Synthetic molecules: Helping to unravel plant signal transduction

Journal of Chemical Biology

Volumn 6, Issue 2, 2013, Pages 43-50

  Xuan, Wei ^a,b   Murphy, Evan ^c   Beeckman, Tom ^a,b   Audenaert, Dominique ^a   De Smet, Ive ^c  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Chemical biology; Plant growth and development; Screening; Small molecules; Translational biology

Indexed keywords

BIKININ; ENDOSIDINS; NAXILLIN; PHYTOHORMONE; PYRABACTIN; UNCLASSIFIED DRUG; [5 (3,4 DICHLOROPHENYL) FURAN 2 YL] PIPERIDINE 1 YLMETHANETHIONE;

ARABIDOPSIS THALIANA; BIOLOGICAL ACTIVITY; CHEMICAL GENETICS; GROWTH REGULATION; HIGH THROUGHPUT SCREENING; MOLECULE; NONHUMAN; PLANT DEFENSE; PLANT GROWTH; PLANT MODEL; PRIORITY JOURNAL; RESEARCH; REVIEW; SIGNAL TRANSDUCTION;

EID: 84874359645     PISSN: 18646158     EISSN: 18646166     Source Type: Journal    
DOI: 10.1007/s12154-013-0091-8     Document Type: Review

References (49)

1. Agler M, Prack M, Zhu Y, Kolb J, Nowak K, Ryseck R, Shen D, Cvijic ME, Somerville J, Nadler S, Chen T (2007) A high-content glucocorticoid receptor translocation assay for compound mechanism-of-action evaluation. J Biomol Screen 12:1029-1041
2. Armstrong JI, Yuan S, Dale JM, Tanner VN, Theologis A (2004) Identification of inhibitors of auxin transcriptional activation by means of chemical genetics in Arabidopsis. Proc Natl Acad Sci U S A 101:14978-14983
3. Arkin MR, Wells JA (2004) Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 3:301-317
4. Bajsa J, Pan Z, Duke SO (2011) Transcriptional responses to cantharidin, a protein phosphatase inhibitor, in Arabidopsis thaliana reveal the involvement of multiple signal transduction pathways. Physiol Plant 143:188-205
5. Barabasz A, Foley B, Otto JC, Scott A, Rice J (2006) The use of highcontent screening for the discovery and characterization of compounds that modulate mitotic index and cell cycle progression by differing mechanisms of action. Assay Drug Dev Technol 4:153-163
6. Baskin TI, Wilson JE (1997) Inhibitors of protein kinases and phosphatases alter root morphology and disorganize cortical microtubules. Plant Physiol 113:493-502
7. Cao H, Glazebrook J, Clarke JD, Volko S, Dong X (1997) The Arabidopsis Npr1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell 88:57-63
8. Chuma M, Sakamoto M, Yasuda J, Fujii G, Nakanishi K, Tsuchiya A, Ohta T, Asaka M, Hirohashi S (2004) Overexpression of cortactin is involved in motility and metastasis of hepatocellular carcinoma. J Hepatol 41:629-636
9. Dai X, Hayashi K, Nozaki H, Cheng Y, Zhao Y (2005) Genetic and chemical analyses of the action mechanisms of sirtinol in Arabidopsis. Proc Natl Acad Sci U S A 102:3129-3134
10. De Rybel B, Audenaert D, Beeckman T, Kepinski S (2009) The past, present, and future of chemical biology in auxin research. ACS Chem Biol 4:987-998
11. De Rybel B, Audenaert D, Vert G, Rozhon W, Mayerhofer J, Peelman F, Coutuer S, Denayer T, Jansen L, Nguyen L, Vanhoutte I, Beemster GT, Vleminckx K, Jonak C, Chory J, Inze D, Russinova E, Beeckman T (2009) Chemical inhibition of a subset of Arabidopsis thaliana Gsk3-like kinases activates brassinosteroid signaling. Chem Biol 16:594-604
12. De Rybel B, Audenaert D, Xuan W, Overvoorde P, Strader LC, Kepinski S, Hoye R, Brisbois R, Parizot B, Vanneste S, Liu X, Gilday A, Graham IA, Nguyen L, Jansen L, Njo MF, Inze D, Bartel B, Beeckman T (2012) A role for the root cap in root branching revealed by the non-auxin probe naxillin. Nat Chem Biol 8:798-805
13. Demidov D, Van Damme D, Geelen D, Blattner FR, Houben A (2005) Identification and dynamics of two classes of aurora-like kinases in Arabidopsis and other plants. Plant Cell 17:836-848
14. Deruere J, Jackson K, Garbers C, Soll D, Delong A (1999) The Rcn1-encoded a subunit of protein phosphatase 2a increases phosphatase activity in vivo. Plant J 20:389-399
15. Drakakaki G, Robert S, Szatmari AM, Brown MQ, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid SL, Russinova E, Friml J, Raikhel NV, Hicks GR (2011) Clusters of bioactive compounds target dynamic endomembrane networks in vivo. Proc Natl Acad Sci U S A 108:17850-17855
16. Finkelstein RR, Gampala SS, Rock CD (2002) Abscisic acid signaling in seeds and seedlings. Plant Cell 14(Suppl):S15-S45
17. Fujii H, Verslues PE, Zhu JK (2007) Identification of two protein kinases required for abscisic acid regulation of seed germination, root growth, and gene expression in Arabidopsis. Plant Cell 19:485-494
18. Hayashi K, Tan X, Zheng N, Hatate T, Kimura Y, Kepinski S, Nozaki H (2008) Small-molecule agonists and antagonists of Fbox protein-substrate interactions in auxin perception and signaling. Proc Natl Acad Sci U S A 105:5632-5637
19. Huggins DJ, Venkitaraman AR, Spring DR (2011) Rational methods for the selection of diverse screening compounds. ACS Chem Biol 6:208-217
20. Iorio F, Isacchi A, di Bernardo D, Brunetti-Pierri N (2010) Identification of small molecules enhancing autophagic function from drug network analysis. Autophagy 6:1204-1205
21. Jonak C, Hirt H (2002) Glycogen synthase kinase 3/shaggy-like kinases in plants: an emerging family with novel functions. Trends Plant Sci 7:457-461
22. Kalin RE, Banziger-Tobler NE, Detmar M, Brandli AW (2009) An in vivo chemical library screen in Xenopus tadpoles reveals novel pathways involved in angiogenesis and lymphangiogenesis. Blood 114:1110-1122
23. Kim TH, Hauser F, Ha T, Xue S, Bohmer M, Nishimura N, Munemasa S, Hubbard K, Peine N, Lee BH, Lee S, Robert N, Parker JE, Schroeder JI (2011) Chemical genetics reveals negative regulation of abscisic acid signaling by a plant immune response pathway. Curr Biol 21:990-997
24. Kobayashi H, Harada H, Nakamura M, Futamura Y, Ito A, Yoshida M, Iemura S, Shin-Ya K, Doi T, Takahashi T, Natsume T, Imoto M, Sakakibara Y (2012) Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications. BMC Chem Biol 12:2
25. Licitra EJ, Liu JO (1996) A three-hybrid system for detecting small ligand-protein receptor interactions. Proc Natl Acad Sci U S A 93:12817-12821
26. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46:3-26
27. Liu D, McIlvain HB, Fennell M, Dunlop J, Wood A, Zaleska MM, Graziani EI, Pong K (2007) Screening of immunophilin ligands by quantitative analysis of neurofilament expression and neurite outgrowth in cultured neurons and cells. J Neurosci Methods 163:310-320
28. Ma Y, Szostkiewicz I, Korte A, Moes D, Yang Y, Christmann A, Grill E (2009) Regulators of Pp2c phosphatase activity function as abscisic acid sensors. Science 324:1064-1068
29. Marshall A, Aalen RB, Audenaert D, Beeckman T, Broadley MR, Butenko MA, Cano-Delgado AI, de Vries S, Dresselhaus T, Felix G, Graham NS, Foulkes J, Granier C, Greb T, Grossniklaus U, Hammond JP, Heidstra R, Hodgman C, Hothorn M, Inze D, Ostergaard L, Russinova E, Simon R, Skirycz A, Stahl Y, Zipfel C, De Smet I (2012) Tackling drought stress: receptor-like kinases present new approaches. Plant Cell 24:2262
30. Melcher K, Xu Y, Ng LM, Zhou XE, Soon FF, Chinnusamy V, Suino-Powell KM, Kovach A, Tham FS, Cutler SR, Li J, Yong EL, Zhu JK, Xu HE (2010) Identification and mechanism of ABA receptor antagonism. Nat Struct Mol Biol 17:1102-1108
31. Mortlock AA, Keen NJ, Jung FH, Heron NM, Foote KM, Wilkinson RW, Green S (2005) Progress in the development of selective inhibitors of Aurora kinases. Curr Top Med Chem 5:807-821
32. Mosquna A, Peterson FC, Park SY, Lozano-Juste J, Volkman BF, Cutler SR (2011) Potent and selective activation of abscisic acid receptors in vivo by mutational stabilization of their agonist-bound conformation. Proc Natl Acad Sci U S A 108:20838-20843
33. Noutoshi Y, Okazaki M, Kida T, Nishina Y, Morishita Y, Ogawa T, Suzuki H, Shibata D, Jikumaru Y, Hanada A, Kamiya Y, Shirasu K (2012) Novel plant immune-priming compounds identified via high-throughput chemical screening target salicylic acid glucosyltransferases in Arabidopsis. Plant Cell 24:3795-3804
34. Pandey UB, Nichols CD (2011) Human disease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery. Pharmacol Rev 63:411-436
35. Park SY, Fung P, Nishimura N, Jensen DR, Fujii H, Zhao Y, Lumba S, Santiago J, Rodrigues A, Chow TF, Alfred SE, Bonetta D, Finkelstein R, Provart NJ, Desveaux D, Rodriguez PL, McCourt P, Zhu JK, Schroeder JI, Volkman BF, Cutler SR (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324:1068-1071
36. Robert S, Chary SN, Drakakaki G, Li S, Yang Z, Raikhel NV, Hicks GR (2008) Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor Bri1 and the auxin transporters Pin2 and Aux1. Proc Natl Acad Sci U S A 105:8464-8469
37. Robert S, Raikhel NV, Hicks GR (2009) Powerful partners: Arabidopsis and chemical genomics. Arabidopsis Book 7:e0109
38. Savaldi-Goldstein S, Baiga TJ, Pojer F, Dabi T, Butterfield C, Parry G, Santner A, Dharmasiri N, Tao Y, Estelle M, Noel JP, Chory J (2008) New auxin analogs with growth-promoting effects in intact plants reveal a chemical strategy to improve hormone delivery. Proc Natl Acad Sci U S A 105:15190-15195
39. Sun Y, Dong Z, Khodabakhsh H, Chatterjee S, Guo S (2012) Zebrafish chemical screening reveals the impairment of dopaminergic neuronal survival by cardiac glycosides. PLoS One 7:e35645
40. Tice CM (2001) Selecting the right compounds for screening: does Lipinski’s Rule of 5 for pharmaceuticals apply to agrochemicals? Pest Manag Sci 57:3-16
41. Trask OJ (2004) Nuclear factor kappa B (Nf-Kappab) translocation assay development and validation for high content screening. In: Sittampalam GS, Gal-Edd N, Arkin M, Auld D, Austin C, Bejcek B, Glicksman M, Inglese J, Lemmon V, Li Z, McGee J, McManus O, Minor L, Napper A, Riss T, Trask OJ, Weidner J (eds) Assay guidance manual. Eli Lilly & Company and the National Center for Advancing Translational Sciences, Bethesda, MD
42. Tsuchiya Y, Vidaurre D, Toh S, Hanada A, Nambara E, Kamiya Y, Yamaguchi S, McCourt P (2010) A small-molecule screen identifies new functions for the plant hormone strigolactone. Nat Chem Biol 6:741-749
43. Van Damme D, De Rybel B, Gudesblat G, Demidov D, Grunewald W, De Smet I, Houben A, Beeckman T, Russinova E (2011) Arabidopsis alpha Aurora kinases function in formative cell division plane orientation. Plant Cell 23:4013-4024
44. Vert JP, Jacob L (2008) Machine learning for in silico virtual screening and chemical genomics: new strategies. Comb Chem High Throughput Screen 11:677-685
45. Yoshida R, Hobo T, Ichimura K, Mizoguchi T, Takahashi F, Aronso J, Ecker JR, Shinozaki K (2002) Aba-activated Snrk2 protein kinase is required for dehydration stress signaling in Arabidopsis. Plant Cell Physiol 43:1473-1483
46. Zhang JH, Chung TD, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4:67-73
47. Zhao Y, Chow TF, Puckrin RS, Alfred SE, Korir AK, Larive CK, Cutler SR (2007) Chemical genetic interrogation of natural variation uncovers a molecule that is glycoactivated. Nat Chem Biol 3:716-721
48. Zhao Y, Dai X, Blackwell HE, Schreiber SL, Chory J (2003) SIR1, an upstream component in auxin signaling identified by chemical genetics. Science 301:1107-1110
49. Zolman BK, Nyberg M, Bartel B (2007) Ibr3, a novel peroxisomal Acyl-Coa dehydrogenase-like protein required for indole-3-butyric acid response. Plant Mol Biol 64:59-72