interactions without the need to modify the ligand molecule. This review provides a comprehensive overview of different approaches and recent advancements for target identification and highlights the significance of chemoproteomics in investigating biological processes and advancing drug discovery processes.
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Affiliation(s)
- Yihui Gao
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Mingzhe Ma
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Wenyang Li
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
- Institute for Cancer ResearchShenzhen Bay LaboratoryShenzhenChina
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15
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Meng Y, Iyamu ID, Ahmed NAM, Huang R. Comparative Analysis of Two NNMT Bisubstrate Inhibitors through Chemoproteomic Studies: Uncovering the Role of Unconventional SAM Analogue Moiety for Improved Selectivity. ACS Chem Biol 2024; 19:89-100. [PMID: 38181447 DOI: 10.1021/acschembio.3c00531] [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: 01/07/2024]
Abstract
Unconventional S-adenosyl-L-methionine (SAM) mimics with enhanced hydrophobicity are an adaptable building block to develop cell-potent inhibitors for SAM-dependent methyltransferases as targeted therapeutics. We recently discovered cell-potent bisubstrate inhibitors for nicotinamide N-methyltransferase (NNMT) by using an unconventional SAM mimic. To delve into the selectivity implications of the unconventional SAM mimic, we employed a chemoproteomic approach to assess two potent NNMT inhibitors LL320 (Ki, app = 6.8 nM) and II399 (containing an unconventional SAM mimic, Ki, app = 5.9 nM) within endogenous proteomes. Our work began with the rational design and synthesis of immobilized probes 1 and 2, utilizing LL320 and II399 as parent compounds. Systematic analysis of protein networks associated with these probes revealed a comprehensive landscape. Notably, NNMT emerged as the top-ranking hit, substantiating the high selectivity of both inhibitors. Meanwhile, we identified additional interacting proteins for LL320 (38) and II399 (17), showcasing the intricate selectivity profiles associated with these compounds. Subsequent experiments confirmed LL320's interactions with RNMT, DPH5, and SAHH, while II399 exhibited interactions with SHMT2 and MEPCE. Importantly, incorporating the unconventional SAM mimic in II399 led to improved selectivity compared to LL320. Our findings underscore the importance of selectivity profiling and validate the utilization of the unconventional SAM mimic as a viable strategy to create highly selective and cell-permeable inhibitors for SAM-dependent methyltransferases.
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Affiliation(s)
- Ying Meng
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Iredia D Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Noha A M Ahmed
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
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16
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Saltzman AB, Chan DW, Holt MV, Wang J, Jaehnig EJ, Anurag M, Singh P, Malovannaya A, Kim BJ, Ellis MJ. Kinase inhibitor pulldown assay (KiP) for clinical proteomics. Clin Proteomics 2024; 21:3. [PMID: 38225548 PMCID: PMC10790396 DOI: 10.1186/s12014-023-09448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/07/2023] [Indexed: 01/17/2024] Open
Abstract
Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential. For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method. Data are available via ProteomeXchange with identifiers PXD044655 and PXD046169.
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Affiliation(s)
- Alexander B Saltzman
- Mass Spectrometry Proteomics Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX, USA
| | - Doug W Chan
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Matthew V Holt
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Junkai Wang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Purba Singh
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Johnson & Johnson, Springhouse, PA, USA
| | - Anna Malovannaya
- Mass Spectrometry Proteomics Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- AstraZeneca, Gaithersburg, MD, 20878, USA.
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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17
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Janda E, Boutin JA, De Lorenzo C, Arbitrio M. Polymorphisms and Pharmacogenomics of NQO2: The Past and the Future. Genes (Basel) 2024; 15:87. [PMID: 38254976 PMCID: PMC10815803 DOI: 10.3390/genes15010087] [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: 11/30/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The flavoenzyme N-ribosyldihydronicotinamide (NRH):quinone oxidoreductase 2 (NQO2) catalyzes two-electron reductions of quinones. NQO2 contributes to the metabolism of biogenic and xenobiotic quinones, including a wide range of antitumor drugs, with both toxifying and detoxifying functions. Moreover, NQO2 activity can be inhibited by several compounds, including drugs and phytochemicals such as flavonoids. NQO2 may play important roles that go beyond quinone metabolism and include the regulation of oxidative stress, inflammation, and autophagy, with implications in carcinogenesis and neurodegeneration. NQO2 is a highly polymorphic gene with several allelic variants, including insertions (I), deletions (D) and single-nucleotide (SNP) polymorphisms located mainly in the promoter, but also in other regulatory regions and exons. This is the first systematic review of the literature reporting on NQO2 gene variants as risk factors in degenerative diseases or drug adverse effects. In particular, hypomorphic 29 bp I alleles have been linked to breast and other solid cancer susceptibility as well as to interindividual variability in response to chemotherapy. On the other hand, hypermorphic polymorphisms were associated with Parkinson's and Alzheimer's disease. The I and D promoter variants and other NQO2 polymorphisms may impact cognitive decline, alcoholism and toxicity of several nervous system drugs. Future studies are required to fill several gaps in NQO2 research.
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Affiliation(s)
- Elzbieta Janda
- Laboratory of Cellular and Molecular Toxicology, Department of Health Science, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy
| | - Jean A. Boutin
- Laboratory of Neuroendocrine Endocrine and Germinal Differentiation and Communication (NorDiC), Université de Rouen Normandie, INSERM, UMR 1239, 76000 Rouen, France;
| | - Carlo De Lorenzo
- Laboratory of Cellular and Molecular Toxicology, Department of Health Science, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy
| | - Mariamena Arbitrio
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 88100 Catanzaro, Italy
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18
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [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: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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19
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Wang Z, Tan J, Li M, Gao C, Li W, Xu J, Guo C, Chen Z, Cai R. Clickable Photoreactive ATP-Affinity Probe for Global Profiling of ATP-Binding Proteins. Anal Chem 2023; 95:17533-17540. [PMID: 37993803 DOI: 10.1021/acs.analchem.3c02694] [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: 11/24/2023]
Abstract
Adenosine triphosphate (ATP) is the major energy carrier in organisms, and there are many cellular proteins that can bind to ATP. Among these proteins, kinases are key regulators in several cell signaling processes, and aberrant kinase signaling contributes to the development of many human diseases, including cancer. Hence, small-molecule kinase inhibitors have been successfully used for the treatment of various diseases. Since the ATP-binding pockets are similar for many kinases, it is very important to evaluate the selectivity of different kinase inhibitors. We report here a clickable ATP photoaffinity probe for the global profiling of ATP-binding proteins. After incubating the protein lysate with the ATP probe followed by ultraviolet (UV) irradiation, ATP-binding proteins were labeled with an alkyne handle for subsequent biotin conjugation through click chemistry. Labeled proteins were enriched with streptavidin beads, digested with trypsin, and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). More than 400 ATP-binding proteins, including approximately 200 kinases, could be identified in a single LC-MS/MS run in the data-dependent acquisition mode. We then applied this method to the analysis of targets of three selected ATP-competitive kinase inhibitors. We were able to successfully identify some of their reported target proteins from label-free quantification results and validated the results using Western blot analyses. Together, we developed a clickable ATP photoaffinity probe for proteome-wide profiling of ATP-binding proteins and demonstrated that this chemoproteomic method is amenable to high-throughput target identification of kinase inhibitors.
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Affiliation(s)
- Zhiming Wang
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
| | - Jing Tan
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
| | - Mengxuan Li
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Can Gao
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Wenwen Li
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Jing Xu
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Changchuan Guo
- Shandong Institute for Food and Drug Control, Jinan 250101, Shandong, China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, Shandong, China
| | - Rong Cai
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
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20
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Lin Z, Gongora J, Liu X, Xie Y, Zhao C, Lv D, Garcia BA. Automation to Enable High-Throughput Chemical Proteomics. J Proteome Res 2023; 22:3676-3682. [PMID: 37917986 PMCID: PMC11037874 DOI: 10.1021/acs.jproteome.3c00467] [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: 11/04/2023]
Abstract
Chemical proteomics utilizes small-molecule probes to covalently engage with their interacting proteins. Since chemical probes are tagged to the active or binding sites of functional proteins, chemical proteomics can be used to profile protein targets, reveal precise binding sites/mechanisms, and screen inhibitors competing with probes in a biological context. These capabilities of chemical proteomics have great potential to enable discoveries of both drug targets and lead compounds. However, chemical proteomics is limited by the time-consuming bottleneck of sample preparations, which are processed manually. With the advancement of robotics and artificial intelligence, it is now possible to automate workflows to make chemical proteomics sample preparation a high-throughput process. An automated robotic system represents a major technological opportunity to speed up advances in proteomics, open new frontiers in drug target discovery, and broaden the future of chemical biology.
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Affiliation(s)
- Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Joanna Gongora
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Xingyu Liu
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Chenfeng Zhao
- McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63110
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
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21
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Swoboda AS, Arfelli VC, Danese A, Windisch R, Kerbs P, Redondo Monte E, Bagnoli JW, Chen-Wichmann L, Caroleo A, Cusan M, Krebs S, Blum H, Sterr M, Enard W, Herold T, Colomé-Tatché M, Wichmann C, Greif PA. CSF3R T618I Collaborates With RUNX1-RUNX1T1 to Expand Hematopoietic Progenitors and Sensitizes to GLI Inhibition. Hemasphere 2023; 7:e958. [PMID: 37841755 PMCID: PMC10569757 DOI: 10.1097/hs9.0000000000000958] [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: 10/17/2022] [Accepted: 08/22/2023] [Indexed: 10/17/2023] Open
Abstract
Activating colony-stimulating factor-3 receptor gene (CSF3R) mutations are recurrent in acute myeloid leukemia (AML) with t(8;21) translocation. However, the nature of oncogenic collaboration between alterations of CSF3R and the t(8;21) associated RUNX1-RUNX1T1 fusion remains unclear. In CD34+ hematopoietic stem and progenitor cells from healthy donors, double oncogene expression led to a clonal advantage, increased self-renewal potential, and blast-like morphology and distinct immunophenotype. Gene expression profiling revealed hedgehog signaling as a potential mechanism, with upregulation of GLI2 constituting a putative pharmacological target. Both primary hematopoietic cells and the t(8;21) positive AML cell line SKNO-1 showed increased sensitivity to the GLI inhibitor GANT61 when expressing CSF3R T618I. Our findings suggest that during leukemogenesis, the RUNX1-RUNXT1 fusion and CSF3R mutation act in a synergistic manner to alter hedgehog signaling, which can be exploited therapeutically.
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Affiliation(s)
- Anja S. Swoboda
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vanessa C. Arfelli
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Danese
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Department of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Germany
| | - Roland Windisch
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Germany
| | - Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Enric Redondo Monte
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes W. Bagnoli
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Martinsried, Germany
| | - Linping Chen-Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Germany
| | - Alessandra Caroleo
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monica Cusan
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Krebs
- Gene Center - Laboratory for Functional Genome Analysis, LMU Munich, Germany
| | - Helmut Blum
- Gene Center - Laboratory for Functional Genome Analysis, LMU Munich, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Center Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Martinsried, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Colomé-Tatché
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Christian Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Germany
| | - Philipp A. Greif
- Department of Medicine III, University Hospital, LMU Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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22
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Zhang X, Ruan C, Wang Y, Wang K, Liu X, Lyu J, Ye M. Integrated Protein Solubility Shift Assays for Comprehensive Drug Target Identification on a Proteome-Wide Scale. Anal Chem 2023; 95:13779-13787. [PMID: 37676971 DOI: 10.1021/acs.analchem.3c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Target proteins are often stabilized after binding with a ligand and thereby typically become more resistant to denaturation. Based on this phenomenon, several methods without the need to covalently modify the ligand have been developed to identify target proteins for a specific ligand. These methods usually employ complicated workflows with high cost and limited throughput. Here, we develop an iso-pH shift assay (ipHSA) method, a proteome-wide target identification method that detects ligand-induced protein solubility shifts by precipitating proteins with a single concentration of acidic agent followed by protein quantification via data-independent acquisition (DIA). Using a pan-kinase inhibitor, staurosporine, we demonstrated that ipHSA increased throughput compared to the previously developed pH-dependent protein precipitation (pHDPP) method. ipHSA was found to have high complementarity in staurosporine target identification compared with the improved isothermal shift assay (iTSA) and isosolvent shift assay (iSSA) using DIA instead of tandem mass tags (TMTs) for quantification. To further improve target identification sensitivity, we developed an integrated protein solubility shift assay (IPSSA) by pooling the supernatants yielded from ipHSA, iTSA, and iSSA methods. IPSSA exhibited increased sensitivity in screening staurosporine targets by 38, 29, and 38% compared to individual methods. Increasing the number of replicate experiments further enhanced the sensitivity of target identification. Meanwhile, IPSSA also improved the throughput and reduced the cost compared with previous methods. As a fast and efficient tool for drug target identification, IPSSA is expected to have broad applications in the study of the mechanism of action.
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Affiliation(s)
- Xiaolei Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chengfei Ruan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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23
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Liu C, Kutchukian P, Nguyen ND, AlQuraishi M, Sorger PK. A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. J Chem Inf Model 2023; 63:5457-5472. [PMID: 37595065 PMCID: PMC10498990 DOI: 10.1021/acs.jcim.3c00347] [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] [Received: 03/06/2023] [Indexed: 08/20/2023]
Abstract
Kinases have been the focus of drug discovery programs for three decades leading to over 70 therapeutic kinase inhibitors and biophysical affinity measurements for over 130,000 kinase-compound pairs. Nonetheless, the precise target spectrum for many kinases remains only partly understood. In this study, we describe a computational approach to unlocking qualitative and quantitative kinome-wide binding measurements for structure-based machine learning. Our study has three components: (i) a Kinase Inhibitor Complex (KinCo) data set comprising in silico predicted kinase structures paired with experimental binding constants, (ii) a machine learning loss function that integrates qualitative and quantitative data for model training, and (iii) a structure-based machine learning model trained on KinCo. We show that our approach outperforms methods trained on crystal structures alone in predicting binary and quantitative kinase-compound interaction affinities; relative to structure-free methods, our approach also captures known kinase biochemistry and more successfully generalizes to distant kinase sequences and compound scaffolds.
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Affiliation(s)
- Changchang Liu
- Laboratory
of Systems Pharmacology, Department of Systems Biology, Harvard Program
in Therapeutic Science, Harvard Medical
School, Boston, Massachusetts 02115, United States
| | - Peter Kutchukian
- Novartis
Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Nhan D. Nguyen
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Mohammed AlQuraishi
- Department
of Systems Biology, Columbia University, New York, New York 10032, United States
| | - Peter K. Sorger
- Laboratory
of Systems Pharmacology, Department of Systems Biology, Harvard Program
in Therapeutic Science, Harvard Medical
School, Boston, Massachusetts 02115, United States
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24
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Herbst SA, White FM. Decrypting the potency of anti-cancer therapeutics by using mass spectrometry to quantify post-translational modifications. CELL REPORTS METHODS 2023; 3:100483. [PMID: 37323574 PMCID: PMC10261922 DOI: 10.1016/j.crmeth.2023.100483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In a recent issue of Science, Zecha et al.1 present decryptM, an approach aimed at defining the mechanisms of action of anti-cancer therapeutics through systems-level analysis of protein post-translational modifications (PTMs). By using a broad range of concentrations, decryptM generates drug response curves for each detected PTM, enabling identification of drug effects at different therapeutic doses.
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Affiliation(s)
- Sophie A. Herbst
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Forest M. White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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25
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Zhu L, Liu H, Dou Y, Luo Q, Gu L, Liu X, Zhou Q, Han J, Wang F. A Photoactivated Ru (II) Polypyridine Complex Induced Oncotic Necrosis of A549 Cells by Activating Oxidative Phosphorylation and Inhibiting DNA Synthesis as Revealed by Quantitative Proteomics. Int J Mol Sci 2023; 24:ijms24097756. [PMID: 37175463 PMCID: PMC10178167 DOI: 10.3390/ijms24097756] [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: 02/14/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
The ruthenium polypyridine complex [Ru(dppa)2(pytp)] (PF6)2 (termed as ZQX-1), where dppa = 4,7-diphenyl-1,10-phenanthroline and pytp = 4'-pyrene-2,2':6',2''-terpyridine, has been shown a high and selective cytotoxicity to hypoxic and cisplatin-resistant cancer cells either under irradiation with blue light or upon two-photon excitation. The IC50 values of ZQX-1 towards A549 cancer cells and HEK293 health cells are 0.16 ± 0.09 µM and >100 µM under irradiation at 420 nm, respectively. However, the mechanism of action of ZQX-1 remains unclear. In this work, using the quantitative proteomics method we identified 84 differentially expressed proteins (DEPs) with |fold-change| ≥ 1.2 in A549 cancer cells exposed to ZQX-1 under irradiation at 420 nm. Bioinformatics analysis of the DEPs revealed that photoactivated ZQX-1 generated reactive oxygen species (ROS) to activate oxidative phosphorylation signaling to overproduce ATP; it also released ROS and pyrene derivative to damage DNA and arrest A549 cells at S-phase, which synergistically led to oncotic necrosis and apoptosis of A549 cells to deplete excess ATP, evidenced by the elevated level of PRAP1 and cleaved capase-3. Moreover, the DNA damage inhibited the expression of DNA repair-related proteins, such as RBX1 and GPS1, enhancing photocytotoxicity of ZQX-1, which was reflected in the inhibition of integrin signaling and disruption of ribosome assembly. Importantly, the photoactivated ZQX-1 was shown to activate hypoxia-inducible factor 1A (HIF1A) survival signaling, implying that combining use of ZQX-1 with HIF1A signaling inhibitors may further promote the photocytotoxicity of the prodrug.
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Affiliation(s)
- Li Zhu
- College of Applied Science and Technology, Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing 100101, China
| | - Hui Liu
- College of Applied Science and Technology, Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing 100101, China
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yang Dou
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhen Gu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xingkai Liu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qianxiong Zhou
- Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Juanjuan Han
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Centre for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
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26
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Tröster A, DiPrima M, Jores N, Kudlinzki D, Sreeramulu S, Gande SL, Linhard V, Ludig D, Schug A, Saxena K, Reinecke M, Heinzlmeir S, Leisegang MS, Wollenhaupt J, Lennartz F, Weiss MS, Kuster B, Tosato G, Schwalbe H. Optimization of the Lead Compound NVP-BHG712 as a Colorectal Cancer Inhibitor. Chemistry 2023; 29:e202203967. [PMID: 36799129 PMCID: PMC10133194 DOI: 10.1002/chem.202203967] [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: 12/19/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
The ephrin type-A receptor 2 (EPHA2) kinase belongs to the largest family of receptor tyrosine kinases. There are several indications of an involvement of EPHA2 in the development of infectious diseases and cancer. Despite pharmacological potential, EPHA2 is an under-examined target protein. In this study, we synthesized a series of derivatives of the inhibitor NVP-BHG712 and triazine-based compounds. These compounds were evaluated to determine their potential as kinase inhibitors of EPHA2, including elucidation of their binding mode (X-ray crystallography), affinity (microscale thermophoresis), and selectivity (Kinobeads assay). Eight inhibitors showed affinities in the low-nanomolar regime (KD <10 nM). Testing in up to seven colon cancer cell lines that express EPHA2 reveals that several derivatives feature promising effects for the control of human colon carcinoma. Thus, we have developed a set of powerful tool compounds for fundamental new research on the interplay of EPH receptors in a cellular context.
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Affiliation(s)
- Alix Tröster
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Michael DiPrima
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), 37 Convent Drive, NIH Bethesda Campus, Building 37, Room 4124, Bethesda, MD 20892, USA
| | - Nathalie Jores
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Santosh L. Gande
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Verena Linhard
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Damian Ludig
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Alexander Schug
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
| | - Stephanie Heinzlmeir
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
| | - Matthias S. Leisegang
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main (Germany)
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Frank Lennartz
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, 12489 Berlin (Germany)
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
- German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Emil-Erlenmeyer-Forum 5, 85354 Freising (Germany)
| | - Giovanna Tosato
- Laboratory of Cellular Oncology, Center for Cancer Research (CCR), National Cancer Institute (NCI), 37 Convent Drive, NIH Bethesda Campus, Building 37, Room 4124, Bethesda, MD 20892, USA
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse7, 60438 Frankfurt am Main (Germany)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg (Germany)
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27
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Li J, Zheng M, Xu Y, Yang X, Kang J. Target proteins profiling of irreversible kinase inhibitor pelitinib and discovery of degradation of PRDX4 by label free chemoproteomics. J Pharm Biomed Anal 2023; 230:115398. [PMID: 37084663 DOI: 10.1016/j.jpba.2023.115398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]
Abstract
Cell-based methods for profiling the kinase inhibitor selectivity are badly needed, especially for the irreversible kinase inhibitors. Here we reported a chemoproteomics approach for profiling the target proteins of irreversible kinase inhibitor with label free quantitative proteomics by using iodoacetamide alkyne as a chemical probe. In total 41 proteins were identified in high confidence (fold change 3.5, p value < 0.05) including PRDX4, STAT3, E2 conjugating enzymes UBE2L3, UBE2K, UBE2N, UBE2V1 and UBE2Z as well as E3 ligase TRIM 25. We validated the interaction between pelitinib and PRDX4 with a cell-based assay, and discovered that pelitinib can induce the degradation of PRDX4. The discovery was confirmed by biochemical assay, cellular thermal shift assay and miRNA knockdown experiment. Our data suggested that pelitinib can be a covalent molecular glue inducing the degradation of PRDX4. In addition, our work demonstrated that identification of the interactions between ligand and ubiquitylation associated proteins by chemoproteomics profiling can be used as a new strategy for identifying molecular glue degraders.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Mengmeng Zheng
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Yao Xu
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Xin Yang
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Jingwu Kang
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China.
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28
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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [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: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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29
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Amaral B, Capacci A, Anderson T, Tezer C, Bajrami B, Lulla M, Lucas B, Chodaparambil JV, Marcotte D, Kumar PR, Murugan P, Spilker K, Cullivan M, Wang T, Peterson AC, Enyedy I, Ma B, Chen T, Yousaf Z, Calhoun M, Golonzhka O, Dillon GM, Koirala S. Elucidation of the GSK3α Structure Informs the Design of Novel, Paralog-Selective Inhibitors. ACS Chem Neurosci 2023; 14:1080-1094. [PMID: 36812145 PMCID: PMC10020971 DOI: 10.1021/acschemneuro.2c00476] [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: 02/24/2023] Open
Abstract
Glycogen synthase kinase 3 (GSK3) remains a therapeutic target of interest for diverse clinical indications. However, one hurdle in the development of small molecule GSK3 inhibitors has been safety concerns related to pan-inhibition of both GSK3 paralogs, leading to activation of the Wnt/β-catenin pathway and potential for aberrant cell proliferation. Development of GSK3α or GSK3β paralog-selective inhibitors that could offer an improved safety profile has been reported but further advancement has been hampered by the lack of structural information for GSK3α. Here we report for the first time the crystal structure for GSK3α, both in apo form and bound to a paralog-selective inhibitor. Taking advantage of this new structural information, we describe the design and in vitro testing of novel compounds with up to ∼37-fold selectivity for GSK3α over GSK3β with favorable drug-like properties. Furthermore, using chemoproteomics, we confirm that acute inhibition of GSK3α can lower tau phosphorylation at disease-relevant sites in vivo, with a high degree of selectivity over GSK3β and other kinases. Altogether, our studies advance prior efforts to develop GSK3 inhibitors by describing GSK3α structure and novel GSK3α inhibitors with improved selectivity, potency, and activity in disease-relevant systems.
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Affiliation(s)
- Brenda Amaral
- Departments of Research, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Andrew Capacci
- Departments of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Trip Anderson
- Departments of Research, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ceren Tezer
- Departments of Research, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Departments of Chemical Biology and Proteomics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Mukesh Lulla
- Departments of Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brian Lucas
- Departments of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jayanth V Chodaparambil
- Departments of Physical Biochemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Douglas Marcotte
- Departments of Physical Biochemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - P Rajesh Kumar
- Departments of Physical Biochemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Departments of Bioassays, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kerri Spilker
- Departments of Physical Biochemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Mike Cullivan
- Departments of Physical Biochemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ti Wang
- Departments of Bioassays, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Anton C Peterson
- Departments of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Istvan Enyedy
- Departments of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bin Ma
- Departments of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - TeYu Chen
- Departments of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Zain Yousaf
- Departments of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Calhoun
- Departments of Research, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Olga Golonzhka
- Departments of Research, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Gregory M Dillon
- Departments of Research, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Samir Koirala
- Departments of Research, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
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30
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Golkowski M, Lius A, Sapre T, Lau HT, Moreno T, Maly DJ, Ong SE. Multiplexed kinase interactome profiling quantifies cellular network activity and plasticity. Mol Cell 2023; 83:803-818.e8. [PMID: 36736316 PMCID: PMC10072906 DOI: 10.1016/j.molcel.2023.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/07/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Dynamic changes in protein-protein interaction (PPI) networks underlie all physiological cellular functions and drive devastating human diseases. Profiling PPI networks can, therefore, provide critical insight into disease mechanisms and identify new drug targets. Kinases are regulatory nodes in many PPI networks; yet, facile methods to systematically study kinase interactome dynamics are lacking. We describe kinobead competition and correlation analysis (kiCCA), a quantitative mass spectrometry-based chemoproteomic method for rapid and highly multiplexed profiling of endogenous kinase interactomes. Using kiCCA, we identified 1,154 PPIs of 238 kinases across 18 diverse cancer lines, quantifying context-dependent kinase interactome changes linked to cancer type, plasticity, and signaling states, thereby assembling an extensive knowledgebase for cell signaling research. We discovered drug target candidates, including an endocytic adapter-associated kinase (AAK1) complex that promotes cancer cell epithelial-mesenchymal plasticity and drug resistance. Our data demonstrate the importance of kinase interactome dynamics for cellular signaling in health and disease.
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Affiliation(s)
- Martin Golkowski
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
| | - Andrea Lius
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Tanmay Sapre
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Taylor Moreno
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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31
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Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types. PLoS Comput Biol 2023; 19:e1010888. [PMID: 36809237 PMCID: PMC9983880 DOI: 10.1371/journal.pcbi.1010888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 03/03/2023] [Accepted: 01/20/2023] [Indexed: 02/23/2023] Open
Abstract
Protein kinases play a vital role in a wide range of cellular processes, and compounds that inhibit kinase activity emerging as a primary focus for targeted therapy development, especially in cancer. Consequently, efforts to characterize the behavior of kinases in response to inhibitor treatment, as well as downstream cellular responses, have been performed at increasingly large scales. Previous work with smaller datasets have used baseline profiling of cell lines and limited kinome profiling data to attempt to predict small molecule effects on cell viability, but these efforts did not use multi-dose kinase profiles and achieved low accuracy with very limited external validation. This work focuses on two large-scale primary data types, kinase inhibitor profiles and gene expression, to predict the results of cell viability screening. We describe the process by which we combined these data sets, examined their properties in relation to cell viability and finally developed a set of computational models that achieve a reasonably high prediction accuracy (R2 of 0.78 and RMSE of 0.154). Using these models, we identified a set of kinases, several of which are understudied, that are strongly influential in the cell viability prediction models. In addition, we also tested to see if a wider range of multiomics data sets could improve the model results and found that proteomic kinase inhibitor profiles were the single most informative data type. Finally, we validated a small subset of the model predictions in several triple-negative and HER2 positive breast cancer cell lines demonstrating that the model performs well with compounds and cell lines that were not included in the training data set. Overall, this result demonstrates that generic knowledge of the kinome is predictive of very specific cell phenotypes, and has the potential to be integrated into targeted therapy development pipelines.
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32
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Global profiling of AMG510 modified proteins identified tumor suppressor KEAP1 as an off-target. iScience 2023; 26:106080. [PMID: 36824285 PMCID: PMC9942120 DOI: 10.1016/j.isci.2023.106080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/30/2022] [Accepted: 01/23/2023] [Indexed: 01/30/2023] Open
Abstract
KRAS inhibitor AMG510 covalently modifies the G12C residue and inactivates the KRAS/G12C function. Because there are many reactive cysteines in the proteome, it is important to characterize AMG510 on-target modification and off-targets. Here, we presented a streamlined workflow to measure abundant AMG510 modified peptides including that of KRAS/G12C by direct profiling, and a pan-AMG510 antibody peptide IP workflow to profile less abundant AMG510 off-targets. We identified over 300 off-target sites with three distinct kinetic patterns, expanding the AMG510 modified proteome involved in the nucleocytoplasmic transport, response to oxidative stress, adaptive immune system, and glycolysis. We found that AMG510 covalently modified cys339 of ALDOA and inhibited its enzyme activity. Moreover, AMG510 modified KEAP1 cys288 and induced NRF2 accumulation in the nuclear of NSCLC cells independent of KRAS/G12C mutation. Our study provides a comprehensive resource of protein off-targets of AMG510 and elucidates potential toxicological sideeffects for this covalent KRASG12C inhibitor.
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33
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Basu D, Pal R, Sarkar M, Barma S, Halder S, Roy H, Nandi S, Samadder A. To Investigate Growth Factor Receptor Targets and Generate Cancer Targeting Inhibitors. Curr Top Med Chem 2023; 23:2877-2972. [PMID: 38164722 DOI: 10.2174/0115680266261150231110053650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/20/2023] [Accepted: 10/02/2023] [Indexed: 01/03/2024]
Abstract
Receptor tyrosine kinase (RTK) regulates multiple pathways, including Mitogenactivated protein kinases (MAPKs), PI3/AKT, JAK/STAT pathway, etc. which has a significant role in the progression and metastasis of tumor. As RTK activation regulates numerous essential bodily processes, including cell proliferation and division, RTK dysregulation has been identified in many types of cancers. Targeting RTK is a significant challenge in cancer due to the abnormal upregulation and downregulation of RTK receptors subfamily EGFR, FGFR, PDGFR, VEGFR, and HGFR in the progression of cancer, which is governed by multiple RTK receptor signalling pathways and impacts treatment response and disease progression. In this review, an extensive focus has been carried out on the normal and abnormal signalling pathways of EGFR, FGFR, PDGFR, VEGFR, and HGFR and their association with cancer initiation and progression. These are explored as potential therapeutic cancer targets and therefore, the inhibitors were evaluated alone and merged with additional therapies in clinical trials aimed at combating global cancer.
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Affiliation(s)
- Debroop Basu
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Riya Pal
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, IndiaIndia
| | - Maitrayee Sarkar
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Soubhik Barma
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sumit Halder
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Harekrishna Roy
- Nirmala College of Pharmacy, Vijayawada, Guntur, Andhra Pradesh, India
| | - Sisir Nandi
- Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur, 244713, India
| | - Asmita Samadder
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
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34
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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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35
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Feng F, Zhang W, Chai Y, Guo D, Chen X. Label-free target protein characterization for small molecule drugs: recent advances in methods and applications. J Pharm Biomed Anal 2023; 223:115107. [DOI: 10.1016/j.jpba.2022.115107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
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36
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Zhang X, Hu L, Ye M. Solvent-Induced Protein Precipitation for Drug Target Discovery. Methods Mol Biol 2023; 2554:35-45. [PMID: 36178619 DOI: 10.1007/978-1-0716-2624-5_4] [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] [Indexed: 06/16/2023]
Abstract
Traditional chemical proteomics approaches for screening drug targets usually require the immobilization/modification of the drug molecules to pull down the interacting proteins. The solvent-induced protein precipitation (SIP) approach provides an alternative way to study drug-protein interaction by using complex cell lysate directly without modifying a compound of interest. It relies on the fact that the ligand-bound proteins have higher resistance to solvent-induced precipitation. This chapter describes the protocol for identifying drug-target protein interactions by performing unbiased SIP with total cell lysate using a mass spectrometry-based proteomic strategy.
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Affiliation(s)
- Xiaolei Zhang
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, China.
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
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37
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Zhai LH, Chen KF, Hao BB, Tan MJ. Proteomic characterization of post-translational modifications in drug discovery. Acta Pharmacol Sin 2022; 43:3112-3129. [PMID: 36372853 PMCID: PMC9712763 DOI: 10.1038/s41401-022-01017-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/07/2022] [Indexed: 11/15/2022] Open
Abstract
Protein post-translational modifications (PTMs), which are usually enzymatically catalyzed, are major regulators of protein activity and involved in almost all celluar processes. Dysregulation of PTMs is associated with various types of diseases. Therefore, PTM regulatory enzymes represent as an attractive and important class of targets in drug research and development. Inhibitors against kinases, methyltransferases, deacetyltransferases, ubiquitin ligases have achieved remarkable success in clinical application. Mass spectrometry-based proteomics technologies serve as a powerful approach for system-wide characterization of PTMs, which facilitates the identification of drug targets, elucidation of the mechanisms of action of drugs, and discovery of biomakers in personalized therapy. In this review, we summarize recent advances of proteomics-based studies on PTM targeting drugs and discuss how proteomics strategies facilicate drug target identification, mechanism elucidation, and new therapy development in precision medicine.
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Affiliation(s)
- Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China
| | - Kai-Feng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing-Bing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China.
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38
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Prokofeva P, Höfer S, Hornisch M, Abele M, Kuster B, Médard G. Merits of Diazirine Photo-Immobilization for Target Profiling of Natural Products and Cofactors. ACS Chem Biol 2022; 17:3100-3109. [PMID: 36302507 PMCID: PMC9680877 DOI: 10.1021/acschembio.2c00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/05/2022] [Indexed: 01/20/2023]
Abstract
Finding the targets of natural products is of key importance in both chemical biology and drug discovery, and deconvolution of cofactor interactomes contributes to the functional annotation of the proteome. Identifying the proteins that underlie natural compound activity in phenotypic screens helps to validate the respective targets and, potentially, expand the druggable proteome. Here, we present a generally applicable protocol for the photoactivated immobilization of unmodified and microgram quantities of natural products on diazirine-decorated beads and their use for systematic affinity-based proteome profiling. We show that among 31 molecules of very diverse reported activity and biosynthetic origin, 25 could indeed be immobilized. Dose-response competition binding experiments using lysates of human or bacterial cells followed by quantitative mass spectrometry recapitulated targets of 9 molecules with <100 μM affinity. Among them, immobilization of coenzyme A produced a tool to interrogate proteins containing a HotDog domain. Surprisingly, immobilization of the cofactor flavin adenine dinucleotide (FAD) led to the identification of nanomolar interactions with dozens of RNA-binding proteins.
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Affiliation(s)
- Polina Prokofeva
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Höfer
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Maximilian Hornisch
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Miriam Abele
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Bernhard Kuster
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Bavarian
Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, 85354 Freising, Germany
| | - Guillaume Médard
- Chair
of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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39
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Ruprecht B, Wei L, Zheng L, Bodea S, Mo X, Maschberger M, Stoehr G, Hahne H, Cornella-Taracido I, Chi A. Chemoproteomic profiling to identify activity changes and functional inhibitors of DNA-binding proteins. Cell Chem Biol 2022; 29:1639-1648.e4. [PMID: 36356585 DOI: 10.1016/j.chembiol.2022.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 07/04/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022]
Abstract
DNA-binding proteins are promising therapeutic targets but are notoriously difficult to drug. Here, we evaluate a chemoproteomic DNA interaction platform as a complementary strategy for parallelized compound profiling. To enable this approach, we determined the proteomic binding landscape of 92 immobilized DNA sequences. Perturbation-induced activity changes of captured transcription factors in disease-relevant settings demonstrated functional relevance of the enriched subproteome. Chemoproteomic profiling of >300 cysteine-directed compounds against a coverage optimized bead mixture, which specifically captures >150 DNA binders, revealed competition of several DNA-binding proteins, including the transcription factors ELF1 and ELF2. We also discovered the first compound that displaces the DNA-repair complex MSH2-MSH3 from DNA. Compound binding to cysteine 252 on MSH3 was confirmed using chemoproteomic reactive cysteine profiling. Overall, these results suggested that chemoproteomic DNA bead pull-downs enable the specific readout of transcription factor activity and can identify functional "hotspots" on DNA binders toward expanding the druggable proteome.
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Affiliation(s)
| | - Lan Wei
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Li Zheng
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Smaranda Bodea
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Xuan Mo
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | | | | | - Hannes Hahne
- OmicScouts GmbH, 85354 Freising, Bavaria, Germany
| | | | - An Chi
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA.
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40
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Screening assays for tyrosine kinase inhibitors:A review. J Pharm Biomed Anal 2022; 223:115166. [DOI: 10.1016/j.jpba.2022.115166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
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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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42
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Zhou W, Chen MM, Liu HL, Si ZL, Wu WH, Jiang H, Wang LX, Vaziri ND, An XF, Su K, Chen C, Tan NH, Zhang ZH. Dihydroartemisinin suppresses renal fibrosis in mice by inhibiting DNA-methyltransferase 1 and increasing Klotho. Acta Pharmacol Sin 2022; 43:2609-2623. [PMID: 35347248 PMCID: PMC9525601 DOI: 10.1038/s41401-022-00898-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/06/2022] [Indexed: 02/07/2023] Open
Abstract
Renal fibrosis is an unavoidable end result of all forms of progressive chronic kidney diseases (CKD). Discovery of efficacious drugs against renal fibrosis is in crucial need. In a preliminary study we found that a derivative of artemisinin, dihydroartemisinin (DHA), exerted strong renoprotection, and reversed renal fibrosis in adenine-induced CKD mouse model. In this study we investigated the anti-fibrotic mechanisms of DHA, particularly its specific target in renal cells. Renal fibrosis was induced in mice by unilateral ureteral obstruction (UUO) or oral administration of adenine (80 mg · kg-1), the mice received DHA (30 mg · kg-1 · d-1, i.g.) for 14 or 21 days, respectively. We showed that DHA administration markedly attenuated the inflammation and fibrotic responses in the kidneys and significantly improved the renal function in both the renal fibrosis mouse models. In adenine-treated mice, DHA was more effective than 5-azacytidine against renal fibrosis. The anti-fibrotic effects of DHA were also observed in TGF-β1-treated HK-2 cells. In order to determine the target protein of DHA, we conducted pull-down technology coupled with shotgun proteomics using a small-molecule probe based on the structure of DHA (biotin-DHA). As a results, DNA methyltransferase 1 (DNMT1) was identified as the anti-fibrotic target of DHA in 3 different types of renal cell lines (HK-2, HEK293 and 3T3). We demonstrated that DHA directly bound to Asn 1529 and Thr 1528 of DNMT1 with a Kd value of 8.18 μM. In primary mouse renal tubular cells, we showed that DHA (10 μM) promoted DNMT1 degradation via the ubiquitin-proteasome pathway. DHA-reduced DNMT1 expression effectively reversed Klotho promoter hypermethylation, which led to the reversal of Klotho protein loss in the kidney of UUO mice. This subsequently resulted in inhibition of the Wnt/β-catenin and TGF-β/Smad signaling pathways and consequently conferred renoprotection in the animals. Knockdown of Klotho abolished the renoprotective effect of DHA in UUO mice. Our study reveals a novel pharmacological activity for DHA, i.e., renoprotection. DHA exhibits this effect by targeting DNMT1 to reverse Klotho repression. This study provides an evidence for the possible clinical application of DHA in the treatment of renal fibrosis.
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Affiliation(s)
- Wei Zhou
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Min-Min Chen
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Hui-Ling Liu
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zi-Lin Si
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Wen-Hui Wu
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Hong Jiang
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Lin-Xiao Wang
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Nosratola D Vaziri
- Division of Nephrology and Hypertension, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Xiao-Fei An
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ke Su
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Cheng Chen
- Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ning-Hua Tan
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Zhi-Hao Zhang
- State Key Laboratory of Natural Medicines, Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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43
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Lin W, Chen G, Mao Y, Ma X, Zhou J, Yu X, Wang C, Liu M. Imperatorin Inhibits Proliferation, Migration, and Inflammation via Blocking the NF-κB and MAPK Pathways in Rheumatoid Fibroblast-like Synoviocytes. ACS OMEGA 2022; 7:29868-29876. [PMID: 36061691 PMCID: PMC9434770 DOI: 10.1021/acsomega.2c02766] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic joint inflammatory disease associated with the aberrant activation of fibroblast-like synoviocytes (FLSs). Searching for natural compounds that may suppress the activation of FLSs has become a complementary approach for RA treatment. Here, we investigated the effects and mechanisms of imperatorin (IPT) on proliferation, migration, and inflammation in primary cultured arthritic FLSs. We found that IPT significantly suppressed TNFα-induced proliferation and migration of arthritic FLSs, but showed little effect on survival and apoptosis. In addition, IPT treatment significantly reduced the TNFα-induced expression of pro-inflammatory cytokines (IL-1β, TNFα, IL-6, and IL-8) in arthritic FLSs. Further mechanism studies suggested that IPT inhibited the activations of p38 and extracellular signal-regulated kinase (ERK). Also, IPT blocked the nuclear factor of κB (NF-κB) activation by suppressing the phosphorylation and degradation of IκBα, thereby preventing the translocation of p65. Collectively, our results demonstrated that IPT could inhibit the over-activated phenotypes of arthritic FLSs via the mitogen-activated protein kinase (MAPK) (p38 and ERK) and NF-κB pathways leading to the down-regulation of pro-inflammatory cytokines, which might be beneficial to the anti-proliferative and anti-migratory activities of FLS cells. These findings suggest that IPT has the potential to be developed as a novel agent for RA treatment.
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Affiliation(s)
- Wei Lin
- Jiangsu
Key Laboratory for Molecular and Medical Biotechnology, College of
Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Spine
and Joint Surgery, People’s Hospital
Affiliated to Shandong First Medical University, Jinan 271199, China
| | - Gang Chen
- Jiangsu
Key Laboratory for Molecular and Medical Biotechnology, College of
Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuhang Mao
- Jiangsu
Key Laboratory for Molecular and Medical Biotechnology, College of
Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xuemei Ma
- Jiangsu
Key Laboratory for Molecular and Medical Biotechnology, College of
Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Junnan Zhou
- Jiangsu
Key Laboratory for Molecular and Medical Biotechnology, College of
Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Xiaolu Yu
- Jiangsu
Key Laboratory for Molecular and Medical Biotechnology, College of
Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Chaoliang Wang
- Spine
and Joint Surgery, People’s Hospital
Affiliated to Shandong First Medical University, Jinan 271199, China
| | - Mei Liu
- Jiangsu
Key Laboratory for Molecular and Medical Biotechnology, College of
Life Sciences, Nanjing Normal University, Nanjing 210023, China
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Abstract
Objective Dasatinib, a second-generation tyrosine kinase inhibitor, is used for chronic myelogenous leukemia (CML) and Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL). It reportedly causes pulmonary arterial hypertension (PAH) and the dose-dependent induction of apoptosis in pulmonary endothelial cells. However, no report has yet discussed the relationship between dasatinib-induced PAH and drug dose. We therefore investigated the incidence of dasatinib-induced PAH and the relationship between dasatinib-PAH and drug dose in consecutive patients with CML and Ph+ ALL who took dasatinib. Methods The clinical data of 128 patients with CML (94 patients) and Ph+ ALL (34 patients) were retrospectively analyzed. Patients All patients (>17 years old) who received dasatinib from January 2009 to March 2020 at Jichi Medical University (Tochigi, Japan) were included. Patients who transferred within one month of starting dasatinib administration were excluded. Results Four (4.3%) and three (8.8%) patients developed pulmonary hypertension (PH), which was considered present when the transtricuspid pressure gradient was ≥40 mmHg, in the CML and ALL groups, respectively. No significant difference was observed between the PH onset and the administration period, cumulative dose, or daily dose of dasatinib. PH occurred in seven patients (5.5%), and the period from the start of dasatinib administration to the PH onset ranged from 7 to 39 (median: 28) months. No patients died from PH in either group. Conclusion Dasatinib-induced PAH does not occur time- or dose-dependently. When administering dasatinib, cardiovascular diagnostic modalities should be routinely checked, and PAH occurrence should be promptly detected.
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Affiliation(s)
- Kana Kubota
- Division of Cardiovascular Medicine, Department of Internal Medicine, Jichi Medical University, Japan
| | - Yasushi Imai
- Division of Cardiovascular Medicine, Department of Internal Medicine, Jichi Medical University, Japan
- Division of Clinical Pharmacology, Department of Pharmacology, Jichi Medical University, Japan
| | - Iekuni Oh
- Division of Hematology, Department of Internal Medicine, Jichi Medical University, Japan
| | - Shuichi Ueno
- Division of Cardiovascular Medicine, Department of Internal Medicine, Jichi Medical University, Japan
- Ueno Clinic, Japan
| | - Yoshinobu Kanda
- Division of Hematology, Department of Internal Medicine, Jichi Medical University, Japan
| | - Kazuomi Kario
- Division of Cardiovascular Medicine, Department of Internal Medicine, Jichi Medical University, Japan
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Sirvent A, Espie K, Papadopoulou E, Naim D, Roche S. New functions of DDR1 collagen receptor in tumor dormancy, immune exclusion and therapeutic resistance. Front Oncol 2022; 12:956926. [PMID: 35936735 PMCID: PMC9355703 DOI: 10.3389/fonc.2022.956926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/28/2022] [Indexed: 01/22/2023] Open
Abstract
The tumor microenvironment facilitates cancer progression and therapeutic resistance. Tumor collagens and their architecture play an essential role in this process. However, little is known about the mechanisms by which tumor cells sense and respond to this extracellular matrix environment. Recently, the Discoidin Domain Receptor 1 (DDR1), a collagen receptor and tyrosine kinase has emerged as an important player in this malignant process, although the underlying signaling mechanisms remain unclear. Here, we review new DDR1 functions in tumor dormancy following dissemination, immune exclusion and therapeutic resistance induced by stromal collagens deposition. We also discuss the signaling mechanisms behind these tumor activities and the therapeutic strategies aiming at targeting these collagens-dependent tumor responses.
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Affiliation(s)
| | | | | | | | - Serge Roche
- *Correspondence: Serge Roche, ; Audrey Sirvent,
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46
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Wilkinson IVL, Pfanzelt M, Sieber SA. Functionalised Cofactor Mimics for Interactome Discovery and Beyond. Angew Chem Int Ed Engl 2022; 61:e202201136. [PMID: 35286003 PMCID: PMC9401033 DOI: 10.1002/anie.202201136] [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: 01/21/2022] [Indexed: 11/09/2022]
Abstract
Cofactors are required for almost half of all enzyme reactions, but their functions and binding partners are not fully understood even after decades of research. Functionalised cofactor mimics that bind in place of the unmodified cofactor can provide answers, as well as expand the scope of cofactor activity. Through chemical proteomics approaches such as activity-based protein profiling, the interactome and localisation of the native cofactor in its physiological environment can be deciphered and previously uncharacterised proteins annotated. Furthermore, cofactors that supply functional groups to substrate biomolecules can be hijacked by mimics to site-specifically label targets and unravel the complex biology of post-translational protein modification. The diverse activity of cofactors has inspired the design of mimics for use as inhibitors, antibiotic therapeutics, and chemo- and biosensors, and cofactor conjugates have enabled the generation of novel enzymes and artificial DNAzymes.
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Affiliation(s)
- Isabel V L Wilkinson
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Martin Pfanzelt
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
| | - Stephan A Sieber
- Centre for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748, Garching, Germany
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47
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Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA. On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. Anal Chem 2022; 94:9508-9513. [PMID: 35729701 PMCID: PMC10654755 DOI: 10.1021/acs.analchem.2c01337] [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: 11/30/2022]
Abstract
The family of deubiquitinases (DUBs) comprises ∼100 enzymes that cleave ubiquitin from substrate proteins and thereby regulate key aspects of human physiology. DUBs have recently emerged as disease-relevant and chemically tractable, although currently there are no approved DUB-targeting drugs and most preclinical small molecules are low-potency and/or multitargeted. We paired a novel capillary electrophoresis microchip containing an integrated, "on-chip" C18 bed (SPE-ZipChip) with a TMT version of our recently described PRM-LIVE acquisition scheme on a timsTOF Pro mass spectrometer to facilitate rapid activity-based protein profiling of DUB inhibitors. We demonstrate the ability of the SPE-ZipChip to improve proteome coverage of complex samples as well as the quantitation integrity of CE-PRM-LIVE for TMT labeled samples. These technologies provide a platform to accurately quantify competitive binding of covalent and reversible inhibitors in a multiplexed assay that spans 49 endogenous DUBs in less than 15 min.
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Affiliation(s)
- He Zhu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Scott Mellors
- 908 Devices Inc., Boston, Massachusetts 02210, United States
| | - Wai Cheung Chan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - J Will Thompson
- 908 Devices Inc., Boston, Massachusetts 02210, United States
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Ariana S Bratt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jens Decker
- Bruker Daltonics GmbH & Co. KG, Bremen 28359, Germany
| | | | - Gary Kruppa
- Bruker S.R.O., District Brno-City 61900 Czech Republic
| | - Sara J Buhrlage
- Department of Cancer Biology, 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
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48
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Wilkinson IVL, Pfanzelt M, Sieber SA. Funktionalisierte Cofaktor‐Analoga für die Erforschung von Interaktomen und darüber hinaus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isabel V. L. Wilkinson
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
| | - Martin Pfanzelt
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
| | - Stephan A. Sieber
- Centre for Functional Protein Assemblies Technische Universität München Ernst-Otto-Fischer-Straße 8 85748 Garching Deutschland
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49
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Therapeutic targeting of TANK-binding kinase signaling towards anticancer drug development: Challenges and opportunities. Int J Biol Macromol 2022; 207:1022-1037. [PMID: 35358582 DOI: 10.1016/j.ijbiomac.2022.03.157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/15/2022]
Abstract
TANK-binding kinase 1 (TBK1) plays a fundamental role in regulating the cellular responses and controlling several signaling cascades. It regulates inflammatory, interferon, NF-κB, autophagy, and Akt pathways. Post-translational modifications (PTM) of TBK1 control its action and subsequent cellular signaling. The dysregulation of the TBK1 pathway is correlated to many pathophysiological conditions, including cancer, that implicates the promising therapeutic advantage for targeting TBK1. The present study summarizes current updates on the molecular mechanisms and cancer-inducing roles of TBK1. Designed inhibitors of TBK1 are considered a potential therapeutic agent for several diseases, including cancer. Data from pre-clinical tumor models recommend that the targeting of TBK1 could be an attractive strategy for anti-tumor therapy. This review further highlighted the therapeutic potential of potent and selective TBK1 inhibitors, including Amlexanox, Compound II, BX795, MRT67307, SR8185 AZ13102909, CYT387, GSK8612, BAY985, and Domainex. These inhibitors may be implicated to facilitate therapeutic management of cancer and TBK1-associated diseases in the future.
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50
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Qing T, Liu J, Liu F, Mitchell DC, Beresis RT, Gordan JD. Methods to assess small molecule allosteric modulators of the STRAD pseudokinase. Methods Enzymol 2022; 667:427-453. [PMID: 35525550 DOI: 10.1016/bs.mie.2022.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
With the increased appreciation of the biological relevance of pseudokinase (PSK) allostery, the broadening of small molecule strategies to target PSK function is of particular importance. We and others have pursued the development of small molecule allosteric modulators of the STRAD pseudokinase by targeting its ATP binding pocket. The purpose of this effort is to modulate the function of the LKB1 tumor suppressor kinase, which exists in a trimer with the STRAD PSK and the adaptor protein MO25. Here we provide detailed guidance regarding the different methods we have used for medium throughput screening to identify STRAD ligands and measure their impact on LKB1 kinase activity. Our experience supports preferential use of direct measurements of LKB1 kinase activity, and demonstrates the limitations of indirect assessment methods in the development trans-acting allosteric modulators.
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Affiliation(s)
- Tingting Qing
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Jin Liu
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Fen Liu
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Dom C Mitchell
- Division of Hematology Oncology and Quantitative Biosciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Richard T Beresis
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - John D Gordan
- Division of Hematology Oncology and Quantitative Biosciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States.
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