1
|
McKenna SM, Florea BI, Zisterer DM, van Kasteren SI, McGouran JF. Probing the metalloproteome: an 8-mercaptoquinoline motif enriches minichromosome maintenance complex components as significant metalloprotein targets in live cells. RSC Chem Biol 2024; 5:776-786. [PMID: 39092446 PMCID: PMC11289876 DOI: 10.1039/d4cb00053f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/18/2024] [Indexed: 08/04/2024] Open
Abstract
Affinity-based probes are valuable tools for detecting binding interactions between small molecules and proteins in complex biological environments. Metalloproteins are a class of therapeutically significant biomolecules which bind metal ions as part of key structural or catalytic domains and are compelling targets for study. However, there is currently a limited range of chemical tools suitable for profiling the metalloproteome. Here, we describe the preparation and application of a novel, photoactivatable affinity-based probe for detection of a subset of previously challenging to engage metalloproteins. The probe, bearing an 8-mercaptoquinoline metal chelator, was anticipated to engage several zinc metalloproteins, including the 26S-proteasome subunit Rpn11. Upon translation of the labelling experiment to mammalian cell lysate and live cell experiments, proteomic analysis revealed that several metalloproteins were competitively enriched. The diazirine probe SMK-24 was found to effectively enrich multiple components of the minichromosome maintenance complex, a zinc metalloprotein assembly with helicase activity essential to DNA replication. Cell cycle analysis experiments revealed that HEK293 cells treated with SMK-24 experienced stalling in G0/G1 phase, consistent with inactivation of the DNA helicase complex. This work represents an important contribution to the library of cell-permeable chemical tools for studying a collection of metalloproteins for which no previous probe existed.
Collapse
Affiliation(s)
- Sean M McKenna
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse St Dublin 2 Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC) Ireland
| | - Bogdan I Florea
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Daniela M Zisterer
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse St Dublin 2 Ireland
| | - Sander I van Kasteren
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Joanna F McGouran
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin 152-160 Pearse St Dublin 2 Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC) Ireland
| |
Collapse
|
2
|
Singh VP, Hirose S, Takemoto M, Farrag AMAS, Sato SI, Honjo T, Chamoto K, Uesugi M. Chemoproteomic Identification of Spermidine-Binding Proteins and Antitumor-Immunity Activators. J Am Chem Soc 2024. [PMID: 38848460 DOI: 10.1021/jacs.3c14615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Cancer immune therapies, particularly programmed cell death protein 1 (PD-1) blockade immunotherapy, falter in aged individuals due to compromised T-cell immunity. Spermidine, a biogenic polyamine that declines along with aging, shows promise in restoring antitumor immunity by enhancing mitochondrial fatty acid oxidation (FAO). Herein, we report a spermidine-based chemoproteomic probe (probe 2) that enables profiling of spermidine-binding proteins and screening for small-molecule enhancers of mitochondrial FAO. Chemoproteomic profiling by the probe revealed 140 proteins engaged in cellular interaction with spermidine, with a significant majority being mitochondrial proteins. Hydroxyl coenzyme A (CoA) dehydrogenase subunits α (HADHA) and other lipid metabolism-linked proteins are among the mitochondrial proteins that have attracted considerable interest. Screening spermidine analogs with the probe led to the discovery of compound 13, which interacts with these lipid metabolism-linked proteins and activates HADHA. This simple and biostable synthetic compound we named "spermimic" mirrors spermidine's ability to enhance mitochondrial bioenergetics and displays similar effectiveness in augmenting PD-1 blockade therapy in mice. This study lays the foundation for developing small-molecule activators of antitumor immunity, offering potential in combination cancer immunotherapy.
Collapse
Affiliation(s)
- Vaibhav Pal Singh
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Shuhei Hirose
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Misao Takemoto
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Asmaa M A S Farrag
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Shin-Ichi Sato
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tasuku Honjo
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Kenji Chamoto
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
- Department of Immuno-Oncology PDT, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Motonari Uesugi
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Kyoto 606-8372, Japan
| |
Collapse
|
3
|
Knörlein A, Xiao Y, David Y. Leveraging histone glycation for cancer diagnostics and therapeutics. Trends Cancer 2023; 9:410-420. [PMID: 36804508 PMCID: PMC10121827 DOI: 10.1016/j.trecan.2023.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 02/22/2023]
Abstract
Cancer cells undergo metabolic reprogramming to rely mostly on aerobic glycolysis (the Warburg effect). The increased glycolytic intake enhances the intracellular levels of reactive sugars and sugar metabolites. These reactive species can covalently modify macromolecules in a process termed glycation. Histones are particularly susceptible to glycation, resulting in substantial alterations to chromatin structure, function, and transcriptional output. Growing evidence suggests a link between dysregulated metabolism of tumors and cancer proliferation through epigenetic changes. This review discusses recent advances in the understanding of histone glycation, its impact on the epigenetic landscape and cellular fate, and its role in cancer. In addition, we investigate the possibility of using histone glycation as biomarkers and targets for anticancer therapeutics.
Collapse
Affiliation(s)
- Anna Knörlein
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yang Xiao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA; Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
4
|
Machine Learning Applied to the Modeling of Pharmacological and ADMET Endpoints. Methods Mol Biol 2021. [PMID: 34731464 DOI: 10.1007/978-1-0716-1787-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The well-known concept of quantitative structure-activity relationships (QSAR) has been gaining significant interest in the recent years. Data, descriptors, and algorithms are the main pillars to build useful models that support more efficient drug discovery processes with in silico methods. Significant advances in all three areas are the reason for the regained interest in these models. In this book chapter we review various machine learning (ML) approaches that make use of measured in vitro/in vivo data of many compounds. We put these in context with other digital drug discovery methods and present some application examples.
Collapse
|