DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
02 Sep 2024
02 Sep 2024
Historique:
received:
13
10
2023
accepted:
11
08
2024
medline:
3
9
2024
pubmed:
3
9
2024
entrez:
2
9
2024
Statut:
epublish
Résumé
Small-molecule compounds that elicit mRNA-selective translation repression have attracted interest due to their potential for expansion of druggable space. However, only a limited number of examples have been reported to date. Here, we show that desmethyl desamino pateamine A (DMDA-PatA) represses translation in an mRNA-selective manner by clamping eIF4A, a DEAD-box RNA-binding protein, onto GNG motifs. By systematically comparing multiple eIF4A inhibitors by ribosome profiling, we found that DMDA-PatA has unique mRNA selectivity for translation repression. Unbiased Bind-n-Seq reveals that DMDA-PatA-targeted eIF4A exhibits a preference for GNG motifs in an ATP-independent manner. This unusual RNA binding sterically hinders scanning by 40S ribosomes. A combination of classical molecular dynamics simulations and quantum chemical calculations, and the subsequent development of an inactive DMDA-PatA derivative reveals that the positive charge of the tertiary amine on the trienyl arm induces G selectivity. Moreover, we identified that DDX3, another DEAD-box protein, is an alternative DMDA-PatA target with the same effects on eIF4A. Our results provide an example of the sequence-selective anchoring of RNA-binding proteins and the mRNA-selective inhibition of protein synthesis by small-molecule compounds.
Identifiants
pubmed: 39223140
doi: 10.1038/s41467-024-51635-9
pii: 10.1038/s41467-024-51635-9
doi:
Substances chimiques
DEAD-box RNA Helicases
EC 3.6.4.13
Eukaryotic Initiation Factor-4A
EC 2.7.7.-
DDX3X protein, human
EC 3.6.1.-
pateamine A
0
RNA, Messenger
0
EIF4A1 protein, human
0
Epoxy Compounds
0
Thiazoles
0
Macrolides
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
7418Subventions
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23H02415
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23H00095
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP23K05648
Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)
ID : JP19H05640
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP20H05784
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP24H02307
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP21H05734
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP23H04268
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP18H05503
Organisme : Ministry of Education, Culture, Sports, Science and Technology (MEXT)
ID : JP21H05281
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23gm1410001
Organisme : Japan Agency for Medical Research and Development (AMED)
ID : JP23gm1410001
Organisme : MEXT | RIKEN
ID : Pioneering Projects
Organisme : MEXT | RIKEN
ID : Incentive Research Projects
Organisme : MEXT | RIKEN
ID : Pioneering Projects
Organisme : MEXT | RIKEN
ID : Pioneering Projects
Informations de copyright
© 2024. The Author(s).
Références
Valeur, E. & Jimonet, P. New modalities, technologies, and partnerships in probe and lead generation: enabling a mode-of-action centric paradigm. J. Med. Chem. 61, 9004–9029 (2018).
pubmed: 29851477
doi: 10.1021/acs.jmedchem.8b00378
Shichino, Y. & Iwasaki, S. Compounds for selective translational inhibition. Curr. Opin. Chem. Biol. 69, 102158 (2022).
pubmed: 35598529
doi: 10.1016/j.cbpa.2022.102158
Vázquez-Laslop, N. & Mankin, A. S. Context-specific action of ribosomal antibiotics. Annu. Rev. Microbiol. 72, 185–207 (2018).
pubmed: 29906204
pmcid: 8742604
doi: 10.1146/annurev-micro-090817-062329
Atanasov, A. G., Zotchev, S. B., Dirsch, V. M., International Natural Product Sciences Taskforce & Supuran, C. T. Natural products in drug discovery: advances and opportunities. Nat. Rev. Drug Discov. 20, 200–216 (2021).
pubmed: 33510482
pmcid: 7841765
doi: 10.1038/s41573-020-00114-z
Lin, J., Zhou, D., Steitz, T. A., Polikanov, Y. S. & Gagnon, M. G. Ribosome-targeting antibiotics: modes of action, mechanisms of resistance, and implications for drug design. Annu. Rev. Biochem. 87, 451–478 (2018).
pubmed: 29570352
pmcid: 9176271
doi: 10.1146/annurev-biochem-062917-011942
Shen, L. & Pelletier, J. Selective targeting of the DEAD-box RNA helicase eukaryotic initiation factor (eIF) 4A by natural products. Nat. Prod. Rep. 37, 609–616 (2020).
pubmed: 31782447
doi: 10.1039/C9NP00052F
Higa, T., Tanaka, J.-I., Tsukitani, Y. & Kikuchi, H. Hippuristanols, cytotoxic polyoxygenated steroids from the gorgonian Isis hippuris. Chem. Lett. 10, 1647–1650 (1981).
doi: 10.1246/cl.1981.1647
Bordeleau, M. E. et al. Functional characterization of IRESes by an inhibitor of the RNA helicase eIF4A. Nat. Chem. Biol. 2, 213–220 (2006).
pubmed: 16532013
doi: 10.1038/nchembio776
Lindqvist, L. et al. Selective pharmacological targeting of a DEAD box RNA helicase. PLoS One 3, e1583 (2008).
pubmed: 18270573
pmcid: 2216682
doi: 10.1371/journal.pone.0001583
Sun, Y. et al. Single-molecule kinetics of the eukaryotic initiation factor 4AI upon RNA unwinding. Structure 22, 941–948 (2014).
pubmed: 24909782
doi: 10.1016/j.str.2014.04.014
Steinberger, J. et al. Identification and characterization of hippuristanol-resistant mutants reveals eIF4A1 dependencies within mRNA 5′ leader regions. Nucleic Acids Res. 48, 9521–9537 (2020).
pubmed: 32766783
pmcid: 7515738
doi: 10.1093/nar/gkaa662
King, M. L. et al. X-Ray crystal structure of rocaglamide, a novel antileulemic 1H-cyclopenta[b]benzofuran from Aglaia elliptifolia. J. Chem. Soc. Chem. Commun. 1, 1150–1151 (1982).
doi: 10.1039/c39820001150
Bordeleau, M. E. et al. Therapeutic suppression of translation initiation modulates chemosensitivity in a mouse lymphoma model. J. Clin. Invest. 118, 2651–2660 (2008).
pubmed: 18551192
pmcid: 2423864
Sadlish, H. et al. Evidence for a functionally relevant rocaglamide binding site on the eIF4A-RNA complex. ACS Chem. Biol. 8, 1519–1527 (2013).
pubmed: 23614532
pmcid: 3796129
doi: 10.1021/cb400158t
Santagata, S. et al. Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science 341, 1238303 (2013).
pubmed: 23869022
pmcid: 3959726
doi: 10.1126/science.1238303
Iwasaki, S., Floor, S. N. & Ingolia, N. T. Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. Nature 534, 558–561 (2016).
pubmed: 27309803
pmcid: 4946961
doi: 10.1038/nature17978
Chu, J. et al. Amidino-rocaglates: a potent class of eIF4A inhibitors. Cell Chem. Biol. 26, 1586–1593.e3 (2019).
pubmed: 31519508
pmcid: 6874763
doi: 10.1016/j.chembiol.2019.08.008
Iwasaki, S. et al. The translation inhibitor rocaglamide targets a bimolecular cavity between eIF4A and polypurine RNA. Mol. Cell 73, 738–748.e9 (2019).
pubmed: 30595437
doi: 10.1016/j.molcel.2018.11.026
Chu, J. et al. Rocaglates induce gain-of-function alterations to eIF4A and eIF4F. Cell Rep. 30, 2481–2488.e5 (2020).
pubmed: 32101697
pmcid: 7077502
doi: 10.1016/j.celrep.2020.02.002
Cencic, R. et al. A second-generation eIF4A RNA helicase inhibitor exploits translational reprogramming as a vulnerability in triple-negative breast cancer. Proc. Natl. Acad. Sci. USA. 121, e2318093121 (2024).
pubmed: 38232291
pmcid: 10823175
doi: 10.1073/pnas.2318093121
Northcote, P. T., Blunt, J. W. & Munro, M. H. G. Pateamine: a potent cytotoxin from the New Zealand Marine sponge, mycale sp. Tetrahedron Lett. 32, 6411–6414 (1991).
doi: 10.1016/0040-4039(91)80182-6
Bordeleau, M. E. et al. Stimulation of mammalian translation initiation factor eIF4A activity by a small molecule inhibitor of eukaryotic translation. Proc. Natl. Acad. Sci. USA. 102, 10460–10465 (2005).
pubmed: 16030146
pmcid: 1176247
doi: 10.1073/pnas.0504249102
Low, W. K. et al. Inhibition of eukaryotic translation initiation by the marine natural product pateamine A. Mol. Cell 20, 709–722 (2005).
pubmed: 16337595
doi: 10.1016/j.molcel.2005.10.008
Bordeleau, M. E. et al. RNA-mediated sequestration of the RNA helicase eIF4A by Pateamine A inhibits translation initiation. Chem. Biol. 13, 1287–1295 (2006).
pubmed: 17185224
doi: 10.1016/j.chembiol.2006.10.005
Low, W. K., Dang, Y., Bhat, S., Romo, D. & Liu, J. O. Substrate-dependent targeting of eukaryotic translation initiation factor 4A by pateamine A: negation of domain-linker regulation of activity. Chem. Biol. 14, 715–727 (2007).
pubmed: 17584618
doi: 10.1016/j.chembiol.2007.05.012
Di Marco, S. et al. The translation inhibitor pateamine A prevents cachexia-induced muscle wasting in mice. Nat. Commun. 3, 896 (2012).
pubmed: 22692539
doi: 10.1038/ncomms1899
Low, W.-K. et al. Second-generation derivatives of the eukaryotic translation initiation inhibitor pateamine A targeting eIF4A as potential anticancer agents. Bioorg. Med. Chem. 22, 116–125 (2014).
pubmed: 24359706
doi: 10.1016/j.bmc.2013.11.046
Popa, A., Lebrigand, K., Barbry, P. & Waldmann, R. Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells. BMC Genomics 17, 52 (2016).
pubmed: 26764022
pmcid: 4712605
doi: 10.1186/s12864-016-2384-0
Chen, R. et al. Creating novel translation inhibitors to target pro-survival proteins in chronic lymphocytic leukemia. Leukemia 33, 1663–1674 (2019).
pubmed: 30700841
pmcid: 8785363
doi: 10.1038/s41375-018-0364-x
Rust, M. et al. A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli. Proc. Natl. Acad. Sci. USA. 117, 9508–9518 (2020).
pubmed: 32291345
pmcid: 7196800
doi: 10.1073/pnas.1919245117
Storey, M. A. et al. Metagenomic exploration of the marine sponge Mycale hentscheli uncovers multiple polyketide-producing bacterial symbionts. MBio 11, e02997–19 (2020).
pubmed: 32209692
pmcid: 7157528
doi: 10.1128/mBio.02997-19
Naineni, S. K. et al. Functional mimicry revealed by the crystal structure of an eIF4A:RNA complex bound to the interfacial inhibitor, desmethyl pateamine A. Cell Chem. Biol.28, 825–834.e6 (2021).
Santos, A. C. & Adkilen, P. The alkaloids of Argemone mexicana. J. Am. Chem. Soc. 54, 2923–2924 (1932).
doi: 10.1021/ja01346a037
Jiang, C. et al. Targeting the N terminus of eIF4AI for inhibition of its catalytic recycling. Cell Chem. Biol. 26, 1417–1426.e5 (2019).
pubmed: 31402318
doi: 10.1016/j.chembiol.2019.07.010
Hinnebusch, A. G. The scanning mechanism of eukaryotic translation initiation. Annu. Rev. Biochem. 83, 779–812 (2014).
pubmed: 24499181
doi: 10.1146/annurev-biochem-060713-035802
Brito Querido, J. et al. Structure of a human 48S translational initiation complex. Science 369, 1220–1227 (2020).
pubmed: 32883864
doi: 10.1126/science.aba4904
Chen, M. et al. Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A. Cell Chem. Biol. 28, 475–486.e8 (2021).
pubmed: 33296667
doi: 10.1016/j.chembiol.2020.11.008
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009).
pubmed: 19213877
pmcid: 2746483
doi: 10.1126/science.1168978
Iwasaki, S. & Ingolia, N. T. The growing toolbox for protein synthesis studies. Trends Biochem. Sci. 42, 612–624 (2017).
pubmed: 28566214
pmcid: 5533619
doi: 10.1016/j.tibs.2017.05.004
Romo, D. et al. Evidence for separate binding and scaffolding domains in the immunosuppressive and antitumor marine natural product, pateamine a: design, synthesis, and activity studies leading to a potent simplified derivative. J. Am. Chem. Soc. 126, 10582–10588 (2004).
pubmed: 15327314
doi: 10.1021/ja040065s
Liu, T. Y. et al. Time-resolved proteomics extends ribosome profiling-based measurements of protein synthesis dynamics. Cell Syst. 4, 636–644.e9 (2017).
pubmed: 28578850
pmcid: 5546878
doi: 10.1016/j.cels.2017.05.001
Chhipi-Shrestha, J. K. et al. Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns. Cell Chem. Biol. 29, 259–275.e10 (2022).
pubmed: 34520743
doi: 10.1016/j.chembiol.2021.07.015
Naineni, S. K. et al. A comparative study of small molecules targeting eIF4A. RNA 26, 541–549 (2020).
pubmed: 32014999
pmcid: 7161356
doi: 10.1261/rna.072884.119
Lambert, N. et al. RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol. Cell 54, 887–900 (2014).
pubmed: 24837674
pmcid: 4142047
doi: 10.1016/j.molcel.2014.04.016
Lambert, N. J., Robertson, A. D. & Burge, C. B. RNA Bind-n-Seq: measuring the binding affinity landscape of RNA-binding proteins. Methods Enzymol. 558, 465–493 (2015).
pubmed: 26068750
pmcid: 5576890
doi: 10.1016/bs.mie.2015.02.007
Linder, P. & Jankowsky, E. From unwinding to clamping—the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol. 12, 505–516 (2011).
pubmed: 21779027
doi: 10.1038/nrm3154
Weis, K. & Hondele, M. The role of DEAD-Box ATPases in gene expression and the regulation of RNA-protein condensates. Annu. Rev. Biochem. 91, 197–219 (2022).
pubmed: 35303788
doi: 10.1146/annurev-biochem-032620-105429
Pestova, T. V. & Kolupaeva, V. G. The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev. 16, 2906–2922 (2002).
pubmed: 12435632
pmcid: 187480
doi: 10.1101/gad.1020902
Wolfe, A. L. et al. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 513, 65–70 (2014).
pubmed: 25079319
pmcid: 4492470
doi: 10.1038/nature13485
Waldron, J. A., Raza, F. & Le Quesne, J. eIF4A alleviates the translational repression mediated by classical secondary structures more than by G-quadruplexes. Nucleic Acids Res. 46, 3075–3087 (2018).
pubmed: 29471358
pmcid: 5888628
doi: 10.1093/nar/gky108
Waldron, J. A. et al. mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity. Genome Biol. 20, 300 (2019).
pubmed: 31888698
pmcid: 6936103
doi: 10.1186/s13059-019-1901-2
Dmitriev, S. E., Pisarev, A. V., Rubtsova, M. P., Dunaevsky, Y. E. & Shatsky, I. N. Conversion of 48S translation preinitiation complexes into 80S initiation complexes as revealed by toeprinting. FEBS Lett. 533, 99–104 (2003).
pubmed: 12505166
doi: 10.1016/S0014-5793(02)03776-6
Shirokikh, N. E. et al. Quantitative analysis of ribosome-mRNA complexes at different translation stages. Nucleic Acids Res. 38, e15 (2010).
pubmed: 19910372
doi: 10.1093/nar/gkp1025
Chen, M. et al. A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants. Elife 12, e81302 (2023).
pubmed: 36852480
pmcid: 9977294
doi: 10.7554/eLife.81302
Kitaura, K., Ikeo, E., Asada, T., Nakano, T. & Uebayasi, M. Fragment molecular orbital method: an approximate computational method for large molecules. Chem. Phys. Lett. 313, 701–706 (1999).
doi: 10.1016/S0009-2614(99)00874-X
Fedorov, D. G., Nagata, T. & Kitaura, K. Exploring chemistry with the fragment molecular orbital method. Phys. Chem. Chem. Phys. 14, 7562–7577 (2012).
pubmed: 22410762
doi: 10.1039/c2cp23784a
Tanaka, S., Mochizuki, Y., Komeiji, Y., Okiyama, Y. & Fukuzawa, K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys. Chem. Chem. Phys. 16, 10310–10344 (2014).
pubmed: 24740821
doi: 10.1039/C4CP00316K
Mochizuki, Y., Tanaka, S. & Fukuzawa, K. Recent Advances of the Fragment Molecular Orbital Method: Enhanced Performance and Applicability (Springer Nature Singapore, 2021).
Handa, Y. et al. Prediction of binding pose and affinity of Nelfinavir, a SARS-CoV-2 main protease repositioned drug, by combining docking, molecular dynamics, and fragment molecular orbital calculations. J. Phys. Chem. B 128, 2249–2265 (2024).
pubmed: 38437183
doi: 10.1021/acs.jpcb.3c05564
Fedorov, D. G. & Kitaura, K. Pair interaction energy decomposition analysis. J. Comput. Chem. 28, 222–237 (2007).
pubmed: 17109433
doi: 10.1002/jcc.20496
Tsukamoto, T. et al. Implementation of pair interaction energy decomposition analysis and its applications to protein-ligand systems. J. Comput. Chem. Jpn. 14, 1–9 (2015).
doi: 10.2477/jccj.2014-0039
Li, F. et al. Reanalysis of ribosome profiling datasets reveals a function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A. Nat. Commun. 14, 553 (2023).
pubmed: 36725859
pmcid: 9891901
doi: 10.1038/s41467-023-36290-w
Mullard, A. Small molecules against RNA targets attract big backers. Nat. Rev. Drug Discov. 16, 813–815 (2017).
pubmed: 29180732
doi: 10.1038/nrd.2017.239
Garber, K. Drugging RNA. Nat. Biotechnol. 41, 745–749 (2023).
pubmed: 37198443
doi: 10.1038/s41587-023-01790-z
Khaperskyy, D. A. et al. Influenza a virus host shutoff disables antiviral stress-induced translation arrest. PLoS Pathog. 10, e1004217 (2014).
pubmed: 25010204
pmcid: 4092144
doi: 10.1371/journal.ppat.1004217
González-Almela, E. et al. Differential action of pateamine A on translation of genomic and subgenomic mRNAs from Sindbis virus. Virology 484, 41–50 (2015).
pubmed: 26057151
doi: 10.1016/j.virol.2015.05.002
Ziehr, B., Lenarcic, E., Cecil, C. & Moorman, N. J. The eIF4AIII RNA helicase is a critical determinant of human cytomegalovirus replication. Virology 489, 194–201 (2016).
pubmed: 26773380
doi: 10.1016/j.virol.2015.12.009
Slaine, P. D., Kleer, M., Smith, N. K., Khaperskyy, D. A. & McCormick, C. Stress granule-inducing eukaryotic translation initiation factor 4A inhibitors block influenza A virus replication. Viruses 9, 388 (2017).
pubmed: 29258238
pmcid: 5744162
doi: 10.3390/v9120388
Lucas, D. M. et al. The novel plant-derived agent silvestrol has B-cell selective activity in chronic lymphocytic leukemia and acute lymphoblastic leukemia in vitro and in vivo. Blood 113, 4656–4666 (2009).
pubmed: 19190247
pmcid: 2680369
doi: 10.1182/blood-2008-09-175430
Alachkar, H. et al. Silvestrol exhibits significant in vivo and in vitro antileukemic activities and inhibits FLT3 and miR-155 expressions in acute myeloid leukemia. J. Hematol. Oncol. 6, 21 (2013).
pubmed: 23497456
pmcid: 3623627
doi: 10.1186/1756-8722-6-21
Boussemart, L. et al. eIF4F is a nexus of resistance to anti-BRAF and anti-MEK cancer therapies. Nature 513, 105–109 (2014).
pubmed: 25079330
doi: 10.1038/nature13572
Wiegering, A. et al. Targeting translation initiation bypasses signaling crosstalk mechanisms that maintain high MYC levels in colorectal cancer. Cancer Discov. 5, 768–781 (2015).
pubmed: 25934076
pmcid: 5166973
doi: 10.1158/2159-8290.CD-14-1040
Manier, S. et al. Inhibiting the oncogenic translation program is an effective therapeutic strategy in multiple myeloma. Sci. Transl. Med. 9, eaal2668 (2017).
pubmed: 28490664
pmcid: 5718051
doi: 10.1126/scitranslmed.aal2668
Cerezo, M. et al. Translational control of tumor immune escape via the eIF4F-STAT1-PD-L1 axis in melanoma. Nat. Med. 24, 1877–1886 (2018).
pubmed: 30374200
doi: 10.1038/s41591-018-0217-1
Chan, K. et al. eIF4A supports an oncogenic translation program in pancreatic ductal adenocarcinoma. Nat. Commun. 10, 5151 (2019).
pubmed: 31723131
pmcid: 6853918
doi: 10.1038/s41467-019-13086-5
Nishida, Y. et al. Inhibition of translation initiation factor eIF4a inactivates heat shock factor 1 (HSF1) and exerts anti-leukemia activity in AML. Leukemia 35, 2469–2481 (2021).
pubmed: 34127794
pmcid: 8764661
doi: 10.1038/s41375-021-01308-z
Skofler, C. et al. Eukaryotic translation initiation factor 4AI: a potential novel target in neuroblastoma. Cells 10, 301 (2021).
pubmed: 33540613
pmcid: 7912938
doi: 10.3390/cells10020301
Thompson, P. A. et al. Targeting oncogene mRNA translation in B-cell malignancies with eFT226, a potent and selective inhibitor of eIF4A. Mol. Cancer Ther. 20, 26–36 (2021).
pubmed: 33037136
doi: 10.1158/1535-7163.MCT-19-0973
Wilmore, S. et al. Targeted inhibition of eIF4A suppresses B-cell receptor-induced translation and expression of MYC and MCL1 in chronic lymphocytic leukemia cells. Cell. Mol. Life Sci. 78, 6337–6349 (2021).
pubmed: 34398253
pmcid: 8429177
doi: 10.1007/s00018-021-03910-x
Kuznetsov, G. et al. Potent in vitro and in vivo anticancer activities of des-methyl, des-amino pateamine A, a synthetic analogue of marine natural product pateamine A. Mol. Cancer Ther. 8, 1250–1260 (2009).
pubmed: 19417157
pmcid: 3026899
doi: 10.1158/1535-7163.MCT-08-1026
Ho, J. J. D. et al. Proteomics reveal cap-dependent translation inhibitors remodel the translation machinery and translatome. Cell Rep 37, 109806 (2021).
pubmed: 34644561
pmcid: 8558842
doi: 10.1016/j.celrep.2021.109806
Romo, D. et al. Total synthesis and immunosuppressive activity of (−)-pateamine A and related compounds: implementation of a β-lactam-based macrocyclization. J. Am. Chem. Soc. 120, 12237–12254 (1998).
doi: 10.1021/ja981846u
Zhuo, C.-X. & Fürstner, A. Catalysis-based total syntheses of pateamine A and DMDA-Pat A. J. Am. Chem. Soc. 140, 10514–10523 (2018).
pubmed: 30056701
doi: 10.1021/jacs.8b05094
Guan, W. et al. Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters. J. Org. Chem. 79, 7199–7204 (2014).
pubmed: 24915498
pmcid: 4120978
doi: 10.1021/jo500773t
McIntosh, M. L., Moore, C. M. & Clark, T. B. Copper-catalyzed diboration of ketones: facile synthesis of tertiary alpha-hydroxyboronate esters. Org. Lett. 12, 1996–1999 (2010).
pubmed: 20392113
doi: 10.1021/ol100468f
Xu, S. et al. Pincer iron hydride complexes for alkene isomerization: catalytic approach to trisubstituted (Z)-alkenyl boronates. ACS Catal. 11, 10138–10147 (2021).
doi: 10.1021/acscatal.1c02432
Sanchez, A. & Maimone, T. J. Taming shapeshifting anions: total synthesis of ocellatusone C. J. Am. Chem. Soc. 144, 7594–7599 (2022).
pubmed: 35420799
doi: 10.1021/jacs.2c02627
Zhuo, C.-X. & Fürstner, A. Concise synthesis of a pateamine A analogue with in vivo anticancer activity based on an iron-catalyzed pyrone ring opening/cross-coupling. Angew. Chem. Int. Ed Engl. 55, 6051–6056 (2016).
pubmed: 27061139
doi: 10.1002/anie.201602125
Mito, M., Mishima, Y. & Iwasaki, S. Protocol for disome profiling to survey ribosome collision in humans and zebrafish. STAR Protoc. 1, 100168 (2020).
pubmed: 33377062
pmcid: 7757362
doi: 10.1016/j.xpro.2020.100168
Kashiwagi, K. et al. eIF2B-capturing viral protein NSs suppresses the integrated stress response. Nat. Commun. 12, 1–12 (2021).
doi: 10.1038/s41467-021-27337-x
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
pubmed: 22388286
pmcid: 3322381
doi: 10.1038/nmeth.1923
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
pubmed: 20979621
pmcid: 3218662
doi: 10.1186/gb-2010-11-10-r106
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886
doi: 10.1093/bioinformatics/bts635
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
pubmed: 30423086
pmcid: 6129281
doi: 10.1093/bioinformatics/bty560
Molecular Operating Environment (MOE). (2022.02 Chemical Computing Group ULC, 910-1010 Sherbrooke St. W., Montreal, QC H3A 2R7, Canada, 2024).
Gerber, P. R. & Müller, K. MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. J. Comput. Aided Mol. Des. 9, 251–268 (1995).
pubmed: 7561977
doi: 10.1007/BF00124456
Case, D. A. et al. Amber 10. (University of California, 2008).
Maier, J. A. et al. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 11, 3696–3713 (2015).
pubmed: 26574453
pmcid: 4821407
doi: 10.1021/acs.jctc.5b00255
Zgarbová, M. et al. Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J. Chem. Theory Comput. 7, 2886–2902 (2011).
pubmed: 21921995
pmcid: 3171997
doi: 10.1021/ct200162x
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004).
pubmed: 15116359
doi: 10.1002/jcc.20035
Wang, J., Wolf, R. M., Caldwell, J. W. & Kollman, P. A. & Case, D. A. Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, “Development and testing of a general amber force field”Journal of Computational Chemistry (2004) 25(9) 1157–1174. J. Comput. Chem. 26, 114–114 (2005).
doi: 10.1002/jcc.20145
He, X., Man, V. H., Yang, W., Lee, T.-S. & Wang, J. A fast and high-quality charge model for the next generation general AMBER force field. J. Chem. Phys. 153, 114502 (2020).
pubmed: 32962378
pmcid: 7728379
doi: 10.1063/5.0019056
Case, D. A. et al. Amber 16 (University of California, 2016).
Mochizuki, Y. et al. A parallelized integral-direct second-order Møller–Plesset perturbation theory method with a fragment molecular orbital scheme. Theor. Chem. Acc. 112, 442–452 (2004).
doi: 10.1007/s00214-004-0602-3
Mochizuki, Y., Koikegami, S., Nakano, T., Amari, S. & Kitaura, K. Large scale MP2 calculations with fragment molecular orbital scheme. Chem. Phys. Lett. 396, 473–479 (2004).
doi: 10.1016/j.cplett.2004.08.082
Takaya, D. et al. FMODB: the world’s first database of quantum mechanical calculations for biomacromolecules based on the fragment molecular orbital method. J. Chem. Inf. Model. 61, 777–794 (2021).
pubmed: 33511845
doi: 10.1021/acs.jcim.0c01062
Saito, H. Custom scripts for DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs. Zenodo. https://doi.org/10.5281/zenodo.11064746 (2024).