Structural insights into the inhibition mechanism of fungal GWT1 by manogepix.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
24 Oct 2024
24 Oct 2024
Historique:
received:
30
04
2024
accepted:
09
10
2024
medline:
25
10
2024
pubmed:
25
10
2024
entrez:
25
10
2024
Statut:
epublish
Résumé
Glycosylphosphatidylinositol (GPI) acyltransferase is crucial for the synthesis of GPI-anchored proteins. Targeting the fungal glycosylphosphatidylinositol acyltransferase GWT1 by manogepix is a promising antifungal strategy. However, the inhibitory mechanism of manogepix remains unclear. Here, we present cryo-EM structures of yeast GWT1 bound to the substrate (palmitoyl-CoA) and inhibitor (manogepix) at 3.3 Å and 3.5 Å, respectively. GWT1 adopts a unique fold with 13 transmembrane (TM) helixes. The palmitoyl-CoA inserts into the chamber among TM4, 5, 6, 7, and 12. The crucial residues (D145 and K155) located on the loop between TM4 and TM5 potentially bind to the GPI precursor, contributing to substrate recognition and catalysis, respectively. The antifungal drug, manogepix, occupies the hydrophobic cavity of the palmitoyl-CoA binding site, suggesting a competitive inhibitory mechanism. Structural analysis of resistance mutations elucidates the drug specificity and selectivity. These findings pave the way for the development of potent and selective antifungal drugs targeting GWT1.
Identifiants
pubmed: 39448635
doi: 10.1038/s41467-024-53512-x
pii: 10.1038/s41467-024-53512-x
doi:
Substances chimiques
Antifungal Agents
0
Acyltransferases
EC 2.3.-
Fungal Proteins
0
glycylpeptide N-tetradecanoyltransferase
EC 2.3.1.97
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
9194Subventions
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32471264
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32100979
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 31971132
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32171211
Informations de copyright
© 2024. The Author(s).
Références
Lockhart, S. R., Chowdhary, A. & Gold, J. A. W. The rapid emergence of antifungal-resistant human-pathogenic fungi. Nat. Rev. Microbiol. 21, 818–832 (2023).
pubmed: 37648790
doi: 10.1038/s41579-023-00960-9
Perfect, J. R. The antifungal pipeline: a reality check. Nat. Rev. Drug Discov. 16, 603–616 (2017).
pubmed: 28496146
pmcid: 5760994
doi: 10.1038/nrd.2017.46
Fisher, M. C., Hawkins, N. J., Sanglard, D. & Gurr, S. J. Worldwide emergence of resistance to antifungal drugs challenges human health and food security. Science 360, 739–742 (2018).
pubmed: 29773744
doi: 10.1126/science.aap7999
Parums, D. V. Editorial: The World Health Organization (WHO) fungal priority pathogens list in response to emerging fungal pathogens during the COVID-19 pandemic. Med. Sci. Monit. 28, e939088 (2022).
pubmed: 36453055
pmcid: 9724454
doi: 10.12659/MSM.939088
Vogt, M. S., Schmitz, G. F., Varon Silva, D., Mosch, H. U. & Essen, L. O. Structural base for the transfer of GPI-anchored glycoproteins into fungal cell walls. Proc. Natl Acad. Sci. Usa. 117, 22061–22067 (2020).
pubmed: 32839341
pmcid: 7486726
doi: 10.1073/pnas.2010661117
Orlean, P. Architecture and biosynthesis of the saccharomyces cerevisiae cell wall. Genetics 192, 775 (2012).
pubmed: 23135325
pmcid: 3522159
doi: 10.1534/genetics.112.144485
Umemura, M. et al. GWT1 gene is required for inositol acylation of glycosylphosphatidylinositol anchors in yeast. J. Biol. Chem. 278, 23639–23647 (2003).
pubmed: 12714589
doi: 10.1074/jbc.M301044200
Tsukahara, K. et al. Medicinal genetics approach towards identifying the molecular target of a novel inhibitor of fungal cell wall assembly. Mol. Microbiol. 48, 1029–1042 (2003).
pubmed: 12753194
doi: 10.1046/j.1365-2958.2003.03481.x
Miyazaki, M. et al. In vitro activity of E1210, a novel antifungal, against clinically important yeasts and molds. Antimicrob. Agents Chemother. 55, 4652–4658 (2011).
pubmed: 21825291
pmcid: 3186989
doi: 10.1128/AAC.00291-11
Watanabe, N. A. et al. E1210, a new broad-spectrum antifungal, suppresses Candida albicans hyphal growth through inhibition of glycosylphosphatidylinositol biosynthesis. Antimicrob. Agents Chemother. 56, 960–971 (2012).
pubmed: 22143530
pmcid: 3264227
doi: 10.1128/AAC.00731-11
Pfaller, M. et al. In vitro activity of manogepix and comparators against infrequently encountered yeast and mold isolates from the SENTRY Surveillance Program (2017-2022). Antimicrob Agents Chemother, e0113223, https://doi.org/10.1128/aac.01132-23 (2024).
Hodges, M. R. et al. Safety and pharmacokinetics of intravenous and oral fosmanogepix, a first-in-class antifungal agent, in healthy volunteers. Antimicrob. Agents Chemother. 67, e0162322 (2023).
pubmed: 36988461
doi: 10.1128/aac.01623-22
Murakami, Y. et al. PIG-W is critical for inositol acylation but not for flipping of glycosylphosphatidylinositol-anchor. Mol. Biol. Cell 14, 4285–4295 (2003).
pubmed: 14517336
pmcid: 207019
doi: 10.1091/mbc.e03-03-0193
Holm, L., Laiho, A., Toronen, P. & Salgado, M. DALI shines a light on remote homologs: one hundred discoveries. Protein Sci. 32, e4519 (2023).
pubmed: 36419248
pmcid: 9793968
doi: 10.1002/pro.4519
Grevengoed, T. J., Klett, E. L. & Coleman, R. A. Acyl-CoA metabolism and partitioning. Annu. Rev. Nutr. 34, 1–30 (2014).
pubmed: 24819326
pmcid: 5881898
doi: 10.1146/annurev-nutr-071813-105541
Sagane, K. et al. Analysis of membrane topology and identification of essential residues for the yeast endoplasmic reticulum inositol acyltransferase Gwt1p. J. Biol. Chem. 286, 14649–14658 (2011).
pubmed: 21367863
pmcid: 3077662
doi: 10.1074/jbc.M110.193490
Wang, L. et al. Structure and mechanism of human diacylglycerol O-acyltransferase 1. Nature 581, 329–332 (2020).
pubmed: 32433610
pmcid: 7255049
doi: 10.1038/s41586-020-2280-2
Sui, X. W. et al. Structure and catalytic mechanism of a human triacylglycerol-synthesis enzyme. Nature 581, 323 (2020).
pubmed: 32433611
pmcid: 7398557
doi: 10.1038/s41586-020-2289-6
Navratna, V., Kumar, A. & Mosalaganti, S. Structure of the human heparan-α-glucosaminide N-acetyltransferase (HGSNAT). Elife 13, https://doi.org/10.7554/eLife.93510.1 (2024).
Zhao, B. et al. Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome. Nat. Commun. 15, 5388 (2024).
pubmed: 38918376
pmcid: 11199644
doi: 10.1038/s41467-024-49614-1
Xu, R. et al. Structure and mechanism of lysosome transmembrane acetylation by HGSNAT. Nat. Struct. Mol. Biol., https://doi.org/10.1038/s41594-024-01315-5 (2024).
Kapoor, M., Moloney, M., Soltow, Q. A., Pillar, C. M. & Shaw, K. J. Evaluation of resistance development to the Gwt1 inhibitor manogepix (APX001A) in Candida species. Antimicrob. Agents Chemother. 64, https://doi.org/10.1128/AAC.01387-19 (2019).
Nakamoto, K. et al. Synthesis and evaluation of novel antifungal agents-quinoline and pyridine amide derivatives. Bioorg. Med. Chem. Lett. 20, 4624–4626 (2010).
pubmed: 20573507
doi: 10.1016/j.bmcl.2010.06.005
McLellan, C. A. et al. Inhibiting GPI anchor biosynthesis in fungi stresses the endoplasmic reticulum and enhances immunogenicity. ACS Chem. Biol. 7, 1520–1528 (2012).
pubmed: 22724584
doi: 10.1021/cb300235m
Liston, S. D. et al. Antifungal activity of gepinacin scaffold glycosylphosphatidylinositol anchor biosynthesis inhibitors with improved metabolic stability. Antimicrob. Agents Chemother. 64, https://doi.org/10.1128/AAC.00899-20 (2020).
Chiyonobu, T., Inoue, N., Morimoto, M., Kinoshita, T. & Murakami, Y. Glycosylphosphatidylinositol (GPI) anchor deficiency caused by mutations in PIGW is associated with West syndrome and hyperphosphatasia with mental retardation syndrome. J. Med. Genet. 51, 203–207 (2014).
pubmed: 24367057
doi: 10.1136/jmedgenet-2013-102156
Pierce, M. R. & Hougland, J. L. A rising tide lifts all MBOATs: recent progress in structural and functional understanding of membrane bound O-acyltransferases. Front. Physiol. 14, 1167873 (2023).
pubmed: 37250116
pmcid: 10213974
doi: 10.3389/fphys.2023.1167873
Jiang, Y., Benz, T. L. & Long, S. B. Substrate and product complexes reveal mechanisms of Hedgehog acylation by HHAT. Science 372, 1215–1219 (2021).
pubmed: 34112694
pmcid: 8734478
doi: 10.1126/science.abg4998
Coupland, C. E. et al. Structure, mechanism, and inhibition of Hedgehog acyltransferase. Mol. Cell 81, 5025–5038.e5010 (2021).
pubmed: 34890564
pmcid: 8693861
doi: 10.1016/j.molcel.2021.11.018
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290 (2017).
pubmed: 28165473
doi: 10.1038/nmeth.4169
Pettersen, E. F. et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
pubmed: 32881101
doi: 10.1002/pro.3943
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010).
pubmed: 20383002
pmcid: 2852313
doi: 10.1107/S0907444910007493
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010).
pubmed: 20124702
pmcid: 2815670
doi: 10.1107/S0907444909052925
Croll, T. I. : a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D. 74, 519–530 (2018).
doi: 10.1107/S2059798318002425
Thompson, J. D., Higgins, D. G. & Gibson, T. J. Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994).
pubmed: 7984417
pmcid: 308517
doi: 10.1093/nar/22.22.4673
Koes, D. R., Baumgartner, M. P. & Camacho, C. J. Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. J. Chem. Inf. Model. 53, 1893–1904 (2013).
pubmed: 23379370
pmcid: 3726561
doi: 10.1021/ci300604z
Trott, O. & Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455–461 (2010).
pubmed: 19499576
pmcid: 3041641
doi: 10.1002/jcc.21334
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).
pubmed: 29788355
pmcid: 6030848
doi: 10.1093/nar/gky427
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).
doi: 10.1063/1.445869
Huang, J. & MacKerell, A. D. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J. Comput. Chem. 34, 2135–2145 (2013).
pubmed: 23832629
doi: 10.1002/jcc.23354
Vanommeslaeghe, K. et al. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 31, 671–690 (2010).
pubmed: 19575467
pmcid: 2888302
doi: 10.1002/jcc.21367
Brooks, B. R. et al. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545–1614 (2009).
pubmed: 19444816
pmcid: 2810661
doi: 10.1002/jcc.21287
Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005).
pubmed: 16222654
pmcid: 2486339
doi: 10.1002/jcc.20289
Martyna, G. J., Tobias, D. J. & Klein, M. L. Constant-pressure molecular-dynamics algorithms. J. Chem. Phys. 101, 4177–4189 (1994).
doi: 10.1063/1.467468
Feller, S. E., Zhang, Y. H., Pastor, R. W. & Brooks, B. R. Constant-pressure molecular-dynamics simulation - the langevin piston method. J. Chem. Phys. 103, 4613–4621 (1995).
doi: 10.1063/1.470648
Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995).
doi: 10.1063/1.470117
Shirts, M. R., Mobley, D. L., Chodera, J. D. & Pande, V. S. Accurate and efficient corrections for missing dispersion interactions in molecular Simulations. J. Phys. Chem. B 111, 13052–13063 (2007).
pubmed: 17949030
doi: 10.1021/jp0735987