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Jones LH. Advances in sulfonyl exchange chemical biology: expanding druggable target space. Chem Sci 2025:d5sc02647d. [PMID: 40443986 PMCID: PMC12117709 DOI: 10.1039/d5sc02647d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2025] [Accepted: 05/05/2025] [Indexed: 06/02/2025] Open
Abstract
Targeted covalent inhibitors possess advantages over reversible binding drugs, that include higher potency, enhanced selectivity and prolonged pharmacodynamic duration. The standard paradigm for covalent inhibitor discovery relies on the use of α,β-unsaturated carbonyl electrophiles to engage the nucleophilic cysteine thiol, but due to its rarity in binding sites, the amino acid is often not available for targeting. 10 years ago we highlighted the emerging potential of sulfonyl fluoride chemical probes that were initially found to serendipitously modify residues beyond cysteine, including tyrosine, lysine, histidine, serine and threonine. Since then, the rational application of sulfonyl fluorides and related sulfonyl exchange warheads to site-specifically target diverse amino acid residues in proteins using small molecules, oligonucleotides, peptides and proteins, has made considerable progress, which has significantly advanced covalent therapeutic discovery. Additionally, sulfonyl exchange chemistry has recently shown utility in the labeling of RNA and carbohydrates, further expanding the biomolecular diversity of addressable targets. This Perspective provides not only a timely update regarding this exciting area of research, thus serving as a useful resource to scientists working in the field, but areas of challenge and opportunity are highlighted that may stimulate new research at the chemistry-biology interface.
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Affiliation(s)
- Lyn H Jones
- Dana-Farber Cancer Institute Boston MA USA
- Harvard Medical School Boston MA USA
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2
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Peters-Clarke TM, Liang Y, Mertz KL, Lee KW, Westphall MS, Hinkle JD, McAlister GC, Syka JEP, Kelly RT, Coon JJ. Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags. J Proteome Res 2025; 24:1539-1548. [PMID: 38713017 PMCID: PMC12068060 DOI: 10.1021/acs.jproteome.4c00076] [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: 05/08/2024]
Abstract
Single-cell proteomics is a powerful approach to precisely profile protein landscapes within individual cells toward a comprehensive understanding of proteomic functions and tissue and cellular states. The inherent challenges associated with limited starting material demand heightened analytical sensitivity. Just as advances in sample preparation maximize the amount of material that makes it from the cell to the mass spectrometer, we strive to maximize the number of ions that make it from ion source to the detector. In isobaric tagging experiments, limited reporter ion generation limits quantitative accuracy and precision. The combination of infrared photoactivation and ion parking circumvents the m/z dependence inherent in HCD, maximizing reporter generation and avoiding unintended degradation of TMT reporter molecules in infrared-tandem mass tags (IR-TMT). The method was applied to single-cell human proteomes using 18-plex TMTpro, resulting in 4-5-fold increases in reporter signal compared to conventional SPS-MS3 approaches. IR-TMT enables faster duty cycles, higher throughput, and increased peptide identification and quantification. Comparative experiments showcase 4-5-fold lower injection times for IR-TMT, providing superior sensitivity without compromising accuracy. In all, IR-TMT enhances the dynamic range of proteomic experiments and is compatible with gas-phase fractionation and real-time searching, promising increased gains in the study of cellular heterogeneity.
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Affiliation(s)
- Trenton M. Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yiran Liang
- Department of Chemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Keaton L. Mertz
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kenneth W. Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | | | | | - Ryan T. Kelly
- Department of Chemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA
- Morgridge Institute for Research, Madison, WI, 53515, USA
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3
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Lyu B, Gou W, Xu F, Chen L, Wang Z, Ren Z, Liu G, Li Y, Hou W. Target Discovery Driven by Chemical Biology and Computational Biology. CHEM REC 2025; 25:e202400182. [PMID: 39811950 DOI: 10.1002/tcr.202400182] [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: 09/09/2024] [Revised: 12/06/2024] [Indexed: 01/16/2025]
Abstract
Target identification is crucial for drug screening and development because it can reveal the mechanism of drug action and ensure the reliability and accuracy of the results. Chemical biology, an interdisciplinary field combining chemistry and biology, can assist in this process by studying the interactions between active molecular compounds and proteins and their physiological effects. It can also help predict potential drug targets or candidates, develop new biomarker assays and diagnostic reagents, and evaluate the selectivity and range of active compounds to reduce the risk of off-target effects. Chemical biology can achieve these goals using techniques such as changing protein thermal stability, enzyme sensitivity, and molecular structure and applying probes, isotope labeling and mass spectrometry. Concurrently, computational biology employs a diverse array of computational models to predict drug targets. This approach also offers innovative avenues for repurposing existing drugs. In this paper, we review the reported chemical biology and computational biology techniques for identifying different types of targets that can provide valuable insights for drug target discovery.
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Affiliation(s)
- Bohai Lyu
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Wenfeng Gou
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Feifei Xu
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Leyuan Chen
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Zhiyun Wang
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Zhonghao Ren
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Gaiting Liu
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yiliang Li
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Wenbin Hou
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
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Shikwana F, Heydari BS, Ofori S, Truong C, Turmon AC, Darrouj J, Holoidovsky L, Gustafson JL, Backus KM. CySP3-96 enables scalable, streamlined, and low-cost sample preparation for cysteine chemoproteomic applications. Mol Cell Proteomics 2024:100898. [PMID: 39706478 DOI: 10.1016/j.mcpro.2024.100898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 11/19/2024] [Accepted: 12/06/2024] [Indexed: 12/23/2024] Open
Abstract
Cysteine chemoproteomic screening platforms are widely utilized for chemical probe and drug discovery campaigns. Chemoproteomic compound screens, which use a mass spectrometry-based proteomic readout, can interrogate the structure activity relationship (SAR) for thousands of proteins in parallel across the proteome. The versatility of chemoproteomic screens has been demonstrated across electrophilic, nucleophilic, and reversible classes of molecules. However, a key bottleneck that remains for these approaches is the low throughput nature of most established sample preparation workflows, which rely on many time-intensive and often error prone steps. Addressing these challenges, here we establish a novel workflow, termed CySP3-96, that pairs single-pot, solid-phase-enhanced, sample preparation (SP3) with a customized 96-well sample cleanup workflow to achieve streamlined multiplexed sample preparation. Our CySP3-96 method addresses prior volume limitations of SP3, which allows for seamless 96-well chemoproteomic sample preparation, including for large input amounts that are incompatible with prior methods. By deploying CySP3-96 to screen a focused set of 16 cysteine-reactive compounds, we identify 2633 total ligandable cysteines, including 21 not captured in CysDB. Chemoproteomic analysis of a pair of atropisomeric electrophilic kinase inhibitors reveals striking stereoselective cysteine ligandability for 67 targets across the proteome. When paired with our innovative budget friendly magnetic resin, CySP3-96 represents a versatile, low cost, and highly reproducible screening platform with widespread applications spanning all types of chemoproteomic studies.
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Affiliation(s)
- Flowreen Shikwana
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Beeta S Heydari
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA. 92182, USA
| | - Samuel Ofori
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Cindy Truong
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Joelle Darrouj
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Lara Holoidovsky
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Jeffrey L Gustafson
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA. 92182, USA; Stony Brook University, Stony Brook NY, 11794, USA
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA.
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Wiest A, Kielkowski P. Improved deconvolution of natural products' protein targets using diagnostic ions from chemical proteomics linkers. Beilstein J Org Chem 2024; 20:2323-2341. [PMID: 39290210 PMCID: PMC11406061 DOI: 10.3762/bjoc.20.199] [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: 04/05/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
Identification of interactions between proteins and natural products or similar active small molecules is crucial for understanding of their mechanism of action on a molecular level. To search elusive, often labile, and low-abundant conjugates between proteins and active compounds, chemical proteomics introduces a feasible strategy that allows to enrich and detect these conjugates. Recent advances in mass spectrometry techniques and search algorithms provide unprecedented depth of proteome coverage and the possibility to detect desired modified peptides with high sensitivity. The chemical 'linker' connecting an active compound-protein conjugate with a detection tag is the critical component of all chemical proteomic workflows. In this review, we discuss the properties and applications of different chemical proteomics linkers with special focus on their fragmentation releasing diagnostic ions and how these may improve the confidence in identified active compound-peptide conjugates. The application of advanced search options improves the identification rates and may help to identify otherwise difficult to find interactions between active compounds and proteins, which may result from unperturbed conditions, and thus are of high physiological relevance.
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Affiliation(s)
- Andreas Wiest
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Pavel Kielkowski
- LMU Munich, Department of Chemistry, Butenandtstr. 5-13, 81377 Munich, Germany
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Burton NR, Backus KM. Functionalizing tandem mass tags for streamlining click-based quantitative chemoproteomics. Commun Chem 2024; 7:80. [PMID: 38600184 PMCID: PMC11006884 DOI: 10.1038/s42004-024-01162-x] [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: 12/01/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Mapping the ligandability or potential druggability of all proteins in the human proteome is a central goal of mass spectrometry-based covalent chemoproteomics. Achieving this ambitious objective requires high throughput and high coverage sample preparation and liquid chromatography-tandem mass spectrometry analysis for hundreds to thousands of reactive compounds and chemical probes. Conducting chemoproteomic screens at this scale benefits from technical innovations that achieve increased sample throughput. Here we realize this vision by establishing the silane-based cleavable linkers for isotopically-labeled proteomics-tandem mass tag (sCIP-TMT) proteomic platform, which is distinguished by early sample pooling that increases sample preparation throughput. sCIP-TMT pairs a custom click-compatible sCIP capture reagent that is readily functionalized in high yield with commercially available TMT reagents. Synthesis and benchmarking of a 10-plex set of sCIP-TMT reveal a substantial decrease in sample preparation time together with high coverage and high accuracy quantification. By screening a focused set of four cysteine-reactive electrophiles, we demonstrate the utility of sCIP-TMT for chemoproteomic target hunting, identifying 789 total liganded cysteines. Distinguished by its compatibility with established enrichment and quantification protocols, we expect sCIP-TMT will readily translate to a wide range of covalent chemoproteomic applications.
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Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles CA, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles CA, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
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