1
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Ritzefeld M, Zhang L, Xiao Z, Andrei SA, Boyd O, Masumoto N, Rodgers UR, Artelsmair M, Sefer L, Hayes A, Gavriil ES, Raynaud FI, Burke R, Blagg J, Rzepa HS, Siebold C, Magee AI, Lanyon-Hogg T, Tate EW. Design, Synthesis, and Evaluation of Inhibitors of Hedgehog Acyltransferase. J Med Chem 2024; 67:1061-1078. [PMID: 38198226 PMCID: PMC10823475 DOI: 10.1021/acs.jmedchem.3c01363] [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: 07/28/2023] [Revised: 11/08/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Hedgehog signaling is involved in embryonic development and cancer growth. Functional activity of secreted Hedgehog signaling proteins is dependent on N-terminal palmitoylation, making the palmitoyl transferase Hedgehog acyltransferase (HHAT), a potential drug target and a series of 4,5,6,7-tetrahydrothieno[3,2-c]pyridines have been identified as HHAT inhibitors. Based on structural data, we designed and synthesized 37 new analogues which we profiled alongside 13 previously reported analogues in enzymatic and cellular assays. Our results show that a central amide linkage, a secondary amine, and (R)-configuration at the 4-position of the core are three key factors for inhibitory potency. Several potent analogues with low- or sub-μM IC50 against purified HHAT also inhibit Sonic Hedgehog (SHH) palmitoylation in cells and suppress the SHH signaling pathway. This work identifies IMP-1575 as the most potent cell-active chemical probe for HHAT function, alongside an inactive control enantiomer, providing tool compounds for validation of HHAT as a target in cellular assays.
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Affiliation(s)
- Markus Ritzefeld
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Leran Zhang
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Zhangping Xiao
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | | | - Olivia Boyd
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Naoko Masumoto
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Ursula R. Rodgers
- National
Heart and Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
| | - Markus Artelsmair
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Lea Sefer
- Division
of Structural Biology, University of Oxford, Oxford OX3 7BN, U.K.
| | - Angela Hayes
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | | | - Florence I. Raynaud
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Burke
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Julian Blagg
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Henry S. Rzepa
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Christian Siebold
- Division
of Structural Biology, University of Oxford, Oxford OX3 7BN, U.K.
| | - Anthony I. Magee
- National
Heart and Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
| | | | - Edward W. Tate
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
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2
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Schonbrun AR, Resh MD. A Direct in vitro Fatty Acylation Assay for Hedgehog Acyltransferase. Bio Protoc 2022; 12:e4573. [PMID: 36618094 PMCID: PMC9797357 DOI: 10.21769/bioprotoc.4573] [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: 08/24/2022] [Revised: 09/20/2022] [Accepted: 11/26/2022] [Indexed: 12/24/2022] Open
Abstract
Several assays have been developed to monitor the in vitro catalytic activity of Hedgehog acyltransferase (Hhat), an enzyme critical to the Hedgehog signaling pathway in cells. However, the majority of these previously reported assays involve radioactive fatty acyl donor substrates, multiple steps to achieve product readout, or specialized equipment. To increase safety, efficiency, and convenience, we developed a direct, fluorescent in vitro assay to monitor Hhat activity. Our assay utilizes purified Hhat, a fluorescently labeled fatty acyl-CoA donor substrate, and a Sonic hedgehog (Shh) peptide recipient substrate sufficient for fatty acylation. The protocol is a straightforward process that yields direct readout of fatty acylated Shh peptide via fluorescence detection of the transferred fatty acyl group. This protocol was validated in: J Biol Chem (2022), DOI: 10.1016/j.jbc.2022.102422 Graphical abstract Graphical abstract adapted from Schonbrun and Resh (2022).
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Affiliation(s)
- Adina R. Schonbrun
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
,
Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
| | - Marilyn D. Resh
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
,
Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
,
Biochemistry, Cell Biology and Molecular Biology Graduate Program, Weill-Cornell Graduate School of Medical Sciences, New York, NY, USA
,
*For correspondence:
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3
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Schonbrun AR, Resh MD. Hedgehog acyltransferase catalyzes a random sequential reaction and utilizes multiple fatty acyl-CoA substrates. J Biol Chem 2022; 298:102422. [PMID: 36030053 PMCID: PMC9513256 DOI: 10.1016/j.jbc.2022.102422] [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: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Sonic hedgehog (Shh) signaling is a key component of embryonic development and is a driving force in several cancers. Hedgehog acyltransferase (Hhat), a member of the membrane-bound O-acyltransferase family of enzymes, catalyzes the attachment of palmitate to the N-terminal cysteine of Shh, a posttranslation modification critical for Shh signaling. The activity of Hhat has been assayed in cells and in vitro, and cryo-EM structures of Hhat have been reported, yet several unanswered questions remain regarding the enzyme’s reaction mechanism, substrate specificity, and the impact of the latter on Shh signaling. Here, we present an in vitro acylation assay with purified Hhat that directly monitors attachment of a fluorescently tagged fatty acyl chain to Shh. Our kinetic analyses revealed that the reaction catalyzed by Hhat proceeds through a random sequential mechanism. We also determined that Hhat can utilize multiple fatty acyl-CoA substrates for fatty acid transfer to Shh, with comparable affinities and turnover rates for myristoyl-CoA, palmitoyl-CoA, palmitoleoyl-CoA, and oleoyl-CoA. Furthermore, we investigated the functional consequence of differential fatty acylation of Shh in a luciferase-based Shh reporter system. We found that the potency of the signaling response in cells was higher for Shh acylated with saturated fatty acids compared to monounsaturated fatty acids. These findings demonstrate that Hhat can attach fatty acids other than palmitate to Shh and suggest that heterogeneous fatty acylation has the potential to impact Shh signaling in the developing embryo and/or cancer cells.
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Affiliation(s)
- Adina R Schonbrun
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY; Gerstner Sloan Kettering Graduate School
| | - Marilyn D Resh
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY; Gerstner Sloan Kettering Graduate School; Biochemistry, Cell Biology and Molecular Biology Graduate Program, Weill-Cornell Graduate School of Medical Sciences, New York, NY.
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4
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Evaluating Hedgehog Acyltransferase Activity and Inhibition Using the Acylation-coupled Lipophilic Induction of Polarization (Acyl-cLIP) Assay. Methods Mol Biol 2022; 2374:13-26. [PMID: 34562239 DOI: 10.1007/978-1-0716-1701-4_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Palmitoylation of the Hedgehog family of proteins is a critical step in the Hedgehog signaling pathway and is performed by the membrane-bound O-acyltransferase enzyme Hedgehog acyltransferase (HHAT). Measurement of HHAT activity has traditionally relied on radiolabeled fatty acid substrates, which imposes considerable constraints on throughput, cost, and safety, consequently hindering the efficient identification and development of small-molecule HHAT inhibitors. The Acylation-coupled Lipophilic Induction of Polarisation (Acyl-cLIP) assay was recently developed in our lab as a novel platform to evaluate lipidation of peptides in real time and high throughput. In this chapter, we describe the isolation of active HHAT from HEK293a cells and application of the Acyl-cLIP assay to characterize HHAT inhibitors. Our methodology uses standard chemical biology lab equipment and yields high-quality kinetic data from minimal sample volumes. The assay uses standard 384-well plates and is easily adapted to medium- or high-throughput screening formats.
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5
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Kallemeijn WW, Lanyon-Hogg T, Panyain N, Goya Grocin A, Ciepla P, Morales-Sanfrutos J, Tate EW. Proteome-wide analysis of protein lipidation using chemical probes: in-gel fluorescence visualization, identification and quantification of N-myristoylation, N- and S-acylation, O-cholesterylation, S-farnesylation and S-geranylgeranylation. Nat Protoc 2021; 16:5083-5122. [PMID: 34707257 DOI: 10.1038/s41596-021-00601-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 07/05/2021] [Indexed: 02/08/2023]
Abstract
Protein lipidation is one of the most widespread post-translational modifications (PTMs) found in nature, regulating protein function, structure and subcellular localization. Lipid transferases and their substrate proteins are also attracting increasing interest as drug targets because of their dysregulation in many disease states. However, the inherent hydrophobicity and potential dynamic nature of lipid modifications makes them notoriously challenging to detect by many analytical methods. Chemical proteomics provides a powerful approach to identify and quantify these diverse protein modifications by combining bespoke chemical tools for lipidated protein enrichment with quantitative mass spectrometry-based proteomics. Here, we report a robust and proteome-wide approach for the exploration of five major classes of protein lipidation in living cells, through the use of specific chemical probes for each lipid PTM. In-cell labeling of lipidated proteins is achieved by the metabolic incorporation of a lipid probe that mimics the specific natural lipid, concomitantly wielding an alkyne as a bio-orthogonal labeling tag. After incorporation, the chemically tagged proteins can be coupled to multifunctional 'capture reagents' by using click chemistry, allowing in-gel fluorescence visualization or enrichment via affinity handles for quantitative chemical proteomics based on label-free quantification (LFQ) or tandem mass-tag (TMT) approaches. In this protocol, we describe the application of lipid probes for N-myristoylation, N- and S-acylation, O-cholesterylation, S-farnesylation and S-geranylgeranylation in multiple cell lines to illustrate both the workflow and data obtained in these experiments. We provide detailed workflows for method optimization, sample preparation for chemical proteomics and data processing. A properly trained researcher (e.g., technician, graduate student or postdoc) can complete all steps from optimizing metabolic labeling to data processing within 3 weeks. This protocol enables sensitive and quantitative analysis of lipidated proteins at a proteome-wide scale at native expression levels, which is critical to understanding the role of lipid PTMs in health and disease.
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Affiliation(s)
- Wouter W Kallemeijn
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- The Francis Crick Institute, London, UK
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Nattawadee Panyain
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Global Health Institute, Faculty of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Goya Grocin
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- The Francis Crick Institute, London, UK
| | - Paulina Ciepla
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Julia Morales-Sanfrutos
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Proteomics Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK.
- The Francis Crick Institute, London, UK.
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6
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Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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7
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Resh MD. Palmitoylation of Hedgehog proteins by Hedgehog acyltransferase: roles in signalling and disease. Open Biol 2021; 11:200414. [PMID: 33653085 PMCID: PMC8061759 DOI: 10.1098/rsob.200414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hedgehog acyltransferase (Hhat), a member of the membrane-bound O-acyltransferase (MBOAT) family, catalyses the covalent attachment of palmitate to the N-terminus of Hedgehog proteins. Palmitoylation is a post-translational modification essential for Hedgehog signalling. This review explores the mechanisms involved in Hhat acyltransferase enzymatic activity, similarities and differences between Hhat and other MBOAT enzymes, and the role of palmitoylation in Hedgehog signalling. In vitro and cell-based assays for Hhat activity have been developed, and residues within Hhat and Hedgehog essential for palmitoylation have been identified. In cells, Hhat promotes the transfer of palmitoyl-CoA from the cytoplasmic to the luminal side of the endoplasmic reticulum membrane, where Shh palmitoylation occurs. Palmitoylation is required for efficient delivery of secreted Hedgehog to its receptor Patched1, as well as for the deactivation of Patched1, which initiates the downstream Hedgehog signalling pathway. While Hhat loss is lethal during embryogenesis, mutations in Hhat have been linked to disease states or abnormalities in mice and humans. In adults, aberrant re-expression of Hedgehog ligands promotes tumorigenesis in an Hhat-dependent manner in a variety of different cancers, including pancreatic, breast and lung. Targeting hedgehog palmitoylation by inhibition of Hhat is thus a promising, potential intervention in human disease.
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Affiliation(s)
- Marilyn D Resh
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 143, New York, NY 10065, USA
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8
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Lanyon-Hogg T, Ritzefeld M, Sefer L, Bickel JK, Rudolf AF, Panyain N, Bineva-Todd G, Ocasio CA, O'Reilly N, Siebold C, Magee AI, Tate EW. Acylation-coupled lipophilic induction of polarisation (Acyl-cLIP): a universal assay for lipid transferase and hydrolase enzymes. Chem Sci 2019; 10:8995-9000. [PMID: 31762980 PMCID: PMC6855259 DOI: 10.1039/c9sc01785b] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/16/2019] [Indexed: 12/12/2022] Open
Abstract
Posttranslational attachment of lipids to proteins is important for many cellular functions, and the enzymes responsible for these modifications are implicated in many diseases, from cancer to neurodegeneration. Lipid transferases and hydrolases are increasingly tractable therapeutic targets, but present unique challenges for high-throughput biochemical enzyme assays which hinder development of new inhibitors. We present Acylation-coupled Lipophilic Induction of Polarisation (Acyl-cLIP) as the first universally applicable biochemical lipidation assay, exploiting the hydrophobic nature of lipidated peptides to drive a polarised fluorescence readout. Acyl-cLIP allows sensitive, accurate, real-time measurement of S- or N-palmitoylation, N-myristoylation, S-farnesylation or S-geranylgeranylation. Furthermore, it is applicable to transfer and hydrolysis reactions, and we demonstrate its extension to a high-throughput screening format. We anticipate that Acyl-cLIP will greatly expedite future drug discovery efforts against these challenging targets.
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Affiliation(s)
- Thomas Lanyon-Hogg
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
| | - Markus Ritzefeld
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
| | - Lea Sefer
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , Oxford , OX3 7BN , UK
| | - Jasmine K Bickel
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
| | - Amalie F Rudolf
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , Oxford , OX3 7BN , UK
| | - Nattawadee Panyain
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
| | | | | | | | - Christian Siebold
- Division of Structural Biology , Wellcome Centre for Human Genetics , University of Oxford , Oxford , OX3 7BN , UK
| | - Anthony I Magee
- Molecular Medicine Section , National Heart & Lung Institute , Imperial College London , London , SW7 2AZ , UK
| | - Edward W Tate
- Department of Chemistry , Imperial College London , London , W12 0BZ , UK . ; ; Tel: +44 0207 5943752 ; Tel: +44 0207 5945821
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9
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Gao X, Hannoush RN. A Decade of Click Chemistry in Protein Palmitoylation: Impact on Discovery and New Biology. Cell Chem Biol 2017; 25:236-246. [PMID: 29290622 DOI: 10.1016/j.chembiol.2017.12.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/10/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]
Abstract
Protein palmitoylation plays diverse roles in regulating the trafficking, stability, and activity of cellular proteins. The advent of click chemistry has propelled the field of protein palmitoylation forward by providing specific, sensitive, rapid, and easy-to-handle methods for studying protein palmitoylation. This year marks the 10th anniversary since the first click chemistry-based fatty acid probes for detecting protein lipid modifications were reported. The goal of this review is to highlight key biological advancements in the field of protein palmitoylation during the past 10 years. In particular, we discuss the impact of click chemistry on enabling protein palmitoylation proteomics methods, uncovering novel lipid modifications on proteins and elucidating their functions, as well as the development of non-radioactive biochemical and enzymatic assays. In addition, this review provides context for building and exploring new research avenues in protein palmitoylation through the use of clickable fatty acid probes.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.
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10
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Lanyon-Hogg T, Faronato M, Serwa RA, Tate EW. Dynamic Protein Acylation: New Substrates, Mechanisms, and Drug Targets. Trends Biochem Sci 2017; 42:566-581. [PMID: 28602500 DOI: 10.1016/j.tibs.2017.04.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/06/2017] [Accepted: 04/13/2017] [Indexed: 01/04/2023]
Abstract
Post-translational attachment of lipids to proteins is found in all organisms, and is important for many biological processes. Acylation with myristic and palmitic acids are among the most common lipid modifications, and understanding reversible protein palmitoylation dynamics has become a particularly important goal. Linking acyltransferase enzymes to disease states can be challenging due to a paucity of robust models, compounded by functional redundancy between many palmitoyl transferases; however, in cases such as Wnt or Hedgehog signalling, small molecule inhibitors have been identified, with some progressing to clinical trials. In this review, we present recent developments in our understanding of protein acylation in human health and disease through use of chemical tools, global profiling of acylated proteomes, and functional studies of specific protein targets.
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Affiliation(s)
- Thomas Lanyon-Hogg
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Monica Faronato
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Remigiusz A Serwa
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Edward W Tate
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London SW7 2AZ, UK.
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