1
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Bourner LA, Chung LA, Long H, McGettrick AF, Xiao J, Roth K, Bailey JD, Strickland M, Tan B, Cunningham J, Lutzke B, McGee J, Otero FJ, Gemperline DC, Zhang L, Wang YC, Chalmers MJ, Yang CW, Gutierrez JA, O'Neill LAJ, Dorsey FC. Endogenously produced itaconate negatively regulates innate-driven cytokine production and drives global ubiquitination in human macrophages. Cell Rep 2024; 43:114570. [PMID: 39093697 DOI: 10.1016/j.celrep.2024.114570] [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: 10/24/2022] [Revised: 05/13/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
A wide variety of electrophilic derivatives of itaconate, the Kreb's cycle-derived metabolite, are immunomodulatory, yet these derivatives have overlapping and sometimes contradictory activities. Therefore, we generated a genetic system to interrogate the immunomodulatory functions of endogenously produced itaconate in human macrophages. Endogenous itaconate is driven by multiple innate signals restraining inflammatory cytokine production. Endogenous itaconate directly targets cysteine 13 in IRAK4 (disrupting IRAK4 autophosphorylation and activation), drives the degradation of nuclear factor κB, and modulates global ubiquitination patterns. As a result, cells unable to make itaconate overproduce inflammatory cytokines such as tumor necrosis factor alpha (TNFα), interleukin-6 (IL-6), and IL-1β in response to these innate activators. In contrast, the production of interferon (IFN)β, downstream of LPS, requires the production of itaconate. These data demonstrate that itaconate is a critical arbiter of inflammatory cytokine production downstream of multiple innate signaling pathways, laying the groundwork for the development of itaconate mimetics for the treatment of autoimmunity.
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Affiliation(s)
- Luke A Bourner
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Linda A Chung
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Haiyan Long
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Anne F McGettrick
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, D02 PN40 Dublin, Ireland
| | - Junpeng Xiao
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Kenneth Roth
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Jade D Bailey
- Sitryx Therapeutics Limited, Bellhouse Building, Magdalen Centre, The Oxford Science Park, Oxford OX4 4GA, UK
| | - Marie Strickland
- Sitryx Therapeutics Limited, Bellhouse Building, Magdalen Centre, The Oxford Science Park, Oxford OX4 4GA, UK
| | - Bo Tan
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Jason Cunningham
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Barry Lutzke
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - James McGee
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Francella J Otero
- Eli Lilly and Company, Lilly Biotechnology Center, San Diego, CA 92121, USA
| | - David C Gemperline
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Lin Zhang
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Ying C Wang
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Michael J Chalmers
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Chiao-Wen Yang
- Eli Lilly and Company, Lilly Biotechnology Center, San Diego, CA 92121, USA
| | - Jesus A Gutierrez
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, D02 PN40 Dublin, Ireland
| | - Frank C Dorsey
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.
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2
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Li Z, Jiang J, Ficarro SB, Beyett TS, To C, Tavares I, Zhu Y, Li J, Eck MJ, Jänne PA, Marto JA, Zhang T, Che J, Gray NS. Molecular Bidents with Two Electrophilic Warheads as a New Pharmacological Modality. ACS CENTRAL SCIENCE 2024; 10:1156-1166. [PMID: 38947214 PMCID: PMC11212140 DOI: 10.1021/acscentsci.3c01245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 07/02/2024]
Abstract
A systematic strategy to develop dual-warhead inhibitors is introduced to circumvent the limitations of conventional covalent inhibitors such as vulnerability to mutations of the corresponding nucleophilic residue. Currently, all FDA-approved covalent small molecules feature one electrophile, leaving open a facile route to acquired resistance. We conducted a systematic analysis of human proteins in the protein data bank to reveal ∼400 unique targets amendable to dual covalent inhibitors, which we term "molecular bidents". We demonstrated this strategy by targeting two kinases: MKK7 and EGFR. The designed compounds, ZNL-8162 and ZNL-0056, are ATP-competitive inhibitors that form two covalent bonds with cysteines and retain potency against single cysteine mutants. Therefore, molecular bidents represent a new pharmacological modality with the potential for improved selectivity, potency, and drug resistance profile.
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Affiliation(s)
- Zhengnian Li
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Jie Jiang
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Scott B. Ficarro
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s
Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tyler S. Beyett
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Ciric To
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Isidoro Tavares
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Yingde Zhu
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jiaqi Li
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Michael J. Eck
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Pasi A. Jänne
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jarrod A. Marto
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s
Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tinghu Zhang
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Jianwei Che
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Nathanael S. Gray
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
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3
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McCarthy WJ, van der Zouwen AJ, Bush JT, Rittinger K. Covalent fragment-based drug discovery for target tractability. Curr Opin Struct Biol 2024; 86:102809. [PMID: 38554479 DOI: 10.1016/j.sbi.2024.102809] [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: 02/07/2024] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 04/01/2024]
Abstract
An important consideration in drug discovery is the prioritization of tractable protein targets that are not only amenable to binding small molecules, but also alter disease biology in response to small molecule binding. Covalent fragment-based drug discovery has emerged as a powerful approach to aid in the identification of such protein targets. The application of irreversible binding mechanisms enables the identification of fragment hits for challenging-to-target proteins, allows proteome-wide screening in a cellular context, and makes it possible to determine functional effects with modestly potent ligands without the requirement for extensive compound optimization. Here, we provide an overview of recent approaches to covalent fragment-based screening and discuss how these have been applied to establish the tractability of unexplored binding sites on protein targets.
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Affiliation(s)
- William J McCarthy
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Antonie J van der Zouwen
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jacob T Bush
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK. https://twitter.com/Jake_T_Bush
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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4
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Lamontagne F, Paz-Trejo C, Zamorano Cuervo N, Grandvaux N. Redox signaling in cell fate: Beyond damage. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119722. [PMID: 38615720 DOI: 10.1016/j.bbamcr.2024.119722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/20/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024]
Abstract
This review explores the nuanced role of reactive oxygen species (ROS) in cell fate, challenging the traditional view that equates ROS with cellular damage. Through significant technological advancements in detecting localized redox states and identifying oxidized cysteines, a paradigm shift has emerged: from ROS as merely damaging agents to crucial players in redox signaling. We delve into the intricacies of redox mechanisms, which, although confined, exert profound influences on cellular physiological responses. Our analysis extends to both the positive and negative impacts of these mechanisms on cell death processes, including uncontrolled and programmed pathways. By unraveling these complex interactions, we argue against the oversimplified notion of a 'stress response', advocating for a more nuanced understanding of redox signaling. This review underscores the importance of localized redox states in determining cell fate, highlighting the sophistication and subtlety of ROS functions beyond mere damage.
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Affiliation(s)
- Felix Lamontagne
- CRCHUM - Centre de Recherche du Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal H2X 0A9, Québec, Canada
| | - Cynthia Paz-Trejo
- CRCHUM - Centre de Recherche du Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal H2X 0A9, Québec, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal H3C 3J7, Québec, Canada
| | - Natalia Zamorano Cuervo
- CRCHUM - Centre de Recherche du Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal H2X 0A9, Québec, Canada
| | - Nathalie Grandvaux
- CRCHUM - Centre de Recherche du Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal H2X 0A9, Québec, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal H3C 3J7, Québec, Canada.
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5
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Liu Z, Remsberg JR, Li H, Njomen E, DeMeester KE, Tao Y, Xia G, Hayward RE, Yoo M, Nguyen T, Simon GM, Schreiber SL, Melillo B, Cravatt BF. Proteomic Ligandability Maps of Spirocycle Acrylamide Stereoprobes Identify Covalent ERCC3 Degraders. J Am Chem Soc 2024; 146:10393-10406. [PMID: 38569115 PMCID: PMC11211653 DOI: 10.1021/jacs.3c13448] [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: 04/05/2024]
Abstract
Covalent chemistry coupled with activity-based protein profiling (ABPP) offers a versatile way to discover ligands for proteins in native biological systems. Here, we describe a set of stereo- and regiochemically defined spirocycle acrylamides and the analysis of these electrophilic "stereoprobes" in human cancer cells by cysteine-directed ABPP. Despite showing attenuated reactivity compared to structurally related azetidine acrylamide stereoprobes, the spirocycle acrylamides preferentially liganded specific cysteines on diverse protein classes. One compound termed ZL-12A promoted the degradation of the TFIIH helicase ERCC3. Interestingly, ZL-12A reacts with the same cysteine (C342) in ERCC3 as the natural product triptolide, which did not lead to ERCC3 degradation but instead causes collateral loss of RNA polymerases. ZL-12A and triptolide cross-antagonized one another's protein degradation profiles. Finally, we provide evidence that the antihypertension drug spironolactone─previously found to promote ERCC3 degradation through an enigmatic mechanism─also reacts with ERCC3_C342. Our findings thus describe monofunctional degraders of ERCC3 and highlight how covalent ligands targeting the same cysteine can produce strikingly different functional outcomes.
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Affiliation(s)
- Zhonglin Liu
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Haoxin Li
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Yongfeng Tao
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Guoqin Xia
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Minjin Yoo
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | | | - Stuart L. Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
| | - Benjamin F. Cravatt
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
- Vividion Therapeutics, San Diego, CA 92121, USA
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6
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Ali MY, Bar-Peled L. Chemical proteomics to study metabolism, a reductionist approach applied at the systems level. Cell Chem Biol 2024; 31:446-451. [PMID: 38518745 DOI: 10.1016/j.chembiol.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/02/2023] [Accepted: 02/28/2024] [Indexed: 03/24/2024]
Abstract
Cellular metabolism encompasses a complex array of interconnected biochemical pathways that are required for cellular homeostasis. When dysregulated, metabolism underlies multiple human pathologies. At the heart of metabolic networks are enzymes that have been historically studied through a reductionist lens, and more recently, using high throughput approaches including genomics and proteomics. Merging these two divergent viewpoints are chemical proteomic technologies, including activity-based protein profiling, which combines chemical probes specific to distinct enzyme families or amino acid residues with proteomic analysis. This enables the study of metabolism at the network level with the precision of powerful biochemical approaches. Herein, we provide a primer on how chemical proteomic technologies custom-built for studying metabolism have unearthed fundamental principles in metabolic control. In parallel, these technologies have leap-frogged drug discovery through identification of novel targets and drug specificity. Collectively, chemical proteomics technologies appear to do the impossible: uniting systematic analysis with a reductionist approach.
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Affiliation(s)
- Md Yousuf Ali
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
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7
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Ogasawara D, Konrad DB, Tan ZY, Carey KL, Luo J, Won SJ, Li H, Carter T, DeMeester KE, Njomen E, Schreiber SL, Xavier RJ, Melillo B, Cravatt BF. Chemical tools to expand the ligandable proteome: diversity-oriented synthesis-based photoreactive stereoprobes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582206. [PMID: 38464067 PMCID: PMC10925180 DOI: 10.1101/2024.02.27.582206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Chemical proteomics enables the global assessment of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, been limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically-defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these 'photo-stereoprobes' interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible nanoBRET assays. Integrated phenotypic analysis and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and discovering and characterizing bioactive small molecules by cell-based screening.
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8
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Bak DW, Weerapana E. A Chemoproteomic Approach to Monitor Native Iron-Sulfur Cluster Binding. Methods Mol Biol 2024; 2839:261-289. [PMID: 39008260 DOI: 10.1007/978-1-0716-4043-2_16] [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: 07/16/2024]
Abstract
Iron-sulfur (Fe-S) clusters are essential redox-active metallocofactors participating in electron transfer, radical chemistry, primary metabolism, and gene regulation. Successful trafficking and incorporation of Fe-S clusters into target proteins are critical to proper cellular function. While biophysical studies of isolated Fe-S proteins provide insight into the structure and function of these inorganic cofactors, few strategies currently exist to directly interrogate Fe-S cluster binding within a cellular environment. Here, we describe a chemoproteomic platform to report on Fe-S cluster incorporation and occupancy directly within a native proteome, enabling the characterization of Fe-S biogenesis pathways and the identification of undiscovered Fe-S proteins.
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Affiliation(s)
- Daniel W Bak
- Boston College, Department of Chemistry, Chestnut Hill, MA, USA
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9
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Evbuomwan IO, Alejolowo OO, Elebiyo TC, Nwonuma CO, Ojo OA, Edosomwan EU, Chikwendu JI, Elosiuba NV, Akulue JC, Dogunro FA, Rotimi DE, Osemwegie OO, Ojo AB, Ademowo OG, Adeyemi OS, Oluba OM. In silico modeling revealed phytomolecules derived from Cymbopogon citratus (DC.) leaf extract as promising candidates for malaria therapy. J Biomol Struct Dyn 2024; 42:101-118. [PMID: 36974933 DOI: 10.1080/07391102.2023.2192799] [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: 01/02/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
The emergence of varying levels of resistance to currently available antimalarial drugs significantly threatens global health. This factor heightens the urgency to explore bioactive compounds from natural products with a view to discovering and developing newer antimalarial drugs with novel mode of actions. Therefore, we evaluated the inhibitory effects of sixteen phytocompounds from Cymbopogon citratus leaf extract against Plasmodium falciparum drug targets such as P. falciparum circumsporozoite protein (PfCSP), P. falciparum merozoite surface protein 1 (PfMSP1) and P. falciparum erythrocyte membrane protein 1 (PfEMP1). In silico approaches including molecular docking, pharmacophore modeling and 3D-QSAR were adopted to analyze the inhibitory activity of the compounds under consideration. The molecular docking results indicated that a compound swertiajaponin from C. citratus exhibited a higher binding affinity (-7.8 kcal/mol) to PfMSP1 as against the standard artesunate-amodiaquine (-6.6 kcal/mol). Swertiajaponin also formed strong hydrogen bond interactions with LYS29, CYS30, TYR34, ASN52, GLY55 and CYS28 amino acid residues. In addition, quercetin another compound from C. citratus exhibited significant binding energies -6.8 and -8.3 kcal/mol with PfCSP and PfEMP1, respectively but slightly lower than the standard artemether-lumefantrine with binding energies of -7.4 kcal/mol against PfCSP and -8.7 kcal/mol against PfEMP1. Overall, the present study provides evidence that swertiajaponin and other phytomolecules from C. citratus have modulatory properties toward P. falciparum drug targets and thus may warrant further exploration in early drug discovery efforts against malaria. Furthermore, these findings lend credence to the folkloric use of C. citratus for malaria treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ikponmwosa Owen Evbuomwan
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
- Department of Food Science and Microbiology, Landmark University, Omu-Aran, Nigeria
| | - Omokolade Oluwaseyi Alejolowo
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | | | - Charles Obiora Nwonuma
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | - Oluwafemi Adeleke Ojo
- Phytomedicine, Molecular Toxicology and Computational Biochemistry Research Group, Department of Biochemistry, Bowen University, Iwo, Nigeria
| | - Evelyn Uwa Edosomwan
- Department of Animal and Environmental Biology, University of Benin, Benin City, Nigeria
| | | | | | | | | | - Damilare Emmanuel Rotimi
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | | | | | - Olusegun George Ademowo
- Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Nigeria
- Drug Research Laboratory, Institute of Advanced Medical Research and Training (IMRAT), College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oluyomi Stephen Adeyemi
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Olarewaju Michael Oluba
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
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10
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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11
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Michels J, Venkatesh D, Liu C, Budhu S, Zhong H, George MM, Thach D, Yao ZK, Ouerfelli O, Liu H, Stockwell BR, Campesato LF, Zamarin D, Zappasodi R, Wolchok JD, Merghoub T. APR-246 increases tumor antigenicity independent of p53. Life Sci Alliance 2024; 7:e202301999. [PMID: 37891002 PMCID: PMC10610029 DOI: 10.26508/lsa.202301999] [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: 02/18/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
We previously reported that activation of p53 by APR-246 reprograms tumor-associated macrophages to overcome immune checkpoint blockade resistance. Here, we demonstrate that APR-246 and its active moiety, methylene quinuclidinone (MQ) can enhance the immunogenicity of tumor cells directly. MQ treatment of murine B16F10 melanoma cells promoted activation of melanoma-specific CD8+ T cells and increased the efficacy of a tumor cell vaccine using MQ-treated cells even when the B16F10 cells lacked p53. We then designed a novel combination of APR-246 with the TLR-4 agonist, monophosphoryl lipid A, and a CD40 agonist to further enhance these immunogenic effects and demonstrated a significant antitumor response. We propose that the immunogenic effect of MQ can be linked to its thiol-reactive alkylating ability as we observed similar immunogenic effects with the broad-spectrum cysteine-reactive compound, iodoacetamide. Our results thus indicate that combination of APR-246 with immunomodulatory agents may elicit effective antitumor immune response irrespective of the tumor's p53 mutation status.
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Affiliation(s)
- Judith Michels
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Divya Venkatesh
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Cailian Liu
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sadna Budhu
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hong Zhong
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Mariam M George
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Daniel Thach
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Zhong-Ke Yao
- The Organic Synthesis Core Facility, MSK, New York, NY, USA
| | | | - Hengrui Liu
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Luis Felipe Campesato
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dmitriy Zamarin
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Jedd D Wolchok
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell, New York, NY, USA
| | - Taha Merghoub
- https://ror.org/02r109517 Department of Pharmacology, Swim Across America and Ludwig Collaborative Laboratory, Weill Cornell Medicine, New York, NY, USA
- https://ror.org/02r109517 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell, New York, NY, USA
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12
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Anantharajan J, Tan QW, Fulwood J, Sifang W, Huang Q, Ng HQ, Koh X, Xu W, Cherian J, Baburajendran N, Kang C, Ke Z. Identification and characterization of inhibitors covalently modifying catalytic cysteine of UBE2T and blocking ubiquitin transfer. Biochem Biophys Res Commun 2023; 689:149238. [PMID: 37979329 DOI: 10.1016/j.bbrc.2023.149238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023]
Abstract
UBE2T is an E2 ubiquitin ligase critical for ubiquitination of substrate and plays important roles in many diseases. Despite the important function, UBE2T is considered as an undruggable target due to lack of a pocket for binding to small molecules with satisfied properties for clinical applications. To develop potent and specific UBE2T inhibitors, we adopted a high-throughput screening assay and two compounds-ETC-6152 and ETC-9004 containing a sulfone tetrazole scaffold were identified. Solution NMR study demonstrated the direct interactions between UBE2T and compounds in solution. Further co-crystal structures reveal the binding modes of these compounds. Both compound hydrolysation and formation of a hydrogen bond with the thiol group of the catalytic cysteine were observed. The formation of covalent complex was confirmed with mass spectrometry. As these two compounds inhibit ubiquitin transfer, our study provides a strategy to develop potent inhibitors of UBE2T.
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Affiliation(s)
- Jothi Anantharajan
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Qian Wen Tan
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Justina Fulwood
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Wang Sifang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Hui Qi Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Xiaoying Koh
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Weijun Xu
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Joseph Cherian
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore.
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore.
| | - Zhiyuan Ke
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore.
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13
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Rochet LNC, Bahou C, Wojciechowski JP, Koutsopetras I, Britton P, Spears RJ, Thanasi IA, Shao B, Zhong L, Bučar DK, Aliev AE, Porter MJ, Stevens MM, Baker JR, Chudasama V. Use of pyridazinediones for tuneable and reversible covalent cysteine modification applied to peptides, proteins and hydrogels. Chem Sci 2023; 14:13743-13754. [PMID: 38075666 PMCID: PMC10699563 DOI: 10.1039/d3sc04976k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/27/2023] [Indexed: 05/02/2024] Open
Abstract
Reversible cysteine modification has been found to be a useful tool for a plethora of applications such as selective enzymatic inhibition, activity-based protein profiling and/or cargo release from a protein or a material. However, only a limited number of reagents display reliable dynamic/reversible thiol modification and, in most cases, many of these reagents suffer from issues of stability, a lack of modularity and/or poor rate tunability. In this work, we demonstrate the potential of pyridazinediones as novel reversible and tuneable covalent cysteine modifiers. We show that the electrophilicity of pyridazinediones correlates to the rates of the Michael addition and retro-Michael deconjugation reactions, demonstrating that pyridazinediones provide an enticing platform for readily tuneable and reversible thiol addition/release. We explore the regioselectivity of the novel reaction and unveil the reason for the fundamental increased reactivity of aryl bearing pyridazinediones by using DFT calculations and corroborating findings with SCXRD. We also applied this fundamental discovery to making more rapid disulfide rebridging agents in related work. We finally provide the groundwork for potential applications in various areas with exemplification using readily functionalised "clickable" pyridazinediones on clinically relevant cysteine and disulfide conjugated proteins, as well as on a hydrogel material.
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Affiliation(s)
- Léa N C Rochet
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Calise Bahou
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Jonathan P Wojciechowski
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - Ilias Koutsopetras
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Phyllida Britton
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Richard J Spears
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Ioanna A Thanasi
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Baihao Shao
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - Lisha Zhong
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - Dejan-Krešimir Bučar
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Abil E Aliev
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Michael J Porter
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London London SW7 2AZ UK
| | - James R Baker
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Vijay Chudasama
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
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14
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Qin Z, Zhang K, He P, Zhang X, Xie M, Fu Y, Gu C, Zhu Y, Tong A, Wei H, Zhang C, Xiang Y. Discovering covalent inhibitors of protein-protein interactions from trillions of sulfur(VI) fluoride exchange-modified oligonucleotides. Nat Chem 2023; 15:1705-1714. [PMID: 37653229 DOI: 10.1038/s41557-023-01304-z] [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: 06/04/2022] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
Molecules that covalently engage target proteins are widely used as activity-based probes and covalent drugs. The performance of these covalent inhibitors is, however, often compromised by the paradox of efficacy and risk, which demands a balance between reactivity and selectivity. The challenge is more evident when targeting protein-protein interactions owing to their low ligandability and undefined reactivity. Here we report sulfur(VI) fluoride exchange (SuFEx) in vitro selection, a general platform for high-throughput discovery of covalent inhibitors from trillions of SuFEx-modified oligonucleotides. With SuFEx in vitro selection, we identified covalent inhibitors that cross-link distinct residues of the SARS-CoV-2 spike protein at its protein-protein interaction interface with the human angiotensin-converting enzyme 2. A separate suite of covalent inhibitors was isolated for the human complement C5 protein. In both cases, we observed a clear disconnection between binding affinity and cross-linking reactivity, indicating that direct search for the aimed reactivity-as enabled by SuFEx in vitro selection-is vital for discovering covalent inhibitors of high selectivity and potency.
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Affiliation(s)
- Zichen Qin
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Kaining Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Ping He
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xue Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Miao Xie
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Yucheng Fu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunmei Gu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
- Beijing Institute of Collaborative Innovation (BICI), Beijing, China
| | - Yiying Zhu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Aijun Tong
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Xiang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China.
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15
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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16
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Li H, Ma T, Remsberg JR, Won SJ, DeMeester KE, Njomen E, Ogasawara D, Zhao KT, Huang TP, Lu B, Simon GM, Melillo B, Schreiber SL, Lykke-Andersen J, Liu DR, Cravatt BF. Assigning functionality to cysteines by base editing of cancer dependency genes. Nat Chem Biol 2023; 19:1320-1330. [PMID: 37783940 PMCID: PMC10698195 DOI: 10.1038/s41589-023-01428-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/24/2023] [Indexed: 10/04/2023]
Abstract
Covalent chemistry represents an attractive strategy for expanding the ligandability of the proteome, and chemical proteomics has revealed numerous electrophile-reactive cysteines on diverse human proteins. Determining which of these covalent binding events affect protein function, however, remains challenging. Here we describe a base-editing strategy to infer the functionality of cysteines by quantifying the impact of their missense mutation on cancer cell proliferation. The resulting atlas, which covers more than 13,800 cysteines on more than 1,750 cancer dependency proteins, confirms the essentiality of cysteines targeted by covalent drugs and, when integrated with chemical proteomic data, identifies essential, ligandable cysteines in more than 160 cancer dependency proteins. We further show that a stereoselective and site-specific ligand targeting an essential cysteine in TOE1 inhibits the nuclease activity of this protein through an apparent allosteric mechanism. Our findings thus describe a versatile method and valuable resource to prioritize the pursuit of small-molecule probes with high function-perturbing potential.
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Affiliation(s)
- Haoxin Li
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
| | - Tiantai Ma
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Sang Joon Won
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | - Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | - Kevin T Zhao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Bingwen Lu
- Vividion Therapeutics, San Diego, CA, USA
| | | | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jens Lykke-Andersen
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
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17
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Luo P, Zhang Q, Shen S, An Y, Yuan L, Wong YK, Huang S, Huang S, Huang J, Cheng G, Tian J, Chen Y, Zhang X, Li W, He S, Wang J, Du Q. Mechanistic engineering of celastrol liposomes induces ferroptosis and apoptosis by directly targeting VDAC2 in hepatocellular carcinoma. Asian J Pharm Sci 2023; 18:100874. [PMID: 38149060 PMCID: PMC10749887 DOI: 10.1016/j.ajps.2023.100874] [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: 07/01/2023] [Revised: 10/20/2023] [Accepted: 11/08/2023] [Indexed: 12/28/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of most common and deadliest malignancies. Celastrol (Cel), a natural product derived from the Tripterygium wilfordii plant, has been extensively researched for its potential effectiveness in fighting cancer. However, its clinical application has been hindered by the unclear mechanism of action. Here, we used chemical proteomics to identify the direct targets of Cel and enhanced its targetability and anti-tumor capacity by developing a Cel-based liposomes in HCC. We demonstrated that Cel selectively targets the voltage-dependent anion channel 2 (VDAC2). Cel directly binds to the cysteine residues of VDAC2, and induces cytochrome C release via dysregulating VDAC2-mediated mitochondrial permeability transition pore (mPTP) function. We further found that Cel induces ROS-mediated ferroptosis and apoptosis in HCC cells. Moreover, coencapsulation of Cel into alkyl glucoside-modified liposomes (AGCL) improved its antitumor efficacy and minimized its side effects. AGCL has been shown to effectively suppress the proliferation of tumor cells. In a xenograft nude mice experiment, AGCL significantly inhibited tumor growth and promoted apoptosis. Our findings reveal that Cel directly targets VDAC2 to induce mitochondria-dependent cell death, while the Cel liposomes enhance its targetability and reduces side effects. Overall, Cel shows promise as a therapeutic agent for HCC.
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Affiliation(s)
- Piao Luo
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qian Zhang
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shuo Shen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yehai An
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lixia Yuan
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yin-Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sizhe Huang
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shaohui Huang
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jingnan Huang
- Department of Nephrology, Shenzhen key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, China
| | - Guangqing Cheng
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiahang Tian
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yu Chen
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaoyong Zhang
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Weiguang Li
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 100872, China
| | - Songqi He
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jigang Wang
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Department of Nephrology, Shenzhen key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, China
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- National Pharmaceutical Engineering Center for Solid Preparation of Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, China
| | - Qingfeng Du
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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18
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Karkossa I, Fürst S, Großkopf H, von Bergen M, Schubert K. Oxidation is an underappreciated post-translational modification in the regulation of immune responses associated with changes in phosphorylation. Front Immunol 2023; 14:1244431. [PMID: 37809076 PMCID: PMC10559879 DOI: 10.3389/fimmu.2023.1244431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Although macrophages are known to be affected by their redox status, oxidation is not yet a well-recognized post-translational modification (PTM) in regulating macrophages and immune cells in general. While it has been described that the redox status of single cysteines in specific proteins is relevant for macrophage functions, global oxidation information is scarce. Hence, we globally assessed the impact of oxidation on macrophage activation using untargeted proteomics and PTM-omics. We exposed THP-1 macrophages to lipopolysaccharide (LPS) for 4 h and 24 h and applied a sequential iodoTMT labeling approach to get information on overall oxidation as well as reversible oxidation of cysteines. Thus, we identified 10452 oxidation sites, which were integratively analyzed with 5057 proteins and 7148 phosphorylation sites to investigate their co-occurance with other omics layers. Based on this integrative analysis, we found significant upregulation of several immune-related pathways, e.g. toll-like receptor 4 (TLR4) signaling, for which 19 proteins, 7 phosphorylation sites, and 39 oxidation sites were significantly affected, highlighting the relevance of oxidations in TLR4-induced macrophage activation. Co-regulation of oxidation and phosphorylation was observed, as evidenced by multiply modified proteins related to inflammatory pathways. Additionally, we observed time-dependent effects, with differences in the dynamics of oxidation sites compared to proteins and phosphorylation sites. Overall, this study highlights the importance of oxidation in regulating inflammatory processes and provides a method that can be readily applied to study the cellular redoxome globally.
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Affiliation(s)
- Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sabine Fürst
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute of Biochemistry, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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19
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Tallon AM, Xu Y, West GM, am Ende CW, Fox JM. Thiomethyltetrazines Are Reversible Covalent Cysteine Warheads Whose Dynamic Behavior can be "Switched Off" via Bioorthogonal Chemistry Inside Live Cells. J Am Chem Soc 2023; 145:16069-16080. [PMID: 37450839 PMCID: PMC10530612 DOI: 10.1021/jacs.3c04444] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Electrophilic small molecules that can reversibly modify proteins are of growing interest in drug discovery. However, the ability to study reversible covalent probes in live cells can be limited by their reversible reactivity after cell lysis and in proteomic workflows, leading to scrambling and signal loss. We describe how thiomethyltetrazines function as reversible covalent warheads for cysteine modification, and this dynamic labeling behavior can be "switched off" via bioorthogonal chemistry inside live cells. Simultaneously, the tetrazine serves as a bioorthogonal reporter enabling the introduction of tags for fluorescent imaging or affinity purification. Thiomethyltetrazines can label isolated proteins, proteins in cellular lysates, and proteins in live cells with second-order rate constants spanning 2 orders of magnitude (k2, 1-100 M-1 s-1). Reversible modification by thiomethyltetrazines can be switched off upon the addition of trans-cyclooctene in live cells, converting the dynamic thiomethyltetrazine tag into a Diels-Alder adduct which is stable to lysis and proteomic workflows. Time-course quenching experiments were used to demonstrate temporal control over electrophilic modification. Moreover, it is shown that "locking in" the tag through Diels-Alder chemistry enables the identification of protein targets that are otherwise lost during sample processing. Three probes were further evaluated to identify unique pathways in a live-cell proteomic study. We anticipate that discovery efforts will be enabled by the trifold function of thiomethyltetrazines as electrophilic warheads, bioorthogonal reporters, and switches for "locking in" stability.
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Affiliation(s)
- Amanda M. Tallon
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yingrong Xu
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Graham M. West
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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20
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chem Biol 2023; 30:811-827.e7. [PMID: 37419112 PMCID: PMC10510412 DOI: 10.1016/j.chembiol.2023.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/01/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.
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Affiliation(s)
- Tianyang Yan
- 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
| | - Ashley R Julio
- 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
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Andréa B Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Lisa M Boatner
- 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
| | - 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
| | - Kaitlyn B Nguyễn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Stephanie L Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, 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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21
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White MEH, Gil J, Tate EW. Proteome-wide structural analysis identifies warhead- and coverage-specific biases in cysteine-focused chemoproteomics. Cell Chem Biol 2023; 30:828-838.e4. [PMID: 37451266 DOI: 10.1016/j.chembiol.2023.06.021] [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: 11/10/2022] [Revised: 03/20/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Covalent drug discovery has undergone a resurgence over the past two decades and reactive cysteine profiling has emerged in parallel as a platform for ligand discovery through on- and off-target profiling; however, the scope of this approach has not been fully explored at the whole-proteome level. We combined AlphaFold2-predicted side-chain accessibilities for >95% of the human proteome with a meta-analysis of eighteen public cysteine profiling datasets, totaling 44,187 unique cysteine residues, revealing accessibility biases in sampled cysteines primarily dictated by warhead chemistry. Analysis of >3.5 million cysteine-fragment interactions further showed that hit elaboration and optimization drives increased bias against buried cysteine residues. Based on these data, we suggest that current profiling approaches cover a small proportion of potential ligandable cysteine residues and propose future directions for increasing coverage, focusing on high-priority residues and depth. All analysis and produced resources are freely available and extendable to other reactive amino acids.
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Affiliation(s)
- Matthew E H White
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; The Francis Crick Institute, London NW1 1AT, UK.
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22
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Karabulut S, Wijerathne DV, Gauld JW. Computational Insights into the Formation and Structure of S-N Containing Cyclic Peptides. ACS OMEGA 2023; 8:18234-18244. [PMID: 37251184 PMCID: PMC10210182 DOI: 10.1021/acsomega.3c01764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023]
Abstract
Cyclic peptides are known to have biologically important roles and may also be applicable to the pharmaceutical and other industries. Furthermore, thiols and amines, which are found throughout biological systems, can react to form S-N bonds and to date, ∼100 biomolecules containing such a bond have been identified. However, while there are in principle numerous S-N containing peptide-derived rings possible, only a few are presently known to occur in biochemical systems. Density functional theory-based calculations have been used to consider the formation and structure of S-N containing cyclic peptides from systematic series of linear peptides in which a cysteinyl has first been oxidized to a sulfenic or sulfonic acid. In addition, the possible effect of the cysteine's vicinal residue on the free energy of formation has also been considered. In general, when the cysteine is first oxidized to a sulfenic acid, only the formation of smaller S-N containing rings is calculated to be exergonic in aqueous solution. In contrast, when the cysteine is first oxidized to a sulfonic acid, the formation of all rings considered (with one exception) is calculated to be endergonic in aqueous solution. The nature of vicinal residue can influence ring formation through stabilizing or destabilizing intramolecular interactions.
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23
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Lazear MR, Remsberg JR, Jaeger MG, Rothamel K, Her HL, DeMeester KE, Njomen E, Hogg SJ, Rahman J, Whitby LR, Won SJ, Schafroth MA, Ogasawara D, Yokoyama M, Lindsey GL, Li H, Germain J, Barbas S, Vaughan J, Hanigan TW, Vartabedian VF, Reinhardt CJ, Dix MM, Koo SJ, Heo I, Teijaro JR, Simon GM, Ghosh B, Abdel-Wahab O, Ahn K, Saghatelian A, Melillo B, Schreiber SL, Yeo GW, Cravatt BF. Proteomic discovery of chemical probes that perturb protein complexes in human cells. Mol Cell 2023; 83:1725-1742.e12. [PMID: 37084731 PMCID: PMC10198961 DOI: 10.1016/j.molcel.2023.03.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
Abstract
Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such "binding-first" assays affect protein function, nonetheless, often remains unclear. Here, we describe a "function-first" proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.
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Affiliation(s)
- Michael R Lazear
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Martin G Jaeger
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Katherine Rothamel
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Jahan Rahman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Landon R Whitby
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Sang Joon Won
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | | | - Minoru Yokoyama
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Haoxin Li
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Jason Germain
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Sabrina Barbas
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Thomas W Hanigan
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Vincent F Vartabedian
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | | | - Melissa M Dix
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Seong Joo Koo
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Inha Heo
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - John R Teijaro
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Gabriel M Simon
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Brahma Ghosh
- Discovery Chemistry, Janssen Research & Development, Spring House, PA 19477, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Kay Ahn
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Spring House, PA 19477, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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24
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein—Drug Adducts. Pharmaceuticals (Basel) 2023; 16:ph16040547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein–drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein–drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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25
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Kalogirou AS, Oh HJ, Asquith CRM. The Synthesis and Biological Applications of the 1,2,3-Dithiazole Scaffold. Molecules 2023; 28:molecules28073193. [PMID: 37049953 PMCID: PMC10096614 DOI: 10.3390/molecules28073193] [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: 03/07/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
The 1,2,3-dithiazole is an underappreciated scaffold in medicinal chemistry despite possessing a wide variety of nascent pharmacological activities. The scaffold has a potential wealth of opportunities within these activities and further afield. The 1,2,3-dithiazole scaffold has already been reported as an antifungal, herbicide, antibacterial, anticancer agent, antiviral, antifibrotic, and is a melanin and Arabidopsis gibberellin 2-oxidase inhibitor. These structure activity relationships are discussed in detail, along with insights and future directions. The review also highlights selected synthetic strategies developed towards the 1,2,3-dithiazole scaffold, how these are integrated to accessibility of chemical space, and to the prism of current and future biological activities.
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Affiliation(s)
- Andreas S Kalogirou
- Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenis Str., Engomi, P.O. Box 22006, Nicosia 1516, Cyprus
| | - Hans J Oh
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christopher R M Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
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26
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Kumari P, Kaul G, Kumar TA, Akhir A, Shukla M, Sharma S, Kamat SS, Chopra S, Chakrapani H. Heterocyclic Diaryliodonium-Based Inhibitors of Carbapenem-Resistant Acinetobacter baumannii. Microbiol Spectr 2023; 11:e0477322. [PMID: 36976008 PMCID: PMC10101131 DOI: 10.1128/spectrum.04773-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
Finding new therapeutic strategies against Gram-negative pathogens such as Acinetobacter baumannii is challenging. Starting from diphenyleneiodonium (dPI) salts, which are moderate Gram-positive antibacterials, we synthesized a focused heterocyclic library and found a potent inhibitor of patient-derived multidrug-resistant Acinetobacter baumannii strains that significantly reduced bacterial burden in an animal model of infection caused by carbapenem-resistant Acinetobacter baumannii (CRAB), listed as a priority 1 critical pathogen by the World Health Organization. Next, using advanced chemoproteomics platforms and activity-based protein profiling (ABPP), we identified and biochemically validated betaine aldehyde dehydrogenase (BetB), an enzyme that is involved in the metabolism and maintenance of osmolarity, as a potential target for this compound. Together, using a new class of heterocyclic iodonium salts, a potent CRAB inhibitor was identified, and our study lays the foundation for the identification of new druggable targets against this critical pathogen. IMPORTANCE Discovery of novel antibiotics targeting multidrug-resistant (MDR) pathogens such as A. baumannii is an urgent, unmet medical need. Our work has highlighted the potential of this unique scaffold to annihilate MDR A. baumannii alone and in combination with amikacin both in vitro and in animals, that too without inducing resistance. Further in depth analysis identified central metabolism to be a putative target. Taken together, these experiments lay down the foundation for effective management of infections caused due to highly MDR pathogens.
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Affiliation(s)
- Pooja Kumari
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Grace Kaul
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - T. Anand Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Abdul Akhir
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Manjulika Shukla
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Suraj Sharma
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
| | - Sidharth Chopra
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Harinath Chakrapani
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pune, Maharashtra, India
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27
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Li J, Zhou J, Xu H, Tian K, Zhu H, Chen Y, Huang Y, Wang G, Gong Z, Qin H, Ye M. ACR-Based Probe for the Quantitative Profiling of Histidine Reactivity in the Human Proteome. J Am Chem Soc 2023; 145:5252-5260. [PMID: 36848482 DOI: 10.1021/jacs.2c12653] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The quantitative profiling of residue reactivity in proteins promotes the discovery of covalent druggable targets for precise therapy. Histidine (His) residues, accounting for more than 20% of the active sites in enzymes, have not been systematically characterized for their reactivity, due to lack of labeling probes. Herein, we report a chemical proteomics platform for the site-specific quantitative analysis of His reactivity by combination of acrolein (ACR) labeling and reversible hydrazine chemistry enrichment. Based on this platform, in-depth characterization of His residues was conducted for the human proteome, in which the rich content of His residues (>8200) was quantified, including 317 His hyper-reactive residues. Intriguingly, it was observed that the hyper-reactive residues were less likely to be the sites for phosphorylation, and the possible mechanism of this antagonistic effect still needs to be evaluated in further research. Based on the first comprehensive map of His residue reactivity, many more residues could be adopted as the bindable sites to disrupt the activities of a diverse number of proteins; meanwhile, ACR derivatives could also be used as a novel reactive warhead in the development of covalent inhibitors.
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Affiliation(s)
- Jiaying Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,College of Chemical Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Jiahua Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kailu Tian
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - He Zhu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Guosheng Wang
- College of Chemical Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,College of Chemical Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, 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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28
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Ramanathan R, Hatzios SK. Activity-based Tools for Interrogating Host Biology During Infection. Isr J Chem 2023; 63:e202200095. [PMID: 37744997 PMCID: PMC10512441 DOI: 10.1002/ijch.202200095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/18/2023]
Abstract
Host cells sense and respond to pathogens by dynamically regulating cell signaling. The rapid modulation of signaling pathways is achieved by post-translational modifications (PTMs) that can alter protein structure, function, and/or binding interactions. By using chemical probes to broadly profile changes in enzyme function or side-chain reactivity, activity-based protein profiling (ABPP) can reveal PTMs that regulate host-microbe interactions. While ABPP has been widely utilized to uncover microbial mechanisms of pathogenesis, in this review, we focus on more recent applications of this technique to the discovery of host PTMs and enzymes that modulate signaling within infected cells. Collectively, these advances underscore the importance of ABPP as a tool for interrogating the host response to infection and identifying potential targets for host-directed therapies.
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Affiliation(s)
- Renuka Ramanathan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
| | - Stavroula K. Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
- Department of Chemistry, Yale University, New Haven, CT 06520 USA
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29
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Hang HC. Benjamin F. Cravatt III – Chemical Proteomics Trailblazer. Isr J Chem 2023. [DOI: 10.1002/ijch.202200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Howard C. Hang
- Department of Immunology and Microbiology, Scripps Research La Jolla CA 92037
- Department of Chemistry, Scripps Research La Jolla CA 92037
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30
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Brulet JW, Ciancone AM, Yuan K, Hsu K. Advances in Activity‐Based Protein Profiling of Functional Tyrosines in Proteomes. Isr J Chem 2023. [DOI: 10.1002/ijch.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Jeffrey W. Brulet
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Anthony M. Ciancone
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Kun Yuan
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Ku‐Lung Hsu
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
- Department of Pharmacology University of Virginia School of Medicine Charlottesville Virginia 22908 United States
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia 22908 United States
- University of Virginia Cancer Center University of Virginia Charlottesville VA 22903 USA
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31
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525042. [PMID: 36711448 PMCID: PMC9882296 DOI: 10.1101/2023.01.22.525042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxiCat, Biotin Switch, and SP3-Rox, they typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. To obviate requirements for laborious biochemical fractionation, here, we develop and apply an unprecedented two step cysteine capture method to establish the Local Cysteine Capture (Cys-LoC), and Local Cysteine Oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole cell proteomic analysis. Application of the Cys-LOx method to LPS stimulated murine immortalized bone marrow-derived macrophages (iBMDM), revealed previously unidentified mitochondria-specific inflammation-induced cysteine oxidative modifications including those associated with oxidative phosphorylation. These findings shed light on post-translational mechanisms regulating mitochondrial function during the cellular innate immune response.
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Affiliation(s)
- Tianyang Yan
- 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
| | - Ashley R. Julio
- 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
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Anthony E. Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Andréa B. Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Lisa M. Boatner
- 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
| | - 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
| | - Stephanie L. Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Heta S. Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Ajit S. Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, 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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32
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LI J, WANG G, YE M, QIN H. [Advances in applications of activity-based chemical probes in the characterization of amino acid reactivities]. Se Pu 2023; 41:14-23. [PMID: 36633073 PMCID: PMC9837674 DOI: 10.3724/sp.j.1123.2022.05013] [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: 01/13/2023] Open
Abstract
The discovery of novel drug targets enhances the development of novel drugs, and the discovery of novel target proteins depends on highly accurate high-throughput methods of analyzing drug-protein interactions. Protein expression levels, spatial localization, and structural differences directly affect pharmacodynamics. To date, >20000 proteins have been discovered in the human proteome by the genome and proteome projects via gene and protein sequencing. Understanding the biological functions of proteins is critical in identifying and regulating biological processes, with most remaining unidentified. Until recently, >85% of proteins were considered undruggable, mainly because of the lack of binding pockets and active sites targeted by small molecules. Therefore, characterization of the reactive sites of amino acids based on proteomic hierarchy is the key to novel drug design. Recently, with the rapid development of mass spectrometry (MS), the study of drug-target protein interactions based on proteomics technology has been considerably promoted. Activity-based protein profiling (ABPP) is an active chemical probe-based method of detecting functional enzymes and drug targets in complex samples. Compared with classical proteomics strategies, ABPP is based mainly on protein activity. It has been successfully utilized to characterize the activities of numerous protease families with crucial biological functions, such as serine hydrolases, protein kinases, glycosidases, and metalloenzymes. It has also been used to identify key enzymes that are closely related to diseases and develop covalent inhibitors for use in disease treatment. The technology used in proteome analysis ranges from gel electrophoresis to high-throughput MS due to the progress of MS technology. ABPP strategies combined with chemical probe labeling and quantitative MS enable the characterization of amino acid activity, which may enhance the discovery of novel drug targets and the development of lead compounds. Amino acid residues play critical roles in protein structures and functions, and covalent drugs targeting these amino acids are effective in treating numerous diseases. There are 20 main types of natural amino acids, with different reactivities, in the proteins in the human body. In addition, the proteins and amino acids are affected by the spatial microenvironment, leading to significant differences in their spatial reactivities. The key in evaluating the reactivities of amino acids via ABPP is to select those with high reactivities. The core of the ABPP strategy is the use of chemical probes to label amino acid sites that exhibit higher activities in certain environments. The activity-based probe (ABP) at the core of ABPP consists of three components: reactive, reporter groups and a linker. The reactive group is the basis of the ABP and anchors the drug target via strong forces, such as covalent bonds. The reaction exhibits a high specificity and conversion rate and should display a good biocompatibility. Activity probes based on different amino acid residues have been developed, and the screening of amino acid activity combined with isotope labeling is a new focus of research. Currently, different types of ABPs have been developed to target amino acids and characterize amino acid reactivity, such as cysteine labeled with an electrophilic iodoacetamide probe and lysine labeled with activated esters. ABPP facilitates the discovery of potentially therapeutic protein targets, the screening of lead compounds, and the identification of drug targets, thus aiding the design of novel drugs. This review focuses on the development of ABPP methods and the progress in the screening of amino acid reactivity using ABPs, which should be promising methods for use in designing targeted drugs with covalent interactions.
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33
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Protein targeting by the itaconate family in immunity and inflammation. Biochem J 2022; 479:2499-2510. [PMID: 36546613 DOI: 10.1042/bcj20220364] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Immune cells are metabolically plastic and respond to inflammatory stimuli with large shifts in metabolism. Itaconate is one of the most up-regulated metabolites in macrophages in response to the gram negative bacterial product LPS. As such, itaconate has recently been the subject of intense research interest. The artificial derivatives, including 4-Octyl Itaconate (4-OI) and Dimethyl Itaconate (DI) and naturally produced isomers, mesaconate and citraconate, have been tested in relation to itaconate biology with similarities and differences in the biochemistry and immunomodulatory properties of this family of compounds emerging. Both itaconate and 4-OI have been shown to modify cysteines on a range of target proteins, with the modification being linked to a functional change. Targets include KEAP1 (the NRF2 inhibitor), GAPDH, NLRP3, JAK1, and the lysosomal regulator, TFEB. 4-OI and DI are more electrophilic, and are therefore stronger NRF2 activators, and inhibit the production of Type I IFNs, while itaconate inhibits SDH and the dioxygenase, TET2. Additionally, both itaconate and derivates have been shown to be protective across a wide range of mouse models of inflammatory and infectious diseases, through both distinct and overlapping mechanisms. As such, continued research involving the comparison of itaconate and related molecules holds exciting prospects for the study of cysteine modification and pathways for immunomodulation and the potential for new anti-inflammatory therapeutics.
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34
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Omoboyowa DA, Kareem JA, Saibu OA, Bodun DS, Ajayi TM, Oyeneyin OE. Identification of Phyto-Compounds from Ilex kudingcha as Inhibitors of Sterol-14α-Demethylase Protease: A Computational Approach Against Chagas Disease. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00565-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Gai C, Harnor SJ, Zhang S, Cano C, Zhuang C, Zhao Q. Advanced approaches of developing targeted covalent drugs. RSC Med Chem 2022; 13:1460-1475. [PMID: 36561076 PMCID: PMC9749957 DOI: 10.1039/d2md00216g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
In recent years, the development of targeted covalent inhibitors has gained popularity around the world. Specific groups (electrophilic warheads) form irreversible bonds with the side chain of nucleophilic amino acid residues, thus changing the function of biological targets such as proteins. Since the first targeted covalent inhibitor was disclosed in the 1990s, great efforts have been made to develop covalent ligands from known reversible leads or drugs by addition of tolerated electrophilic warheads. However, high reactivity and "off-target" toxicity remain challenging issues. This review covers the concept of targeted covalent inhibition to diseases, discusses traditional and interdisciplinary strategies of cysteine-focused covalent drug discovery, and exhibits newly disclosed electrophilic warheads majorly targeting the cysteine residue. Successful applications to address the challenges of designing effective covalent drugs are also introduced.
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Affiliation(s)
- Conghao Gai
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Suzannah J Harnor
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Shihao Zhang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Céline Cano
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Chunlin Zhuang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Qingjie Zhao
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
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Abstract
Covalent drugs have been used to treat diseases for more than a century, but tools that facilitate the rational design of covalent drugs have emerged more recently. The purposeful addition of reactive functional groups to existing ligands can enable potent and selective inhibition of target proteins, as demonstrated by the covalent epidermal growth factor receptor (EGFR) and Bruton's tyrosine kinase (BTK) inhibitors used to treat various cancers. Moreover, the identification of covalent ligands through 'electrophile-first' approaches has also led to the discovery of covalent drugs, such as covalent inhibitors for KRAS(G12C) and SARS-CoV-2 main protease. In particular, the discovery of KRAS(G12C) inhibitors validates the use of covalent screening technologies, which have become more powerful and widespread over the past decade. Chemoproteomics platforms have emerged to complement covalent ligand screening and assist in ligand discovery, selectivity profiling and target identification. This Review showcases covalent drug discovery milestones with emphasis on the lessons learned from these programmes and how an evolving toolbox of covalent drug discovery techniques facilitates success in this field.
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Affiliation(s)
- Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
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37
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Smith N, Wilson MA. Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography. CRYSTALS 2022; 12:1671. [PMID: 36685087 PMCID: PMC9850494 DOI: 10.3390/cryst12111671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (Mpro) and papain-like (PLpro) cysteine proteases of SARS-CoV-2 as well as other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques such as time-resolved sulfur X-ray spectroscopy that may be able to detect changes in sulfur charge state and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structure and dynamics during catalysis in crystalline samples.
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38
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Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth RD, Broichhagen J, Baik M, Hackenberger CPR. DFT-Guided Discovery of Ethynyl-Triazolyl-Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling. Angew Chem Int Ed Engl 2022; 61:e202205348. [PMID: 35792701 PMCID: PMC9804898 DOI: 10.1002/anie.202205348] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Indexed: 01/09/2023]
Abstract
We report the density functional theory (DFT) guided discovery of ethynyl-triazolyl-phosphinates (ETPs) as a new class of electrophilic warheads for cysteine selective bioconjugation. By using CuI -catalysed azide alkyne cycloaddition (CuAAC) in aqueous buffer, we were able to access a variety of functional electrophilic building blocks, including proteins, from diethynyl-phosphinate. ETP-reagents were used to obtain fluorescent peptide-conjugates for receptor labelling on live cells and a stable and a biologically active antibody-drug-conjugate. Moreover, we were able to incorporate ETP-electrophiles into an azide-containing ubiquitin under native conditions and demonstrate their potential in protein-protein conjugation. Finally, we showcase the excellent cysteine-selectivity of this new class of electrophile in mass spectrometry based, proteome-wide cysteine profiling, underscoring the applicability in homogeneous bioconjugation strategies to connect two complex biomolecules.
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Affiliation(s)
- Christian E. Stieger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Yerin Park
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Mark A. R. de Geus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Dongju Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Christiane Huhn
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - J. Sophia Slenczka
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 12410623BerlinGermany
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Judith M. Müchler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Roderich D. Süssmuth
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 12410623BerlinGermany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Mu‐Hyun Baik
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea,Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany,Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
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Kennedy C, McPhie K, Rittinger K. Targeting the ubiquitin system by fragment-based drug discovery. Front Mol Biosci 2022; 9:1019636. [PMID: 36275626 PMCID: PMC9580268 DOI: 10.3389/fmolb.2022.1019636] [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: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 11/22/2022] Open
Abstract
The ubiquitin system contains a wealth of potential drug targets for many diseases and conditions, including neurodegenerative, immune, metabolic and developmental diseases, as well as multiple cancers. Despite years of research, relatively few clinical inhibitors or specific chemical probes for proteins within the ubiquitin system exist, with many interesting target proteins yet to be explored. Fragment-based drug discovery (FBDD) offers efficient and broad coverage of chemical space with small libraries, using covalent and non-covalent approaches. Coupled with advances in structural biology and proteomics, FBDD now provides a thorough screening platform for inhibitor discovery within the ubiquitin system. In this mini review, we summarise the current scope of FBDD and how it has been applied to ubiquitin-activating (E1), ubiquitin-conjugating (E2), ubiquitin ligase (E3) and deubiquitinating (DUB) enzymes. We also discuss the newest frontiers of FBDD and how they could be applied to enable inhibitor and novel chemical probe discovery and provide functional insight into the ubiquitin system.
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40
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Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry 2022; 61:2165-2176. [PMID: 36161872 PMCID: PMC9583617 DOI: 10.1021/acs.biochem.2c00349] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cysteine side chains
can exist in distinct oxidation
states depending
on the pH and redox potential of the environment, and cysteine oxidation
plays important yet complex regulatory roles. Compared with the effects
of post-translational modifications such as phosphorylation, the effects
of oxidation of cysteine to sulfenic, sulfinic, and sulfonic acid
on protein structure and function remain relatively poorly characterized.
We present an analysis of the role of cysteine reactivity as a regulatory
factor in proteins, emphasizing the interplay between electrostatics
and redox potential as key determinants of the resulting oxidation
state. A review of current computational approaches suggests underdeveloped
areas of research for studying cysteine reactivity through molecular
simulations.
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Affiliation(s)
- Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Emma L Gunderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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41
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Kumar A, Aglyamova G, Yim Y, Bailey AO, Lynch H, Powell R, Nguyen N, Rosenthal Z, Zhao WN, Li Y, Chen J, Fan S, Lee H, Russell W, Stephan C, Robison A, Haggarty S, Nestler E, Zhou J, Machius M, Rudenko G. Chemically targeting the redox switch in AP1 transcription factor ΔFOSB. Nucleic Acids Res 2022; 50:9548-9567. [PMID: 36039764 PMCID: PMC9458432 DOI: 10.1093/nar/gkac710] [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: 05/24/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/24/2022] Open
Abstract
The AP1 transcription factor ΔFOSB, a splice variant of FOSB, accumulates in the brain in response to chronic insults such as exposure to drugs of abuse, depression, Alzheimer's disease and tardive dyskinesias, and mediates subsequent long-term neuroadaptations. ΔFOSB forms heterodimers with other AP1 transcription factors, e.g. JUND, that bind DNA under control of a putative cysteine-based redox switch. Here, we reveal the structural basis of the redox switch by determining a key missing crystal structure in a trio, the ΔFOSB/JUND bZIP domains in the reduced, DNA-free form. Screening a cysteine-focused library containing 3200 thiol-reactive compounds, we identify specific compounds that target the redox switch, validate their activity biochemically and in cell-based assays, and show that they are well tolerated in different cell lines despite their general potential to bind to cysteines covalently. A crystal structure of the ΔFOSB/JUND bZIP domains in complex with a redox-switch-targeting compound reveals a deep compound-binding pocket near the DNA-binding site. We demonstrate that ΔFOSB, and potentially other, related AP1 transcription factors, can be targeted specifically and discriminately by exploiting unique structural features such as the redox switch and the binding partner to modulate biological function despite these proteins previously being thought to be undruggable.
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Affiliation(s)
| | | | - Yun Young Yim
- Nash Family Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Haley M Lynch
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Reid T Powell
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Nghi D Nguyen
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Zachary Rosenthal
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jianping Chen
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shanghua Fan
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hubert Lee
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Clifford Stephan
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Alfred J Robison
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mischa Machius
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gabby Rudenko
- To whom correspondence should be addressed. Tel: +1 409 772 6292; Fax: +1 409 772 9642;
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42
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Feldman HC, Merlini E, Guijas C, DeMeester KE, Njomen E, Kozina EM, Yokoyama M, Vinogradova E, Reardon HT, Melillo B, Schreiber SL, Loreto A, Blankman JL, Cravatt BF. Selective inhibitors of SARM1 targeting an allosteric cysteine in the autoregulatory ARM domain. Proc Natl Acad Sci U S A 2022; 119:e2208457119. [PMID: 35994671 PMCID: PMC9436332 DOI: 10.1073/pnas.2208457119] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/25/2022] [Indexed: 12/23/2022] Open
Abstract
The nicotinamide adenine dinucleotide hydrolase (NADase) sterile alpha toll/interleukin receptor motif containing-1 (SARM1) acts as a central executioner of programmed axon death and is a possible therapeutic target for neurodegenerative disorders. While orthosteric inhibitors of SARM1 have been described, this multidomain enzyme is also subject to intricate forms of autoregulation, suggesting the potential for allosteric modes of inhibition. Previous studies have identified multiple cysteine residues that support SARM1 activation and catalysis, but which of these cysteines, if any, might be selectively targetable by electrophilic small molecules remains unknown. Here, we describe the chemical proteomic discovery of a series of tryptoline acrylamides that site-specifically and stereoselectively modify cysteine-311 (C311) in the noncatalytic, autoregulatory armadillo repeat (ARM) domain of SARM1. These covalent compounds inhibit the NADase activity of WT-SARM1, but not C311A or C311S SARM1 mutants, show a high degree of proteome-wide selectivity for SARM1_C311 and stereoselectively block vincristine- and vacor-induced neurite degeneration in primary rodent dorsal root ganglion neurons. Our findings describe selective, covalent inhibitors of SARM1 targeting an allosteric cysteine, pointing to a potentially attractive therapeutic strategy for axon degeneration-dependent forms of neurological disease.
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Affiliation(s)
| | - Elisa Merlini
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0PY, United Kingdom
| | - Carlos Guijas
- Lundbeck La Jolla Research Center Inc, San Diego, CA 92121
| | | | - Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA 92037
| | - Ellen M Kozina
- Lundbeck La Jolla Research Center Inc, San Diego, CA 92121
| | - Minoru Yokoyama
- Department of Chemistry, Scripps Research, La Jolla, CA 92037
| | | | | | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA 92037
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02138
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Andrea Loreto
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0PY, United Kingdom
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43
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Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth R, Broichhagen J, Baik MH, Hackenberger C. DFT‐Guided Discovery of Ethynyl‐Triazolyl‐Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Ewald Stieger
- Leibniz Institute for Molecular Pharmacology: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Yerin Park
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Mark A. R. de Geus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Dongju Kim
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Christiane Huhn
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chem Bio Probes GERMANY
| | - Julie Sophia Slenczka
- Technische Universität Berlin: Technische Universitat Berlin Institut für Chemie GERMANY
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Judith Maria Müchler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Roderich Süssmuth
- Technische Universität Berlin: Technische Universitat Berlin Institut für Chemie GERMANY
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chem Bio Probes GERMANY
| | - Mu-Hyun Baik
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Christian Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Deptm. of Chemical Biology Robert-Roessle Str. 10 13125 Berlin GERMANY
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44
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Jiang H, Zhang Q, Zhang Y, Feng H, Jiang H, Pu F, Yu R, Zhong Z, Wang C, Fung YME, Blasco P, Li Y, Jiang T, Li X. Triazine-pyridine chemistry for protein labelling on tyrosine. Chem Commun (Camb) 2022; 58:7066-7069. [PMID: 35648412 DOI: 10.1039/d2cc01528e] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we discover the new reactivity of the 1,3,5-triazine moiety reacting with a phenol group and report the development of biocompatible and catalyst-free triazine-pyridine chemistry (TPC) for tyrosine labelling under physiological conditions and profiling in the whole proteome. TPC exhibited high tyrosine chemoselectivity in biological systems after cysteine blocking, displayed potential in tyrosine-guided protein labelling, and had bio-compatibility in live cells.
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Affiliation(s)
- Hongfei Jiang
- Key Laboratory of Marine Drugs Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
| | - Qing Zhang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Yue Zhang
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Huxin Feng
- Key Laboratory of Marine Drugs Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
| | - Hao Jiang
- Key Laboratory of Marine Drugs Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
| | - Fan Pu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Rilei Yu
- Key Laboratory of Marine Drugs Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
| | - Zheng Zhong
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Chaoming Wang
- Key Laboratory of Marine Drugs Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
| | - Yi Man Eva Fung
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Pilar Blasco
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Yongxin Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
| | - Tao Jiang
- Key Laboratory of Marine Drugs Chinese Ministry of Education, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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45
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Hoopes CR, Garcia FJ, Sarkar AM, Kuehl NJ, Barkan DT, Collins NL, Meister GE, Bramhall TR, Hsu CH, Jones MD, Schirle M, Taylor MT. Donor-Acceptor Pyridinium Salts for Photo-Induced Electron-Transfer-Driven Modification of Tryptophan in Peptides, Proteins, and Proteomes Using Visible Light. J Am Chem Soc 2022; 144:6227-6236. [PMID: 35364811 PMCID: PMC10124759 DOI: 10.1021/jacs.1c10536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tryptophan (Trp) plays a variety of critical functional roles in protein biochemistry; however, owing to its low natural frequency and poor nucleophilicity, the design of effective methods for both single protein bioconjugation at Trp as well as for in situ chemoproteomic profiling remains a challenge. Here, we report a method for covalent Trp modification that is suitable for both scenarios by invoking photo-induced electron transfer (PET) as a means of driving efficient reactivity. We have engineered biaryl N-carbamoyl pyridinium salts that possess a donor-acceptor relationship that enables optical triggering with visible light whilst simultaneously attenuating the probe's photo-oxidation potential in order to prevent photodegradation. This probe was assayed against a small bank of eight peptides and proteins, where it was found that micromolar concentrations of the probe and short irradiation times (10-60 min) with violet light enabled efficient reactivity toward surface exposed Trp residues. The carbamate transferring group can be used to transfer useful functional groups to proteins including affinity tags and click handles. DFT calculations and other mechanistic analyses reveal correlations between excited state lifetimes, relative fluorescence quantum yields, and chemical reactivity. Biotinylated and azide-functionalized pyridinium salts were used for Trp profiling in HEK293T lysates and in situ in HEK293T cells using 440 nm LED irradiation. Peptide-level enrichment from live cell labeling experiments identified 290 Trp modifications, with 82% selectivity for Trp modification over other π-amino acids, demonstrating the ability of this method to identify and quantify reactive Trp residues from live cells.
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Affiliation(s)
- Caleb R Hoopes
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Francisco J Garcia
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Akash M Sarkar
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Nicholas J Kuehl
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - David T Barkan
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Nicole L Collins
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Glenna E Meister
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Taylor R Bramhall
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Chien-Hsiang Hsu
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Michael D Jones
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Michael T Taylor
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
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46
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Mazmanian K, Chen T, Sargsyan K, Lim C. From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1607. [PMID: 35600063 PMCID: PMC9111396 DOI: 10.1002/wcms.1607] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 12/20/2022]
Abstract
The COVID‐19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS‐CoV‐2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/continuum calculations led to a novel multi‐targeting strategy against SARS‐CoV‐2, in contrast to developing potent drugs/vaccines against a single viral target such as the spike protein. Specifically, they led to the discovery of reactive cysteines in evolutionary conserved Zn2+‐sites in several SARS‐CoV‐2 proteins that are crucial for viral polypeptide proteolysis as well as viral RNA synthesis, proofreading, and modification. These conserved, reactive cysteines, both free and Zn2+‐bound, can be targeted using the same Zn‐ejector drug (disulfiram/ebselen), which enables the use of broad‐spectrum anti‐virals that would otherwise be removed by the virus's proofreading mechanism. Our strategy of targeting multiple, conserved viral proteins that operate at different stages of the virus life cycle using a Zn‐ejector drug combined with other broad‐spectrum anti‐viral drug(s) could enhance the barrier to drug resistance and antiviral effects, as compared to each drug alone. Since these functionally important nonstructural proteins containing reactive cysteines are highly conserved among coronaviruses, our proposed strategy has the potential to tackle future coronaviruses. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and Catalysis Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Density Functional Theory
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Affiliation(s)
| | - Ting Chen
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan.,Department of Chemistry National Tsing Hua University Hsinchu Taiwan
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47
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Kemper EK, Zhang Y, Dix MM, Cravatt BF. Global profiling of phosphorylation-dependent changes in cysteine reactivity. Nat Methods 2022; 19:341-352. [PMID: 35228727 PMCID: PMC8920781 DOI: 10.1038/s41592-022-01398-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023]
Abstract
Proteomics has revealed that the ~20,000 human genes engender a far greater number of proteins, or proteoforms, that are diversified in large part by post-translational modifications (PTMs). How such PTMs affect protein structure and function is an active area of research but remains technically challenging to assess on a proteome-wide scale. Here, we describe a chemical proteomic method to quantitatively relate serine/threonine phosphorylation to changes in the reactivity of cysteine residues, a parameter that can affect the potential for cysteines to be post-translationally modified or engaged by covalent drugs. Leveraging the extensive high-stoichiometry phosphorylation occurring in mitotic cells, we discover numerous cysteines that exhibit phosphorylation-dependent changes in reactivity on diverse proteins enriched in cell cycle regulatory pathways. The discovery of bidirectional changes in cysteine reactivity often occurring in proximity to serine/threonine phosphorylation events points to the broad impact of phosphorylation on the chemical reactivity of proteins and the future potential to create small-molecule probes that differentially target proteoforms with PTMs.
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Affiliation(s)
- Esther K Kemper
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Yuanjin Zhang
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Melissa M Dix
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin F Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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48
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Uncovering an overlooked consequence of phosphorylation: change in cysteine reactivity. Nat Methods 2022; 19:281-283. [PMID: 35228728 DOI: 10.1038/s41592-022-01414-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Rothweiler EM, Brennan PE, Huber KVM. Covalent fragment-based ligand screening approaches for identification of novel ubiquitin proteasome system modulators. Biol Chem 2022; 403:391-402. [PMID: 35191283 DOI: 10.1515/hsz-2021-0396] [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: 10/21/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a key regulatory mechanism vital for maintenance of cellular homeostasis. Protein degradation is induced by E3 ligases via attachment of ubiquitin chains to substrates. Pharmacological exploitation of this phenomenon via targeted protein degradation (TPD) can be achieved with molecular glues or bifunctional molecules facilitating the formation of ternary complexes between an E3 ligase and a given protein of interest (POI), resulting in ubiquitination of the substrate and subsequent proteolysis by the proteasome. Recently, the development of novel covalent fragment screening approaches has enabled the identification of first-in-class ligands for E3 ligases and deubiquitinases revealing so far unexplored binding sites which highlights the potential of these methods to uncover and expand druggable space for new target classes.
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Affiliation(s)
- Elisabeth M Rothweiler
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
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50
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Function-guided proximity mapping unveils electrophilic-metabolite sensing by proteins not present in their canonical locales. Proc Natl Acad Sci U S A 2022; 119:2120687119. [PMID: 35082156 PMCID: PMC8812531 DOI: 10.1073/pnas.2120687119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Enzyme-assisted posttranslational modifications (PTMs) constitute a major means of signaling across different cellular compartments. However, how nonenzymatic PTMs-despite their direct relevance to covalent drug development-impinge on cross-compartment signaling remains inaccessible as current target-identification (target-ID) technologies offer limited spatiotemporal resolution, and proximity mapping tools are also not guided by specific, biologically-relevant, ligand chemotypes. Here we establish a quantitative and direct profiling platform (Localis-rex) that ranks responsivity of compartmentalized subproteomes to nonenzymatic PTMs. In a setup that contrasts nucleus- vs. cytoplasm-specific responsivity to reactive-metabolite modification (hydroxynonenylation), ∼40% of the top-enriched protein sensors investigated respond in compartments of nonprimary origin or where the canonical activity of the protein sensor is inoperative. CDK9-a primarily nuclear-localized kinase-was hydroxynonenylated only in the cytoplasm. Site-specific CDK9 hydroxynonenylation-which we identified in untreated cells-drives its nuclear translocation, downregulating RNA-polymerase-II activity, through a mechanism distinct from that of commonly used CDK9 inhibitors. Taken together, this work documents an unmet approach to quantitatively profile and decode localized and context-specific signaling/signal-propagation programs orchestrated by reactive covalent ligands.
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