Recent advances in target identification of bioactive natural products

References

• Fleming A. On the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenza. Br J Exp Pathol. 1929;10:226–236.
   Google Scholar
• Kino T1, Hatanaka H, Hashimoto M, et al. FK-506, a novel immunosuppressant isolated from a Streptomyces. I. Fermentation, isolation, and physic-chemical and biological characteristics. J Antibiot (Tokyo). 1987;40(9):1249–1255.
   PubMed Web of Science ®Google Scholar
• Liu J, Farmer JD Jr, Lane WS, et al. Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes. Cell. 1991;66(4):807–815.
   PubMed Web of Science ®Google Scholar
• Spencer DM, Wandless TJ, Schreiber SL, et al. Controlling signal transduction with synthetic ligands. Science. 1993;262(5136):1019–1024.
   PubMed Web of Science ®Google Scholar
• Yoshida M, Nomura S, Beppu T. Effects of trichostatins on differentiation of murine erythroleukemia cells. Cancer Res. 1987;47:3688–3691.
   PubMed Web of Science ®Google Scholar
• Yoshida M, Beppu T. Reversible arrest of proliferation of rat 3Y1 fibroblasts in both the G1 and G2 phases by trichostatin A. Exp Cell Res. 1988;177:122–131.
   PubMed Web of Science ®Google Scholar
• Simanis V, Nurse P. The cell cycle control gene cdc2+ of fission yeast encodes a protein kinase potentially regulated by phosphorylation. Cell. 1986;45(2):261–268.
   PubMed Web of Science ®Google Scholar
• Yoshida M, Kijima M, Akita M, et al. Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by trichostatin A. J Biol Chem. 1990;265:17174–17179.
   PubMed Web of Science ®Google Scholar
• Kijima M, Yoshida M, Sugita K, et al. Trapoxin, an antitumor cyclic tetrapeptide, is an irreversible inhibitor of mammalian histone deacetylase. J Biol Chem. 1993;268:22429–22435.
   PubMed Web of Science ®Google Scholar
• Furumai R, Komatsu Y, Nishino N, et al. Potent histone deacetylase inhibitors built from trichostatin A and cyclic tetrapeptide antibiotics including trapoxin. Proc Natl Acad Sci U S A. 2001;98:87–92.
   PubMed Web of Science ®Google Scholar
• Komatsu Y, Tomizaki KY, Tsukamoto M, et al. Cyclic hydroxamic-acid-containing peptide 31, a potent synthetic histone deacetylase inhibitor with antitumor activity. Cancer Res. 2001;61(11):4459–4466.
   PubMed Web of Science ®Google Scholar
• Allfrey VG, Faulkner R, Mirsky AE. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci U S A. 1964;51:786–794.
   PubMed Web of Science ®Google Scholar
• Taunton J, Hassig CA, Schreiber SL. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science. 1996;272(5260):408–411.
   PubMed Web of Science ®Google Scholar
• Ueda H, Nakajima H, Hori Y, et al. FR901228, a novel antitumor bicyclic depsipeptide produced by Chromobacterium violaceum No. 968. I. Taxonomy, fermentation, isolation, physico-chemical and biological properties, and antitumor activity. J Antibiot (Tokyo). 1994;47(3):301–310.
   PubMed Web of Science ®Google Scholar
• Nakajima H, Kim YB, Terano H, et al. FR901228, a potent antitumor antibiotic, is a novel histone deacetylase inhibitor. Exp Cell Res. 1998;241(1):126–133.
   PubMed Web of Science ®Google Scholar
• Furumai R, Matsuyama A, Kobashi N, et al. FK228 (depsipeptide) as a natural prodrug that inhibits class I histone deacetylases. Cancer Res. 2002;62(17):4916–4921.
   PubMed Web of Science ®Google Scholar
• Richon VM, Emiliani S, Verdin E, et al. A class of hybrid polar inducers of transformed cell differentiation inhibits histone deacetylases. Proc Natl Acad Sci U S A. 1998;95(6):3003–3007.
   PubMed Web of Science ®Google Scholar
• Lamb J, Crawford ED, Peck D, et al. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313(5795):1929–1935.
   PubMed Web of Science ®Google Scholar
• Muroi M, Kazami S, Noda K, et al. Application of proteomic profiling based on 2D-DIGE for classification of compounds according to the mechanism of action. Chem Biol. 2011;17(5):460–470.
   Google Scholar
• Yamori T. Panel of human cancer cell lines provides valuable database for drug discovery and bioinformatics. Cancer Chemother Pharmacol. 2003;52(Suppl 1):S74–79.
   PubMedGoogle Scholar
• Futamura Y, Kawatani M, Kazami S, et al. Morphobase, an encyclopedic cell morphology database, and its use for drug target identification. Chem Biol. 2012;19(12):1620–1630.
   PubMedGoogle Scholar
• Subramanian A, Narayan R, Corsello SM, et al. 4. A next generation connectivity map: L1000 platform and the first 1,000,000 profiles. Cell. 2017;171(6):1437–1452.e17.
   PubMed Web of Science ®Google Scholar
• Fenteany G, Standaert RF, Lane WS, et al. Inhibition of proteasome activities and subunit-specific amino-terminal threonine modification by lactacystin. Science. 1995;268(5211):726–731.
   PubMed Web of Science ®Google Scholar
• Kaida D, Motoyoshi H, Tashiro E, et al. Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat Chem Biol. 2007;3(9):576–583.
   PubMed Web of Science ®Google Scholar
• Yoshimoto R, Kaida D, Furuno M, et al. Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A. RNA. 2017;23(1):47–57.
   Google Scholar
• Ito T, Ando H, Suzuki T, et al. Identification of a primary target of thalidomide teratogenicity. Science. 2010;327(5971):1345–1350.
   PubMed Web of Science ®Google Scholar
• Krönke J1, Udeshi ND, Narla A, et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science. 2014;343(6168):301–305.
   PubMed Web of Science ®Google Scholar
• Lu G, Middleton RE, Sun H, et al. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science. 2014;343(6168):305–309.
   PubMed Web of Science ®Google Scholar
• Kanoh N, Honda K, Simizu S, et al. Photo-cross-linked small-molecule affinity matrix for facilitating forward and reverse chemical genetics. Angew Chem Int Ed Engl. 2005;44(23):3559–3562.
   PubMed Web of Science ®Google Scholar
• Kunz J, Henriquez R, Schneider U, et al. Target of rapamycin in yeast, TOR2, is an essential phosphatidylinositol kinase homolog required for G1 progression. Cell. 1993;73(3):585–596.
   PubMed Web of Science ®Google Scholar
• Hamamoto T, Gunji S, Tsuji H, et al. Leptomycins A and B, new antifungal antibiotics. I. Taxonomy of the producing strain and their fermentation, purification and characterization. J Antibiot (Tokyo). 1983;36(6):639–645.
   PubMed Web of Science ®Google Scholar
• Nishi K, Yoshida M, Fujiwara D, et al. Leptomycin B targets a regulatory cascade of crm1, a fission yeast nuclear protein, involved in control of higher order chromosome structure and gene expression. J Biol Chem. 1994;269(9):6320–6324.
   PubMed Web of Science ®Google Scholar
• Kudo N, Khochbin S, Nishi K, et al. Molecular cloning and cell cycle-dependent expression of mammalian CRM1, a protein involved in nuclear export of proteins. J Biol Chem. 1997;272(47):29742–29751.
   PubMed Web of Science ®Google Scholar
• Fornerod M, Ohno M, Yoshida M, et al. CRM1 is an export receptor for leucine-rich nuclear export signals. Cell. 1997;90(6):1051–1060.
   PubMed Web of Science ®Google Scholar
• Kudo N, Wolff B, Sekimoto T, et al. Leptomycin B inhibition of signal-mediated nuclear export by direct binding to CRM1. Exp Cell Res. 1998;242(2):540–547.
   PubMed Web of Science ®Google Scholar
• Kudo N, Matsumori N, Taoka H, et al. Leptomycin B inactivates CRM1/exportin 1 by covalent modification at a cysteine residue in the central conserved region. Proc Natl Acad Sci U S A. 1999;96(16):9112–9117.
   PubMed Web of Science ®Google Scholar
• Dong X, Biswas A, Süel KE, et al. Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature. 2009;458(7242):1136–1141.
   PubMed Web of Science ®Google Scholar
• Mendonca J, Sharma A, Kim HS, et al. Selective inhibitors of nuclear export (SINE) as novel therapeutics for prostate cancer. Oncotarget. 2014;5(15):6102–6112.
   PubMedGoogle Scholar
• Matsuyama A, Arai R, Yashiroda Y, et al. ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol. 2006;24(7):841–847.
   PubMed Web of Science ®Google Scholar
• Nishimura S, Arita Y, Honda M, et al. Marine antifungal theonellamides target 3beta-hydroxysterol to activate Rho1 signaling. Nat Chem Biol. 2010;6(7):519–526.
   PubMed Web of Science ®Google Scholar
• Parsons AB, Brost RL, Ding H, et al. Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol. 2004;22(1):62–69.
   PubMed Web of Science ®Google Scholar
• Costanzo M, Baryshnikova A, Bellay J, et al. The genetic landscape of a cell. Science. 2010;327(5964):425–431.
   PubMed Web of Science ®Google Scholar
• Piotrowski JS, Li SC, Deshpande R, et al. Functional annotation of chemical libraries across diverse biological processes. Nat Chem Biol. 2017;13(9):982–993.
   PubMed Web of Science ®Google Scholar
• Ohya Y, Sese J, Yukawa M, et al. High-dimensional and large-scale phenotyping of yeast mutants. Proc Natl Acad Sci U S A. 2005;102(52):19015–19020.
   PubMed Web of Science ®Google Scholar
• Takase S, Kurokawa R, Arai D, et al. A quantitative shRNA screen identifies ATP1A1 as a gene that regulates cytotoxicity by aurilide B. Sci Rep. 2017;7(1):2002.
   PubMedGoogle Scholar
• Hart T, Chandrashekhar M, Aregger M, et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell. 2015;163(6):1515–1526.
   PubMed Web of Science ®Google Scholar
• Avior Y, Sagi I, Benvenisty N. Pluripotent stem cells in disease modelling and drug discovery. Nat Rev Mol Cell Biol. 2016;17(3):170–182.
   PubMed Web of Science ®Google Scholar
• Shi Y, Inoue H, Wu JC, et al. Induced pluripotent stem cell technology: a decade of progress. Nat Rev Drug Discov. 2017;16(2):115–130.
   PubMed Web of Science ®Google Scholar