1
|
Verpalen ECJM, Brouwer AJ, Wolfert MA, Boons GJ. Structure-Based Design and Synthesis of Lipid A Derivatives to Modulate Cytokine Responses. Chemistry 2024:e202400429. [PMID: 38587187 DOI: 10.1002/chem.202400429] [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: 01/31/2024] [Revised: 03/28/2024] [Accepted: 04/07/2024] [Indexed: 04/09/2024]
Abstract
Agonists of Toll like receptors (TLRs) have attracted interest as adjuvants and immune modulators. A crystal structure of TLR4/MD2 with E. coli LPS indicates that the fatty acid at C-2 of the lipid A component of LPS induces dimerization of two TLR4-MD2 complexes, which in turn initiates cell signaling leading to the production of (pro)inflammatory cytokines. To probe the importance of the (R)-3-hydroxymyristate at C-2 of lipid A, a range of bis- and mono-phosphoryl lipid A derivatives with different modifications at C-2 were prepared by a strategy in which 2-methylnaphthyl ethers were employed as permanent protecting group that could be readily removed by catalytic hydrogenation. The C-2 amine was protected as 9-fluorenylmethyloxycarbamate, which at a later stage could be removed to give a free amine that was modified by different fatty acids. LPS and the synthetic lipid As induced the same cytokines, however, large differences in activity were observed. A compound having a hexanoyl moiety at C-2 still showed agonistic properties, but further shortening to a butanoyl abolished activity. The modifications had a larger influence on monophosphoryl lipid As. The lipid As having a butanoyl moiety at C-2 could selectively antagonize TRIF associated cytokines induced by LPS or lipid A.
Collapse
Affiliation(s)
- Enrico C J M Verpalen
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Arwin J Brouwer
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Margreet A Wolfert
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Chemistry Department, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
2
|
Ueshima R, Kikuma T, Sano K, Toda N, Greimel P, Takeda Y. Synthesis of azide-modified glycerophospholipid precursor analogs for detection of enzymatic reactions. Chembiochem 2024; 25:e202300699. [PMID: 38061997 DOI: 10.1002/cbic.202300699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/27/2023] [Indexed: 01/10/2024]
Abstract
Glycerophospholipids (GPLs) are major cell membrane components. Although various phosphorylated molecules are attached to lipid moieties as their headgroups, GPLs are biosynthesized from phosphatidic acid (PA) via its derivatives, diacylglycerol (DAG) or cytidine diphosphate diacylglycerol (CDP-DAG). A variety of molecular probes capable of introducing detection tags have been developed to investigate biological events involved in GPLs. In this study, we report the design, synthesis, and evaluation of novel analytical tools suitable to monitor the activity of GPL biosynthetic enzymes in vitro. Our synthetic targets, namely, azide-modified PA, azide-modified DAG, and azide-modified CDP-DAG, were successfully obtained from solketal as their common starting material. Moreover, using CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT), an enzyme that catalyzed the final reaction step in synthesizing phosphatidylinositol, we demonstrated that azide-modified CDP-DAG worked as a substrate for CDIPT.
Collapse
Affiliation(s)
- Rina Ueshima
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Takashi Kikuma
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Kanae Sano
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Nahoko Toda
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Peter Greimel
- RIKEN Center for Brain Science, Wako, 351-0198, Japan
| | - Yoichi Takeda
- Graduate school of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| |
Collapse
|
3
|
Li ZR, Li R, Pasternack L, Chen P, Wong CH. Chemical Synthesis of a Keto Sugar Nucleotide. J Org Chem 2023. [PMID: 37126664 DOI: 10.1021/acs.joc.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Keto sugar nucleotides (KSNs) are common and versatile precursors to various deoxy sugar nucleotides, which are substrates for the corresponding glycosyltransferases involved in the biosynthesis of glycoproteins, glycolipids, and natural products. However, there has been no KSN synthesized chemically due to the inherent instability. Herein, the first chemical synthesis of the archetypal KSN TDP-4-keto-6-deoxy-d-glucose (1) is achieved by an efficient and optimized route, providing feasible access to other KSNs and analogues, thereby opening a new avenue for new applications.
Collapse
Affiliation(s)
- Zhong-Rui Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ruofan Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Laura Pasternack
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Pengxi Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
4
|
Hassan BA, Liu ZA, Milicaj J, Kim MS, Tyson M, Sham YY, Taylor EA. Kinetic Characterization and Computational Modeling of Escherichia coli Heptosyltransferase II: Exploring the Role of Protein Dynamics in Catalysis for GT-B Glycosyltransferase. Biochemistry 2022; 61:1572-1584. [PMID: 35861590 DOI: 10.1021/acs.biochem.2c00329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycosyltransferase (GT) enzymes promote the formation of glycosidic bonds between a sugar molecule and a diversity of substrates. Heptosyltransferase II (HepII) is a GT involved in the lipopolysaccharide (LPS) biosynthetic pathway that transfers the seven-carbon sugar (l-glycero-d-manno-heptose, Hep) onto a lipid-anchored glycopolymer (heptosylated Kdo2-Lipid A, Hep-Kdo2-Lipid A, or HLA). LPS plays a key role in Gram-negative bacterial sepsis, biofilm formation, and host colonization, and as such, LPS biosynthetic enzymes are targets for novel antimicrobial therapeutics. Three heptosyltransferases are involved in the inner-core LPS biosynthesis, with Escherichia coli HepII being the last to be quantitatively characterized in vivo. HepII shares modest sequence similarity with heptosyltransferase I (HepI) while maintaining a high degree of structural homology. Here, we report the first kinetic and biophysical characterization of HepII and demonstrate the properties of HepII that are shared with HepI, including sugar donor promiscuity and sugar acceptor-induced secondary structural changes, which results in significant thermal stabilization. HepII also has an increased catalytic efficiency and a significantly tighter binding affinity for both of its substrates compared to HepI. A structural model of the HepII ternary complex, refined by molecular dynamics simulations, was developed to probe the potentially important substrate-protein contacts. Ligand binding-induced changes in Trp fluorescence in HepII enabled the determination of substrate dissociation constants. Combined, these efforts meaningfully enhance our understanding of the heptosyltransferase family of enzymes and will aid in future efforts to design novel, potent, and specific inhibitors for this family of enzymes.
Collapse
Affiliation(s)
- Bakar A Hassan
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Zhiqi A Liu
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Jozafina Milicaj
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Mia S Kim
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Meka Tyson
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Yuk Y Sham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Department of Integrative Biology and Physiology, Medical School, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Erika A Taylor
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| |
Collapse
|
5
|
Hassan BA, Milicaj J, Ramirez-Mondragon CA, Sham YY, Taylor EA. Ligand-Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamics Simulations of Heptosyltransferase I Complexes. J Chem Inf Model 2022; 62:324-339. [PMID: 34967618 PMCID: PMC8864558 DOI: 10.1021/acs.jcim.1c00868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Understanding the dynamical motions and ligand recognition motifs of heptosyltransferase I (HepI) can be critical to discerning the behavior of other glycosyltransferase (GT) enzymes. Prior studies in our lab have demonstrated that GTs in the GT-B structural class, which are characterized by their connection of two Rossman-like domains by a linker region, have conserved structural fold and dynamical motions, despite low sequence homology, therefore making discoveries found in HepI transferable to other GT-B enzymes. Through molecular dynamics simulations and ligand binding free energy analysis of HepI in the apo and bound complexes (for all kinetically relevant combinations of the native substrates/products), we have determined the energetically favored enzymatic pathway for ligand binding and release. Our principal component, dynamic cross correlation, and network analyses of the simulations have revealed correlated motions involving residues within the N-terminal domain communicating with C-terminal domain residues via both proximal amino acid residues and also functional groups of the bound substrates. Analyses of the structural changes, energetics of substrate/product binding, and changes in pKa have elucidated a variety of inter and intradomain interactions that are critical for enzyme catalysis. These data corroborate our experimental observations of protein conformational changes observed in both presteady state kinetic and circular dichroism analyses of HepI. These simulations provided invaluable structural insights into the regions involved in HepI conformational rearrangement upon ligand binding. Understanding the specific interactions governing conformational changes is likely to enhance our efforts to develop novel dynamics disrupting inhibitors against GT-B structural enzymes in the future.
Collapse
Affiliation(s)
- Bakar A. Hassan
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Jozafina Milicaj
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Carlos Andres Ramirez-Mondragon
- Department of Integrative Biology and Physiology, Medical School and Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yuk Yin Sham
- Department of Integrative Biology and Physiology, Medical School and Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Erika A. Taylor
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| |
Collapse
|
6
|
Abstract
The sugar fucose is expressed on mammalian cell membranes as part of glycoconjugates and mediates essential physiological processes. The aberrant expression of fucosylated glycans has been linked to pathologies such as cancer, inflammation, infection, and genetic disorders. Tools to modulate fucose expression on living cells are needed to elucidate the biological role of fucose sugars and the development of potential therapeutics. Herein, we report a class of fucosylation inhibitors directly targeting de novo GDP-fucose biosynthesis via competitive GMDS inhibition. We demonstrate that cell permeable fluorinated rhamnose 1-phosphate derivatives (Fucotrim I & II) are metabolic prodrugs that are metabolized to their respective GDP-mannose derivatives and efficiently inhibit cellular fucosylation.
Collapse
|
7
|
Liang L, Cao J, Wei TYW, Tsai MD, Vincent SP. Synthesis of a biotinylated heptose 1,7-bisphosphate analogue, a probe to study immunity and inflammation. Org Biomol Chem 2021; 19:4943-4948. [PMID: 33988211 DOI: 10.1039/d1ob00790d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
d-glycero-d-manno-Heptose-1β,7-bisphosphate (HBP) is a bacterial metabolite that can induce a TIFA-dependent innate immune response in mammals. It was recently discovered that after HBP enters into the cytoplasm of the host cell, it is transformed into ADP-heptose-7-phosphate, which then leads to ALPK1-TIFA-dependent inflammatory response. In order to provide a molecular tool allowing the discovery of the proteins involved in this novel inflammatory pathway, we designed and synthesized a biotinylated analogue of HBP. This chemical probe displays an anomeric β-phosphate and a phosphonate at the 7-position, and a d-configured 6-position to which is attached the biotin moiety. To do so, different synthetic strategies were explored and described in this report. Moreover, we demonstrated that the biotinylated version of HBP is still biologically active and can activate the NF-κB pathway in HEK293T cells.
Collapse
Affiliation(s)
- Lina Liang
- Bengbu Medical College, Bengbu, Anhui, China
| | - Jun Cao
- University of Namur (UNamur), NARILIS, Department of Chemistry, rue de Bruxelles 61, 5000 Namur, Belgium.
| | | | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Stéphane P Vincent
- University of Namur (UNamur), NARILIS, Department of Chemistry, rue de Bruxelles 61, 5000 Namur, Belgium.
| |
Collapse
|