RIKEN Center for Sustainable Resource Science Molecular Ligand Target Research Team

Team Director: Charles Boone (Ph.D.)

Japanese Page

Research Summary

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 Fields

Biology

Related Research Fields

Medicine, Dentistry & Pharmacy

Keywords

Chemical Genomics
Target Identification
Yeast

Selected Publications

1. Obara, K., Okada, H., Tan, G., Ohnuki, S., Suzuki, G., Ohtake, H., Kubo, K., Ghanegolmohammadi, F., Ishizaka, S., Yashiroda, Y., Okita, A., Mishiro-Sato, E., Suzuki, K., Tamura, Y., Ashine, R., Ikeda, Y., Kamura, T., van Leeuwen, J., Andrews, B., Bi, E., Noda, N. N., Boone, C., Ohya, Y.:
"Role of Pbr1, a putative oxidoreductase, in the ER quality control and folding of yeast Fks1 glucan synthase"
Proc. Natl. Acad. Sci. USA, 123, e2612792123 (2026)
2. Dutta, A., Garin, M., Loegler, V., Brach, G., Friedrich, A., Yoshimura, M., Hirano, H., Osada, H., Boone, C., Yashiroda, Y., Hou, J., Schacherer, J.:
"Population-scale chemical response revealed by a barcoded yeast collection"
Nat. Commun., 17, 6928 (2026)
3. Billmann, M., Costanzo, M., Zhang, X., Hassan, AZ., Rahman, M., Brown, KR., Chan, KSY., Tong, AHY., Pons, C., Ward, HN., Ross, C., van Leeuwen, J., Aregger, M., Lawson, KA., Mair, B., Roth, AF., Sen, NE., Forster, DT., Tan, G., Mero, P., Masud, SN., Lee, Y., Aguilera-Uribe, M., Ušaj, M., Almeida, SMT., Aulakh, K., Bhojoo, U., Birkadze, S., Budijono, N., Cai, X., Caumanns, JJ., Chalmers, JJ., Chandrashekhar, M., Chang, D., Climie, R., Dasgupta, K., Drazic, A., Echenique, JIR., Gacesa, R., Farias, AG., Habsid, A., Horecka, I., Kantautas, K., Ji, F., Kim, DK., Lee, SY., Liang, W., Lim, HJ., Lin, K., Lu, X., Maier, M., Nami, B., Nixon, A., Mikolajewicz, N., Mokhtaridoost, M., Nedyalkova, L., Rohde, T., Rodrigues, MS., Soste, M., Schultz, E., Wang, W., Seetharaman, A., Shuteriqi, E., Sizova, O., Taylor, DT., Tereshchenko, M., Tieu, D., Turowec, J., Ubhi, T., Varland, S., Wang, KE., Wang, ZY., Wei, J., Xiao, YX., Maass, PG., Reversade, B., Brown, GW., Cravatt, BF., Dixon, SJ., Wyatt, HDM., Röst, HL., Roth, FP., Xia, T., Bader, GD., Loewith, R., Davis, NG., Andrews, B., Myers, CL., Moffat, J., Boone, C.:
"Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles"
Cell, 189(12), 3736-3759.e58 (2026)
4. Li, ST., Kamada, K., Honda, A., Seino, J., Matsuda, T., Suzuki, T., Dohmae, N., Shichino, Y., Iwasaki, S., Noda, Y., Costanzo, M., Boone, C., Suzuki, T.:
"LLP1 is a pyrophosphatase involved in homeostasis/quality control of dolichol-linked oligosaccharide"
J. Cell Biol., 224(11), e202501239 (2025)
5. Diehl, C., Pinzan, CF., de Castro, PA., Delbaje, E., García Carnero, LC., Sánchez-León, E., Bhalla, K., Kronstad, JW., Kim, D-g., Doering, TL., Alkhazraji, S., Mishra, NN., Ibrahim, AS., Yoshimura, M., Vega Isuhuaylas, LA., Pham, LTK., Yashiroda, Y., Boone, C., Dos Reis, TF., Goldman, GH.:
"Brilacidin, a novel antifungal agent against Cryptococcus neoformans"
mBio, 15, e0103124 (2024)
6. Iyer, KR., Li, SC., Revie, NM., Lou, JW., Duncan, D., Fallah, S., Sanchez, H., Skulska, I., Ušaj, MM., Safizadeh, H., Larsen, B., Wong, C., Aman, A., Kiyota, T., Yoshimura, M., Kimura, H., Hirano, H., Yoshida, M., Osada, H., Gingras, AC., Andes, DR., Shapiro, RS., Robbins, N., Mazhab-Jafari, MT., Whitesell, L., Yashiroda, Y., Boone, C., Cowen, LE.:
"Identification of triazenyl indoles as inhibitors of fungal fatty acid biosynthesis with broad- spectrum activity"
Cell Chem. Biol., 30, 795-810 (2023)
7. Forster, DT., Li, SC., Yashiroda, Y., Yoshimura, M., Li, Z., Isuhuaylas, LAV., Itto-Nakama, K., Yamanaka, D., Ohya, Y., Osada, H., Wang, B., Bader, GD., Boone, C.:
"BIONIC: biological network integration using convolutions"
Nat. Methods, 19, 1250-1261 (2022)
8. Persaud, R., Li, SC., Chao, JD., Forestieri, R., Donohue, E., Balgi, AD., Zheng, X., Chao, JT., Yashiroda, Y., Yoshimura, M., Loewen, CJR., Gingras, AC., Boone, C., Av-Gay, Y., Roberge, M., Andersen, RJ.:
"Clionamines stimulate autophagy, inhibit Mycobacterium tuberculosis survival in macrophages, and target Pik1"
Cell Chem. Biol., 29, 870-882 (2021)
9. Tomita, K., Yashiroda, Y., Matsuo, Y., Piotrowski, JS., Li, SC., Okamoto, R., Yoshimura, M., Kimura, H., Kawamura, Y., Kawamukai, M., Boone, C., Yoshida, M., Nojiri, H., Okada, K.:
"Genome-wide screening of genes associated with momilactone B sensitivity in the fission yeast Schizosaccharomyces pombe"
G3 (Bethesda), 11, jkab156 (2021)
10. Piotrowski, JS., Li, SC., Deshpande, R., Simpkins, SW., Nelson, J., Yashiroda, Y., Barber, JM., Safizadeh, H., Wilson, E., Okada, H., Gebre, AA., Kubo, K., Torres, NP., LeBlanc, MA., Andrusiak, K., Okamoto, R., Yoshimura, M., van Leeuwen, J., Shirahige, K., Baryshnikova, A., Brown, GW., Hirano, H., Costanzo, M., Andrews, B., Ohya, Y., Osada, H., Yoshida, M., Myers, CL., and Boone, C.:
"Functional annotation of chemical libraries across diverse biological processes"
Nat. Chem. Biol., 13, 982-993 (2017)