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A small-molecule inhibitor shows that pirin regulates migration of melanoma cells

Abstract

The discovery of small molecules that bind to a specific target and disrupt the function of proteins is an important step in chemical biology, especially for poorly characterized proteins. Human pirin is a nuclear protein of unknown function that is widely expressed in punctate subnuclear structures in human tissues. Here, we report the discovery of a small molecule that binds to pirin. We determined how the small molecule bound to pirin by solving the cocrystal structure. Either knockdown of pirin or treatment with the small molecule inhibited melanoma cell migration. Thus, inhibition of pirin by the small molecule has led to a greater understanding of the function of pirin and represents a new method of studying pirin-mediated signaling pathways.

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Figure 1: Identification of TPh A as a pirin binder.
Figure 2: Crystal structure of the complex formed by pirin and TPh A.
Figure 3: Inhibition of the interaction between pirin and Bcl3 by TPh A in vitro and in cells.
Figure 4: Inhibition of melanoma cell migration by TPh A.
Figure 5: Pirin controls melanoma cell migration through the regulation of SNAI2 expression.
Figure 6: Regulation of SNAI2 promoter activity by pirin.

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Acknowledgements

We thank N. Kanoh, H. Aono, T. Yoshimura, Y. Fukushima, H. Miyatake and Y. Kondoh for suggestions; M. Muroi and H. Kondo for technical assistance with the LC-MS/MS analysis; T. Nakamura and Y. Hongo for mass spectrometry (RIKEN); R. Nakazawa for DNA sequencing (RIKEN); and the Support Unit for Bio-material Analysis, RIKEN BSI Research Resources Center, and K. Fukumoto for DNA microarray analysis. The synchrotron radiation experiments were performed at BL26B2 in SPring-8 with the Mail-in data collection system with the approval of RIKEN (Proposal No. 20090085). This study was supported in part by a Grant-in-Aid from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT).

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I.M., S.S. and H. Osada designed the research; I.M., H. Okumura and S.T. performed the research; and I.M., S.S., H. Okumura and H. Osada wrote the manuscript.

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Correspondence to Hiroyuki Osada.

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Miyazaki, I., Simizu, S., Okumura, H. et al. A small-molecule inhibitor shows that pirin regulates migration of melanoma cells. Nat Chem Biol 6, 667–673 (2010). https://doi.org/10.1038/nchembio.423

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