Centers & Labs

RIKEN Center for Sustainable Resource Science

Molecular Ligand Target Research Team

Team Leader: Charles Boone (Ph.D.)
Charles  Boone(Ph.D.)

Small molecular ligands with unique activities must have the specific target molecules that exist in their cells or organisms. Identification of the target molecules is critical for elucidating the mode of action of the molecular ligands and for drug development. However, drug target identification has been difficult in general, because the mode of interactions between the molecular ligands and their targets is not uniform. Our team aims at developing innovative techniques based on global analysis of yeast genetic interactions, which leads to quick and accurate detection of the ligand-target interactions.

Main Research Field

Biology

Related Research Fields

Medicine, dentistry, and pharmacy

Keywords

  • Chemical Genomics
  • Target Identification
  • Yeast

Selected Publications

  1. Piotrowski, J. S., Li, S. C., Deshpande, R., Simpkins, S. W., Nelson, J., Yashiroda, Y., Barber, J. M., Safizadeh, H., Wilson, E., Okada, H., Gebre, A. A., Kubo, K., Torres, N. P., LeBlanc, M. A., Andrusiak, K., Okamoto, R., Yoshimura, M., van Leeuwen, J., Shirahige, K., Baryshnikova, A., Brown, G. W., Hirano, H., Costanzo, M., Andrews, B., Ohya, Y., Osada, H., Yoshida, M., Myers, C. L., and Boone, C.:
    "Functional annotation of chemical libraries across diverse biological processes."
    Nature Chemical Biology, DOI: 10.1038/nchembio.2436, 2017.
  2. Costanzo, M., VanderSluis, B., Koch, EN., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, SD., Pelechano, V., Styles, EB., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, ZY., Kuzmin, E., Nelson, J., Piotrowski, JS., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, CF., Li, SC., Li, Z., Usaj, MM., Okada, H., Pascoe, N., San Luis, BJ., Sharifpoor, S., Shuteriqi, E., Simpkins, SW., Snider, J., Suresh, HG., Tan, Y., Zhu, H,. Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, OG., Stagljar, I., Xia, T., Ohya, Y., Gingras, AC., Raught, B., Boutros, M., Steinmetz, LM., Moore, CL., Rosebrock, AP., Caudy, AA., Myers, CL., Andrews, B., and Boone, C.:
    "A global genetic interaction network maps a wiring diagram of cellular function."
    Science, 353: aaf1420, 2016.
  3. Dickinson, Q., Bottoms, S., Hinchman, L., McIlwain, S., Li, S., Myers, CL., Boone, C., Coon, JJ., Hebert, A., Sato, TK., Landick, R., and Piotrowski JS.:
    "Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain."
    Microb. Cell Fact., 15: 17, 2016.
  4. Serate, J., Xie, D., Pohlmann, E., Donald, C Jr., Shabani, M., Hinchman, L, Higbee, A., Mcgee, M., La Reau, A., Klinger, GE., Li, S., Myers, CL., Boone, C., Bates, DM., Cavalier, D., Eilert, D., Oates, LG., Sanford, G., Sato, TK., Dale, B., Landick, R., Piotrowski, J., Ong, RG., and Zhang, Y.:
    "Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: effects on hydrolysate composition, microbial response and fermentation."
    Biotechnol. Biofuels, 8: 180, 2015.
  5. Piotrowski, JS., Okada, H., Lu, F., Li, SC., Hinchman, L., Ranjan, A., Smith, DL., Higbee, AJ., Ulbrich, A., Coon, JJ., Deshpande, R., Bukhman, YV., McIlwain, S., Ong, IM., Myers, CL., Boone, C., Landick, R., Ralph, J., Kabbage, M., and Ohya Y.:
    "Plant-derived antifungal agent poacic acid targets β-1,3-glucan."
    Proc. Natl. Acad. Sci. USA, 112: E1490-1497, 2015.
  6. Piotrowski, JS., Simpkins, SW., Li, SC., Deshpande, R., McIlwain, SJ., Ong, IM., Myers, CL., Boone, C., and Andersen, RJ.:
    "Chemical genomic profiling via barcode sequencing to predict compound mode of action."
    Methods Mol. Biol., 1263: 299-318, 2015.
  7. Fung, SY., Sofiyev, V., Schneiderman, J., Hirschfeld, AF., Victor, RE., Woods, K., Piotrowski, JS., Deshpande, R., Li, SC., de Voogd, NJ., Myers, CL., Boone, C., Andersen, RJ., and Turvey, SE.:
    "Unbiased screening of marine sponge extracts for anti-inflammatory agents combined with chemical genomics identifies as an inhibitor of protein synthesis."
    ACS Chem. Biol., 9: 247-257, 2014.
  8. Deshpande, R., Asiedu, MK., Klebig, M., Sutor, S., Kuzmin, E., Nelson, J., Piotrowski, J., Shin, SH., Yoshida, M., Costanzo, M., Boone, C., Wigle, DA., and Myers, CL.:
    "A comparative genomic approach for identifying synthetic lethal interactions in human cancer."
    Cancer Res. 73: 6128-6136, 2013.
  9. Andrusiak, K., Piotrowski, JS., and Boone, C.:
    "Chemical-genomic profiling: systematic analysis of the cellular targets of bioactive molecules."
    Bioorg. Med. Chem. 20: 1952-1960, 2012.
  10. Williams, DE., Dalisay, DS., Patrick, BO., Matainaho T., Andrusiak, K., Deshpande, R., Myers, CL., Piotrowski, JS., Boone, C., Yoshida, M., and Andersen, RJ.:
    "Padanamides A and B, highly modified linear tetrapeptides produced in culture by a Streptomyces sp. isolated from marine sediment collected in Papua New Guinea."
    Org. Lett., 13: 3936-3939, 2011.

Lab Members

Principal Investigator

Charles Boone
Team Leader

Core Members

Yoko Yashiroda
Deputy Team Leader
Sheena Claire Leoncio Li
Research Scientist
Yumi Kawamura
Technical Staff I
Mami Yoshimura
Technical Staff I
Hiromi Kimura
Technical Staff II

Contact information

N202 Sustainable Resource Science Building,
2-1 Hirosawa,
Wako, Saitama
351-0198, Japan

Email: charlieboone [at] riken.jp

Related links

Recent research results

October 6, 2017: RIKEN RESEARCH
A smarter way to screen molecular libraries