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Sueyoshi K, Kishi J, Inuki S, Matsumaru T, Fujimoto Y. Highly Selective Cytokine Induction of Nitrated Lipid-Modified α-GalCer Derivatives Demonstrating High Binding Affinity to the Lipid Antigen Presenting Molecule CD1d. Chemistry 2024:e202403871. [PMID: 39632752 DOI: 10.1002/chem.202403871] [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: 10/19/2024] [Revised: 12/02/2024] [Accepted: 12/03/2024] [Indexed: 12/07/2024]
Abstract
Glycolipid antigens are presented by CD1d on antigen-presenting cells to T cell receptors (TCRs) of natural killer T (NKT) cells, leading to immune responses via cytokine induction. Although various lipid antigens have been found, there are only a limited number of glycolipid antigens having selective cytokine induction. In this study, we identified the glycolipids (α-GalCer nitro-type) that exhibit highly selective induction of Th2 and Th17 type cytokines, with very high binding affinity to CD1d, by introducing nature-inspired nitro-modified fatty acyl groups. The natural nitroalkene moiety of fatty acyl groups in the glycolipids effectively enhances the affinity to CD1d through presumed hydrogen-bonding and NO2-π interactions, leading to the distinctive function in cytokine induction and selectivity.
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Matsumaru T, Iwamatsu T, Ishigami K, Inai M, Kanto W, Ishigaki A, Toyoda A, Shuto S, Maenaka K, Nakagawa S, Maita H. Identification of BAY61-3606 Derivatives With Improved Activity in Splicing Modulation That Induces Inclusion of Cassette Exons Similar to the Splicing Factor 3B Subunit 1 Mutation. Chem Biol Drug Des 2024; 104:e70002. [PMID: 39438141 DOI: 10.1111/cbdd.70002] [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: 05/29/2024] [Revised: 09/24/2024] [Accepted: 09/25/2024] [Indexed: 10/25/2024]
Abstract
Splicing modulation by a small compound offers therapeutic potential for diseases caused by splicing abnormality. However, only a few classes of compounds that can modulate splicing have been identified. We previously identified BAY61-3606, a multiple kinase inhibitor, as a compound that relaxes the splicing fidelity at the 3' splice site recognition. We have also reported the synthesis of derivatives of BAY61-3606. In this study, we tested those compounds for their splicing modulation capabilities and identified two contrasting compounds. These compounds were further investigated for their effects on the whole transcriptome, and analysis of changes in transcription and splicing revealed that the highly active derivative in the splicing reporter assay also showed significantly higher activity in modulating the splicing of endogenously expressed genes. Particularly, cassette exon inclusion was highly upregulated by this compound, and clustering analysis revealed that these effects resembled those in splicing factor 3b subunit 1 (SF3B1) K700E mutant cells but contrasted with those of the splicing inhibitor H3B-8800. Additionally, a group of serine/arginine-rich (SR) protein genes was identified as representatively affected, likely via modulation of poison exon inclusion. This finding could guide further analysis of the mode of action of these compounds on splicing, which could be valuable for developing drugs for diseases associated with splicing abnormalities.
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Furukawa A, Shuchi Y, Wang J, Guillen-Poza PA, Ishizuka S, Kagoshima M, Ikeno R, Kumeta H, Yamasaki S, Matsumaru T, Saitoh T, Maenaka K. Structural basis for plastic glycolipid recognition of the C-type lectin Mincle. Structure 2023; 31:1077-1085.e5. [PMID: 37348496 DOI: 10.1016/j.str.2023.05.018] [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: 05/18/2021] [Revised: 04/26/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor for cord factor, trehalose dimycolate (TDM), which serves as a potent component of adjuvants. The recognition of glycolipids by Mincle, especially their lipid parts, is poorly understood. Here, we performed nuclear magnetic resonance analysis, revealing that titration of trehalose harboring a linear short acyl chain showed a chemical shift perturbation of hydrophobic residues next to the Ca-binding site. Notably, there were split signals for Tyr201 upon complex formation, indicating two binding modes for the acyl chain. In addition, most Mincle residues close to the Ca-binding site showed no observable signals, suggesting their mobility on an ∼ ms scale even after complex formation. Mutagenesis study supported two putative lipid-binding modes for branched acyl-chain TDM binding. These results provide novel insights into the plastic-binding modes of Mincle toward a wide range of glycol- and glycerol-lipids, important for rational adjuvant development.
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Kimishima A, Ando H, Sennari G, Noguchi Y, Sekikawa S, Kojima T, Ohara M, Watanabe Y, Inahashi Y, Takada H, Sugawara A, Matsumaru T, Iwatsuki M, Hirose T, Sunazuka T. Chemical Degradation-Inspired Total Synthesis of the Antibiotic Macrodiolide, Luminamicin. J Am Chem Soc 2022; 144:23148-23157. [DOI: 10.1021/jacs.2c10856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Matsumaru T, Sueyoshi K, Okubo K, Fujii S, Sakuratani K, Saito R, Ueki K, Yamasaki S, Fujimoto Y. Trehalose diesters containing a polar functional group-modified lipid moiety: Synthesis and evaluation of Mincle-mediated signaling activity. Bioorg Med Chem 2022; 75:117045. [PMID: 36327694 DOI: 10.1016/j.bmc.2022.117045] [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: 08/31/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022]
Abstract
Mincle, a C-type lectin receptor (CLR), activates the innate immune system by recognizing certain complex lipid compounds. In this study, we designed and synthesized trehalose disteate (TDS) and dibehenate (TDB), containing a polar-functional group in the middle of fatty acid moieties, based on a model of the Mincle-glycolipids interaction. The modified fatty acids were prepared using hydroxy fatty acids as common intermediates, and conjugated with an appropriate trehalose moiety to synthesize the desired trehalose diesters. TDE derivatives containing the modified fatty acid have different Mincle-mediated signaling activities depending on the position of the functional group and the length of the lipids. The newly developed TDE derivatives exhibit signaling activity comparable or superior to that of TDS or TDB, and the results suggest that Mincle tolerates polar functional groups at a certain position of the lipid chain of TDE. The introduction of the polar functional groups into the lipid moiety of the glycolipids also resulted in improved solubility in polar solvents, which would be advantageous for various analyses and applications.
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Matsumaru T. Lipid Conjugates as Ligands for the C-type Lectin Receptor Mincle. TRENDS GLYCOSCI GLYC 2022. [DOI: 10.4052/tigg.2029.1j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Matsumaru T. Lipid Conjugates as Ligands for the C-type Lectin Receptor Mincle. TRENDS GLYCOSCI GLYC 2022. [DOI: 10.4052/tigg.2029.1e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Matsumaru T, Sakuratani K, Yanaka S, Kato K, Yamasaki S, Fujimoto Y. Fungal β‐mannosyloxymannitol glycolipids and their analogues: synthesis and Mincle‐mediated signaling activity. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Matsumaru T, Ikeno R, Shuchi Y, Iwamatsu T, Tadokoro T, Yamasaki S, Fujimoto Y, Furukawa A, Maenaka K. Correction: Synthesis of glycerolipids containing simple linear acyl chains or aromatic rings and evaluation of their Mincle signaling activity. Chem Commun (Camb) 2022; 58:2580. [PMID: 35113118 DOI: 10.1039/d2cc90023h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'Synthesis of glycerolipids containing simple linear acyl chains or aromatic rings and evaluation of their Mincle signaling activity' by Takanori Matsumaru et al., Chem. Commun., 2019, 55, 711-714, DOI: 10.1039/C8CC07322H.
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Miyachi H, Kanamitsu K, Ishii M, Watanabe E, Katsuyama A, Otsuguro S, Yakushiji F, Watanabe M, Matsui K, Sato Y, Shuto S, Tadokoro T, Kita S, Matsumaru T, Matsuda A, Hirose T, Iwatsuki M, Shigeta Y, Nagano T, Kojima H, Ichikawa S, Sunazuka T, Maenaka K. Structure, solubility, and permeability relationships in a diverse middle molecule library. Bioorg Med Chem Lett 2021; 37:127847. [PMID: 33571648 DOI: 10.1016/j.bmcl.2021.127847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/07/2021] [Accepted: 01/30/2021] [Indexed: 10/22/2022]
Abstract
To develop methodology to predict the potential druggability of middle molecules, we examined the structure, solubility, and permeability relationships of a diverse library (HKDL ver.1) consisting of 510 molecules (359 natural product derivatives, 76 non-natural products, 46 natural products, and 29 non-natural product derivatives). The library included peptides, depsipeptides, macrolides, and lignans, and 476 of the 510 compounds had a molecular weight in the range of 500-2000 Da. The solubility and passive diffusion velocity of the middle molecules were assessed using the parallel artificial membrane permeability assay (PAMPA). Quantitative values of solubility of 471 molecules and passive diffusion velocity of 287 molecules were obtained, and their correlations with the structural features of the molecules were examined. Based on the results, we propose a method to predict the passive diffusion characteristics of middle molecules from their three-dimensional structural features.
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Sugawara A, Takada H, Hirose T, Kimishima A, Yamada T, Toda M, Kojima T, Matsumaru T, Sunazuka T. Pd-catalyzed Regio- and Stereoselective Hydrostannylation of an Alkyl Ethynyl Ether/One-Pot Stille Coupling Enables the Synthesis of 14-Membered Macrolactone of Luminamicin. Org Lett 2021; 23:1758-1763. [PMID: 33591766 DOI: 10.1021/acs.orglett.1c00183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Regio- and stereoselective hydrostannylation of alkyl ethynyl ethers generates alkenyl ethers, which are useful building blocks in organic synthesis. This efficient synthetic method, however, is limited. Here, we report not only an efficient method for a highly regio- and stereoselective Pd-catalyzed hydrostannylation of alkyl ethynyl ethers but also a scalable synthesis and construction of the core framework of luminamicin possessing all functional groups and stereocenters.
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Terasawa Y, Sataka C, Sato T, Yamamoto K, Fukushima Y, Nakajima C, Suzuki Y, Katsuyama A, Matsumaru T, Yakushiji F, Yokota SI, Ichikawa S. Elucidating the Structural Requirement of Uridylpeptide Antibiotics for Antibacterial Activity. J Med Chem 2020; 63:9803-9827. [PMID: 32787111 DOI: 10.1021/acs.jmedchem.0c00973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The synthesis and biological evaluation of analogues of uridylpeptide antibiotics were described, and the molecular interaction between the 3'-hydroxy analogue of mureidomycin A (3'-hydroxymureidomycin A) and its target enzyme, phospho-MurNAc-pentapeptide transferase (MraY), was analyzed in detail. The structure-activity relationship (SAR) involving MraY inhibition suggests that the side chain at the urea-dipeptide moiety does not affect the MraY inhibition. However, the anti-Pseudomonas aeruginosa activity is in great contrast and the urea-dipeptide motif is a key contributor. It is also suggested that the nucleoside peptide permease NppA1A2BCD is responsible for the transport of 3'-hydroxymureidomycin A into the cytoplasm. A systematic SAR analysis of the urea-dipeptide moiety of 3'-hydroxymureidomycin A was further conducted and the antibacterial activity was determined. This study provides a guide for the rational design of analogues based on uridylpeptide antibiotics.
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Arai Y, Torigoe S, Matsumaru T, Yamasaki S, Fujimoto Y. The key entity of a DCAR agonist, phosphatidylinositol mannoside Ac 1PIM 1: its synthesis and immunomodulatory function. Org Biomol Chem 2020; 18:3659-3663. [PMID: 32356529 DOI: 10.1039/c9ob02724f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ac1PIM1 is a potential biosynthetic intermediate for phosphatidylinositol mannosides (PIMs) from Mycobacterium tuberculosis. We achieved the first synthesis of Ac1PIM1 by utilizing an allyl-type protecting group strategy and regioselective phosphorylation of inositol. A very potent agonist of an innate immune receptor DCAR, which is better than previously known agonists, is demonstrated.
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Inuki S, Sato K, Zui N, Yamaguchi R, Matsumaru T, Fujimoto Y. Synthetic Studies on FNC-RED and Its Analogues Containing an All syn-Cyclopentanetetrol Moiety. J Org Chem 2019; 84:12680-12685. [PMID: 31507185 DOI: 10.1021/acs.joc.9b02101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FNC-RED exhibits innate immune receptor Toll-like receptor 4 (TLR4)/myeloid differentiation factor-2 (MD2) stimulatory activity. We have developed a divergent synthetic route to FNC-RED derivatives containing various alkyl side chains. Key features of the synthetic study include stepwise palladium catalyzed cross-coupling reactions and the construction of an all syn-cyclopentanetetrol moiety.
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Yamamoto K, Sato T, Hikiji Y, Katsuyama A, Matsumaru T, Yakushiji F, Yokota SI, Ichikawa S. Synthesis and biological evaluation of a MraY selective analogue of tunicamycins. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:349-364. [PMID: 31566068 DOI: 10.1080/15257770.2019.1649696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Tunicamycins, which are nucleoside natural products, inhibit both bacterial phospho-N-acetylmuraminic acid (MurNAc)-pentapeptide translocase (MraY) and human UDP-N-acetylglucosamine (GlcNAc): polyprenol phosphate translocase (GPT). The improved synthesis and detailed biological evaluation of an MraY-selective inhibitor, 2, where the GlcNAc moiety was modified to a MurNAc amide, has been described.
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Matsumaru T, Ikeno R, Shuchi Y, Iwamatsu T, Tadokoro T, Yamasaki S, Fujimoto Y, Furukawa A, Maenaka K. Synthesis of glycerolipids containing simple linear acyl chains or aromatic rings and evaluation of their Mincle signaling activity. Chem Commun (Camb) 2019; 55:711-714. [DOI: 10.1039/c8cc07322h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesized glycerolipid derivatives possessing simple alkyl chains can stimulate a Mincle-mediated signaling assay relevant for the innate immune system.
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Matsumaru T, Yasuda D. [Young Innovators Driving the Next Generation of Academic Drug Discovery]. YAKUGAKU ZASSHI 2018; 138:1025-1026. [PMID: 30068842 DOI: 10.1248/yakushi.17-00211-f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Katsuyama A, Sato K, Yakushiji F, Matsumaru T, Ichikawa S. Solid-Phase Modular Synthesis of Park Nucleotide and Lipids I and II Analogues. Chem Pharm Bull (Tokyo) 2018; 66:84-95. [PMID: 29311516 DOI: 10.1248/cpb.c17-00828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A solid-phase synthesis of Park nucleotide as well as lipids I and II analogues, which is applicable to the synthesis of a range of analogues, is described in this work. This technique allows highly functionalized macromolecules to be modularly labeled. Multiple steps are used in a short time (4 d) with a single purification step to synthesize the molecules by solid-phase synthesis.
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Ando H, Kimishima A, Ohara M, Hirose T, Matsumaru T, Takada H, Morodome K, Miyamoto T, Sugawara A, Ōmura S, Sunazuka T. Toward the total synthesis of luminamicin; an anaerobic antibiotic: construction of highly functionalized cis-decalin containing a bridged ether moiety. J Antibiot (Tokyo) 2017; 71:268-272. [PMID: 28676718 DOI: 10.1038/ja.2017.77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 11/09/2022]
Abstract
Synthesis of a cis-decalin moiety, containing an oxa-bridged cis-decalin ring system (11-oxatricyclo(5.3.1.1,703,8)undecane), as a key intermediate of the total synthesis of luminamicin (1) was accomplished. One of the essential steps in our synthetic route is construction of a cis-decaline framework using a one-pot Michael addition-aldol reaction. Additionally, the bridged ether moiety was obtained by an intramolecular 1,6-oxa-Michael reaction of a conjugated aldehyde.
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Matsumaru T, Inai M, Ishigami K, Iwamatsu T, Maita H, Otsuguro S, Nomura T, Matsuda A, Ichikawa S, Sakaitani M, Shuto S, Maenaka K, Kan T. Divergent synthesis of kinase inhibitor derivatives, leading to discovery of selective Gck inhibitors. Bioorg Med Chem Lett 2017; 27:2144-2147. [DOI: 10.1016/j.bmcl.2017.03.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/11/2017] [Accepted: 03/22/2017] [Indexed: 12/01/2022]
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McCallum ME, Smith GM, Matsumaru T, Kong K, Enquist JA, Wood JL. Synthetic studies toward citrinadin A: construction of the pentacyclic core. J Antibiot (Tokyo) 2016; 69:331-6. [PMID: 26956798 PMCID: PMC6501190 DOI: 10.1038/ja.2016.25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 01/13/2016] [Accepted: 01/16/2016] [Indexed: 11/20/2022]
Abstract
This manuscript describes the preparation of an advanced intermediate toward the total synthesis of citrinadin A, featuring a [3+2] cycloaddition employing in situ generation of the dipole.
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Matsumaru T. Drug Discovery Assisted by Kinetic Target Guided Synthesis. J SYN ORG CHEM JPN 2015. [DOI: 10.5059/yukigoseikyokaishi.73.1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Matsumaru T, McCallum ME, Enquist JA, Smith GM, Kong K, Wood JL. Synthetic studies toward the citrinadins: enantioselective preparation of an advanced spirooxindole intermediate. Tetrahedron 2014; 70:4089-4093. [PMID: 31827307 DOI: 10.1016/j.tet.2014.02.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This manuscript describes the enantioselective preparation of a spirooxindole that is suited for advancedment to either Citrinadin A or B.
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Kong K, Enquist JA, McCallum ME, Smith GM, Matsumaru T, Menhaji-Klotz E, Wood JL. An enantioselective total synthesis and stereochemical revision of (+)-citrinadin B. J Am Chem Soc 2013; 135:10890-3. [PMID: 23837485 DOI: 10.1021/ja405548b] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This manuscript describes an enantioselective synthesis of the naturally occurring alkaloid citrinadin B. The synthetic effort revealed an anomaly in the original structural assignment that has led to the proposal of a stereochemical revision. This revision is consistent with the structures previously reported for a closely related family of alkaloids, PF1270A-C. The synthesis is convergent and employs a stereoselective intermolecular nitrone cyloaddition reaction as a key step.
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