1
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Matoba H, Oba K, Li H, Mizuno Y, Wang Q, Yoritate M, Aso M, Sodeoka M, Yoshida M, Yashiroda Y, Hirai G. Structure-activity relationship study of nitrogen signaling factors. Bioorg Med Chem Lett 2024; 109:129857. [PMID: 38909706 DOI: 10.1016/j.bmcl.2024.129857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
We have synthesized 10 analogs of oxylipins, which are nitrogen signaling factors (NSFs) that mediate cell-to-cell communication in the fission yeast Schizosaccharomyces pombe, and evaluated their structure-activity relationships with the aim of developing molecular probes for NSFs. We found that the OH or OAc group at C10 could be replaced with a compact amide (17) or carbamate (19). Introducing an alkyne as a detection tag at C10 led to decreased, though still sufficient, activity. Introducing an alkyne at the C18 position showed a similar trend, suggesting tolerance is relatively low even for compact functional groups such as alkynes. Although introduction of a diazirine moiety as a photoreactive group at the C5 position decreased the activity, we found that introducing diazirine at the C13 position was acceptable, and compound 38 exhibited potent NSF activity. These findings will be helpful in the development of molecular probes for NSFs.
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Affiliation(s)
- Hiroaki Matoba
- Graduate Schools of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kouhei Oba
- Graduate Schools of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Huanlin Li
- RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan
| | - Yuta Mizuno
- Graduate Schools of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Qianqian Wang
- RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan
| | - Makoto Yoritate
- Graduate Schools of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mariko Aso
- Graduate Schools of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mikiko Sodeoka
- RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan; RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan; RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan; Office of University Professors, The University of Tokyo, Bunkyo-ku, 113-8657 Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan; RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan.
| | - Go Hirai
- Graduate Schools of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; RIKEN Center for Sustainable Resource Sciences (CSRS), Saitama, Japan.
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2
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Farley SE, Hashimoto R, Evangelista J, Stein F, Haberkant P, Kikuchi K, Tafesse FG, Schultz C. Trifunctional fatty acid derivatives: the impact of diazirine placement. Chem Commun (Camb) 2024; 60:6651-6654. [PMID: 38856656 DOI: 10.1039/d4cc00974f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Functionalized lipid probes are a critical new tool to interrogate the function of individual lipid species, but the structural parameters that constrain their utility have not been thoroughly described. Here, we synthesize three palmitic acid derivatives with a diazirine at different positions on the acyl chain and examine their metabolism, subcellular localization, and protein interactions. We demonstrate that while they produce very similar metabolites and subcellular distributions, probes with the diazirine at either end pulldown distinct subsets of proteins after photo-crosslinking. This highlights the importance of thoughtful diazirine placement when developing probes based on biological molecules.
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Affiliation(s)
- Scotland E Farley
- Oregon Health & Science University, Department of Chemical Physiology and Biochemistry, USA.
- Oregon Health & Science University, Department of Molecular Microbiology and Immunology, Portland, OR, 97239, USA.
| | - Ryu Hashimoto
- Oregon Health & Science University, Department of Chemical Physiology and Biochemistry, USA.
- Osaka University, Department of Applied Chemistry, Graduate School of Engineering, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Judah Evangelista
- Oregon Health & Science University, Department of Chemical Physiology and Biochemistry, USA.
- Oregon Health & Science University, Department of Molecular Microbiology and Immunology, Portland, OR, 97239, USA.
| | - Frank Stein
- European Molecular Biology Laboratory, Proteomics Core Facility, 69117, Heidelberg, Germany
| | - Per Haberkant
- European Molecular Biology Laboratory, Proteomics Core Facility, 69117, Heidelberg, Germany
| | - Kazuya Kikuchi
- Osaka University, Department of Applied Chemistry, Graduate School of Engineering, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fikadu G Tafesse
- Oregon Health & Science University, Department of Molecular Microbiology and Immunology, Portland, OR, 97239, USA.
| | - Carsten Schultz
- Oregon Health & Science University, Department of Chemical Physiology and Biochemistry, USA.
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3
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Farley SE, Hashimoto R, Evangelista J, Stein F, Haberkant P, Kikuchi K, Tafesse FG, Schultz C. Trifunctional fatty acid derivatives demonstrate the impact of diazirine placement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594383. [PMID: 38798378 PMCID: PMC11118520 DOI: 10.1101/2024.05.15.594383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Functionalized lipid probes are a critical new tool to interrogate the function of individual lipid species, but the structural parameters that constrain their utility have not been thoroughly described. Here, we synthesize three palmitic acid derivatives with a diazirine at different positions on the acyl chain and examine their metabolism, subcellular localization, and protein interactions. We demonstrate that while they produce very similar metabolites and subcellular distributions, probes with the diazirine at either end pulldown distinct subsets of proteins after photo-crosslinking. This highlights the importance of thoughtful diazirine placement when developing probes based on biological molecules.
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4
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Farley S, Stein F, Haberkant P, Tafesse FG, Schultz C. Trifunctional Sphinganine: A New Tool to Dissect Sphingolipid Function. ACS Chem Biol 2024; 19:336-347. [PMID: 38284972 PMCID: PMC10878393 DOI: 10.1021/acschembio.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/30/2024]
Abstract
Functions and cell biology of the sphingolipids sphingosine and sphinganine in cells are not well understood. While some signaling roles for sphingosine have been elucidated, the closely related sphinganine has been described only insofar as it does not elicit many of the same signaling responses. Here, we prepared multifunctionalized derivatives of the two lipid species that differ only in a single double bond of the carbon backbone. Using these novel probes, we were able to define their spatiotemporal distributions within cells. Furthermore, we used these tools to systematically map the protein interactomes of both lipids. The lipid-protein conjugates, prepared through photo-crosslinking in live cells and extraction via click chemistry to azide beads, revealed significant differences in the captured proteins, highlighting their distinct roles in various cellular processes. This work elucidates mechanistic differences between these critical lipids and sets the foundation for further studies of the cellular functions of sphingosine and sphinganine.
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Affiliation(s)
- Scotland Farley
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
- Department
of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Frank Stein
- European
Molecular Biology Laboratory, Proteomics
Core Facility, Heidelberg 69117, Germany
| | - Per Haberkant
- European
Molecular Biology Laboratory, Proteomics
Core Facility, Heidelberg 69117, Germany
| | - Fikadu G. Tafesse
- Department
of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Carsten Schultz
- Department
of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
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5
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Uematsu M, Baskin JM. Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level. Cold Spring Harb Perspect Biol 2023; 15:a041407. [PMID: 37604586 PMCID: PMC10691496 DOI: 10.1101/cshperspect.a041407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.
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Affiliation(s)
- Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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6
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Abstract
Lipids are key components of all organisms. We are well educated in their use as fuel and their essential role to form membranes. We also know much about their biosynthesis and metabolism. We are also aware that most lipids have signaling character meaning that a change in their concentration or location constitutes a signal that helps a living cell to respond to changes in the environment or to fulfill its specific function ranging from secretion to cell division. What is much less understood is how lipids change location in cells over time and what other biomolecules they interact with at each stage of their lifetime. Due to the large number of often quite similar lipid species and the sometimes very short lifetime of signaling lipids, we need highly specific tools to manipulate and visualize lipids and lipid-protein interactions. If successfully applied, these tools provide fabulous opportunities for discovery.In this Account, I summarize the development of synthetic tools from our lab that were designed to address crucial properties that allow them to function as tools in live cell experiments. Techniques to change the concentration of lipids by adding a small molecule or by light are described and complemented by examples of biological findings made when applying the tools. This ranges from chemical dimerizer-based systems to synthetic "caged" lipid derivatives. Furthermore, I discuss the problem of locating a lipid in an intact cell. Synthetic molecular probes are described that help to unravel the lipid location and to determine their binding proteins. These location studies require in-cell lipid tagging by click chemistry, photo-cross-linking to prevent further movement and the "caging" groups to avoid premature metabolism. The combination of these many technical features in a single tool allows for the analysis of not only lipid fluxes through metabolism but also lipid transport from one membrane to another as well as revealing the lipid interactome in a cell-dependent manner. This latter point is crucial because with these multifunctional tools in combination with lipidomics we can now address differences in healthy versus diseased cells and ultimately find the changes that are essential for disease development and new therapeutics that prevent these changes.
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Affiliation(s)
- Carsten Schultz
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
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7
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Jiménez-López C, Nadler A. Caged lipid probes for controlling lipid levels on subcellular scales. Curr Opin Chem Biol 2023; 72:102234. [PMID: 36493527 DOI: 10.1016/j.cbpa.2022.102234] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
Lipids exert their cellular functions in individual organelles, in some cases on the scale of even smaller, specialized membrane domains. Thus, the experimental capacity to precisely manipulate lipid levels at the subcellular level is crucial for studying lipid-related processes in cell biology. Photo-caged lipid probes which partition into specific cellular membranes prior to photoactivation have emerged as key tools for localized and selective perturbation of lipid concentration in living cells. In this review, we provide an overview of the recent advances in the area and outline which developments are still required for the methodology to be more widely implemented in the wider membrane biology community.
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Affiliation(s)
| | - André Nadler
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany.
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8
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Ge J, Du S, Yao SQ. Bifunctional Lipid-Derived Affinity-Based Probes (A fBPs) for Analysis of Lipid-Protein Interactome. Acc Chem Res 2022; 55:3663-3674. [PMID: 36484537 DOI: 10.1021/acs.accounts.2c00593] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although lipids are not genetically encoded, they are fundamental building blocks of cell membranes and essential components of cell metabolites. Lipids regulate various biological processes, including energy storage, membrane trafficking, signal transduction, and protein secretion; therefore, their metabolic imbalances cause many diseases. Approximately 47 000 lipid species with diverse structures have been identified, but little is known about their crucial roles in cellular systems. Particularly the structural, metabolic, and signaling functions of lipids often arise from interactions with proteins. Lipids attach to proteins not only by covalent bonds but also through noncovalent interactions, which also influence protein functions and localization. Therefore, it is important to explore this lipid-protein "interactome" to understand its roles in health and disease, which may further provide insight for medicinal development. However, lipid structures are generally quite complicated, rendering the systematic characterization of lipid-protein interactions much more challenging.Chemoproteomics is a well-known chemical biology platform in which small-molecule chemical probes are utilized in combination with high-resolution, quantitative mass spectrometry to study protein-ligand interactions in living cells or organisms, and it has recently been applied to the study of protein-lipid interactions as well. The study of these complicated interactions has been advanced by the development of bifunctional lipid probes, which not only enable probes to form covalent cross-links with lipid-interacting proteins under UV irradiation, but are also capable of enriching these proteins through bioorthogonal reactions.In this Account, we will discuss recent developments in bifunctional lipid-derived, affinity-based probes (AfBP)s that have been developed to investigate lipid-protein interactions in live cell systems. First, we will give a brief introduction of fundamental techniques based on AfBPs which are related to lipid research. Then, we will focus on three aspects, including probes developed on the basis of lipidation, lipid-derived probes with different modification positions (e.g., hydrophobic or hydrophilic parts of a lipid), and, finally, in situ biosynthesis of probes through intrinsic metabolic pathways by using chemically modified building blocks. We will present some case studies to describe these probes' design principles and cellular applications. At the end, we will also highlight key limitations of current approaches so as to provide inspirations for future improvement. The lipid probes that have been constructed are only the tip of the iceberg, and there are still plenty of lipid species that have yet to be explored. We anticipate that AfBP-based chemoproteomics and its further advancement will pave the way for a deep understanding of lipid-protein interactions in the future.
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Affiliation(s)
- Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
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9
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Wegner T, Laskar R, Glorius F. Lipid mimetics: A versatile toolbox for lipid biology and beyond. Curr Opin Chem Biol 2022; 71:102209. [PMID: 36122522 DOI: 10.1016/j.cbpa.2022.102209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Being the principal component of biological membranes lipids are essential building blocks of life. Given their huge biological importance, the investigation of lipids, their properties, interactions and metabolic pathways is of prime importance for the fundamental understanding of living cells and organisms as well as the emergence of diseases. Different strategies have been applied to investigate lipid-mediated biological processes, one of them being the use of lipid mimetics. They structurally resemble their natural counterparts but are equipped with functionality that can be used to probe or manipulate lipid-mediated biological processes and biomembranes. Lipid mimetics therefore constitute an indispensable toolbox for lipid biology and membrane research but also beyond for potential applications in medicine or synthetic biology. Herein, we highlight recent advances in the development and application of lipid-mimicking compounds.
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Affiliation(s)
- Tristan Wegner
- Institute of Organic Chemistry, University of Münster, Münster, Germany
| | - Ranjini Laskar
- Institute of Organic Chemistry, University of Münster, Münster, Germany
| | - Frank Glorius
- Institute of Organic Chemistry, University of Münster, Münster, Germany.
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10
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Yu W, Baskin JM. Photoaffinity labeling approaches to elucidate lipid-protein interactions. Curr Opin Chem Biol 2022; 69:102173. [PMID: 35724595 DOI: 10.1016/j.cbpa.2022.102173] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022]
Abstract
Lipid-protein interactions serve as the basis for many of the diverse roles of lipids. However, these noncovalent binding events are often weak, transient, or dependent upon environmental cues. Photoaffinity labeling can preserve these interactions under native conditions, enabling their biochemical profiling. Typically, photoaffinity labeling probes contain a diazirine photocrosslinker and a click chemistry handle for enrichment and downstream analysis. In this review, we summarize recent advances in the understanding the mechanisms of diazirine photocrosslinking, and we provide an overview of recent applications of photoaffinity labeling to reveal the interactions of diverse types of lipids with specific members of the proteome.
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Affiliation(s)
- Weizhi Yu
- Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, 14853, NY, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, 14853, NY, USA.
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11
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Nieto-Garai JA, Contreras FX, Arboleya A, Lorizate M. Role of Protein-Lipid Interactions in Viral Entry. Adv Biol (Weinh) 2022; 6:e2101264. [PMID: 35119227 DOI: 10.1002/adbi.202101264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/19/2021] [Indexed: 12/25/2022]
Abstract
The viral entry consists of several sequential events that ensure the attachment of the virus to the host cell and the introduction of its genetic material for the continuation of the replication cycle. Both cellular and viral lipids have gained a wider focus in recent years in the field of viral entry, as they are found to play key roles in different steps of the process. The specific role is summarized that lipids and lipid membrane nanostructures play in viral attachment, fusion, and immune evasion and how they can be targeted with antiviral therapies. Finally, some of the limitations of techniques commonly used for protein-lipid interactions studies are discussed, and new emerging tools are reviewed that can be applied to this field.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, E-48940, Spain
| | - Francesc-Xabier Contreras
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, E-48940, Spain.,Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - Aroa Arboleya
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, E-48940, Spain.,Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain.,Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, E-48940, Spain
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, E-48940, Spain.,Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain
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12
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Abstract
Phosphoinositides are signalling lipids derived from phosphatidylinositol, a ubiquitous phospholipid in the cytoplasmic leaflet of eukaryotic membranes. Initially discovered for their roles in cell signalling, phosphoinositides are now widely recognized as key integrators of membrane dynamics that broadly impact on all aspects of cell physiology and on disease. The past decade has witnessed a vast expansion of our knowledge of phosphoinositide biology. On the endocytic and exocytic routes, phosphoinositides direct the inward and outward flow of membrane as vesicular traffic is coupled to the conversion of phosphoinositides. Moreover, recent findings on the roles of phosphoinositides in autophagy and the endolysosomal system challenge our view of lysosome biology. The non-vesicular exchange of lipids, ions and metabolites at membrane contact sites in between organelles has also been found to depend on phosphoinositides. Here we review our current understanding of how phosphoinositides shape and direct membrane dynamics to impact on cell physiology, and provide an overview of emerging concepts in phosphoinositide regulation.
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13
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Simon C, Feng S, Riezman H. Chemical Biology Tools to Study Lipids and their Metabolism with Increased Spatial and Temporal Resolution. Chimia (Aarau) 2021; 75:1012-1016. [PMID: 34920769 DOI: 10.2533/chimia.2021.1012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lipids are important cellular components providing many essential functions. To fulfill these various functions evolution has selected for a diverse set of lipids and this diversity is seen at the organismal, cellular and subcellular level. Understanding how cells maintain this complex lipid organization is a very challenging problem, which for lipids, is not easily addressed using biochemical and genetic techniques. Therefore, chemical tools have an important role to play in our quest to understand the complexities of lipid metabolism. Here we discuss new chemical tools to study lipids, their distribution and metabolism with increased spatial and temporal resolution.
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Affiliation(s)
- Clémence Simon
- NCCR Chemical Biology, University of Geneva, CH-1211 Geneva
| | - Suihan Feng
- NCCR Chemical Biology, University of Geneva, CH-1211 Geneva; Current Address : Center for Microbes, Health and Development (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, China
| | - Howard Riezman
- NCCR Chemical Biology, University of Geneva, CH-1211 Geneva;,
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14
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Burton NR, Kim P, Backus KM. Photoaffinity labelling strategies for mapping the small molecule-protein interactome. Org Biomol Chem 2021; 19:7792-7809. [PMID: 34549230 PMCID: PMC8489259 DOI: 10.1039/d1ob01353j] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.
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Affiliation(s)
- Nikolas R Burton
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
| | - Phillip Kim
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
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