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Letters in Drug Design & Discovery


ISSN (Print): 1570-1808
ISSN (Online): 1875-628X

Research Article

Design and Synthesis of the Diazirine-based Clickable Photo-affinity Probe Targeting Sphingomyelin Synthase 2

Author(s): Penghui Wang, Zhining Li, Lulu Jiang, Lu Zhou* and Deyong Ye*

Volume 16, Issue 6, 2019

Page: [678 - 684] Pages: 7

DOI: 10.2174/1570180816666181106154601


Background: SMS family plays a very important role in sphingolipids metabolism and is involved in the membrane mobility and signaling transduction.

Methods: SMS2 subtype was related to a variety of diseases and could be regarded as a promising potential drug target. However, the uncertainty of the binding sites and the molecular mechanism of action limited the development of SMS2 inhibitors. Herein, we discovered a photo-affinity probe PAL-1 targeting SMS2.

Results: The enzyme inhibitory activity and the photo-affinity labeling experiments showed that PAL-1 could be mono-labeled on SMS2.

Conclusion: In summary, starting from the N-arylbenzamides core structure and the minimalist terminal alkyne-containing diazirine photo-crosslinker, we designed and synthesized a photoaffinity probe PAL-1 targeting SMS2. The enzymatic inhibitory activity study showed that PAL-1 exhibited superior selectivities for SMS2 with an IC50 of 0.37 µM over SMS1.

Keywords: Sphingomyelin synthase 2, sphingomyelin, photo-affinity labeling, diazirine, phosphatidylcholine, phosphoethanolamine.

Graphical Abstract
Holthuis, J.; Ternes, P.; van den Dikkenberg, J.; Huitema, K. The sphingomyelin synthase family: Identification and biological implications. FASEB J., 2005, 19(5), A1371-A1371.
Tafesse, F.G.; Ternes, P.; Holthuis, J.C.M. The multigenic sphingomyelin synthase family. J. Biol. Chem., 2006, 281(40), 29421-29425.
Chen, Y.; Cao, Y. The sphingomyelin synthase family: proteins, diseases, and inhibitors. Biol. Chem., 2017, 398(12), 1319-1325.
Yano, M.; Watanabe, K.; Yamamoto, T.; Ikeda, K.; Senokuchi, T.; Lu, M.H.; Kadomatsu, T.; Tsukano, H.; Ikawa, M.; Okabe, M.; Yamaoka, S.; Okazaki, T.; Umehara, H.; Gotoh, T.; Song, W.J.; Node, K.; Taguchi, R.; Yamagata, K.; Oike, Y. Mitochondrial dysfunction and increased reactive oxygen species impair insulin secretion in sphingomyelin synthase 1-null mice. J. Biol. Chem., 2011, 286(5), 3992-4002.
Lu, M.H.; Takemoto, M.; Watanabe, K.; Luo, H.; Nishimura, M.; Yano, M.; Tomimoto, H.; Okazaki, T.; Oike, Y.; Song, W.J. Deficiency of sphingomyelin synthase-1 but not sphingomyelin synthase-2 causes hearing impairments in mice. J. Physiol., 2012, 590(16), 4029-4044.
Wittmann, A.; Grimm, M.O.W.; Scherthan, H.; Horsch, M.; Beckers, J.; Fuchs, H.; Gailus-Durner, V.; de Angelis, M.H.; Ford, S.J.; Burton, N.C.; Razansky, D.; Trumbach, D.; Aichler, M.; Walch, A.K.; Calzada-Wack, J.; Neff, F.; Wurst, W.; Hartmann, T.; Floss, T. Sphingomyelin synthase 1 is essential for male fertility in mice. PLoS One, 2016, 11(10), e0164298.
Zhao, Y.R.; Dong, J.B.; Li, Y.; Wu, M.P. Sphingomyelin synthase 2 over-expression induces expression of aortic inflammatory biomarkers and decreases circulating EPCs in ApoE KO mice. Life Sci., 2012, 90(21-22), 867-873.
Liu, J.; Zhang, H.Q.; Li, Z.Q.; Hailemariam, T.K.; Chakraborty, M.; Jiang, K.L.; Qiu, D.; Bui, H.H.; Peake, D.A.; Kuo, M.S.; Wadgaonkar, R.; Cao, G.Q.; Jiang, X.C. Sphingomyelin synthase 2 is one of the determinants for plasma and liver sphingomyelin levels in mice. Arterioscl. Throm. Vas., 2009, 29(6), 850-U189.
Wang, X.G.; Dong, J.B.; Zhao, Y.R.; Li, Y.; Wu, M.P. Adenovirus-mediated sphingomyelin synthase 2 increases atherosclerotic lesions in ApoE KO mice. Lipids Health Dis., 2011, 10, 7.
Mitsutake, S.; Zama, K.; Yokota, H.; Yoshida, T.; Tanaka, M.; Mitsui, M.; Ikawa, M.; Okabe, M.; Tanaka, Y.; Yamashita, T.; Takemoto, H.; Okazaki, T.; Watanabe, K.; Igarashi, Y. Dynamic modification of sphingomyelin in lipid microdomains controls development of obesity, fatty liver, and type 2 diabetes. J. Biol. Chem., 2011, 286(32), 28544-28555.
Mitsutake, S.; Yokota, H.; Zama, K.; Yoshida, T.; Yamashita, T.; Okazaki, T.; Watanabe, K.; Igarashi, Y. Sphingomyelin synthase 2 is responsible for obesity and lipid droplet formation in liver and is a novel regulator of membrane microdomain. Chem. Phys. Lipids, 2011, 164, S16-S16.
Gowda, S.; Yeang, C.; Wadgaonkar, S.; Anjum, F.; Grinkina, N.; Cutaia, M.; Jiang, X.C.; Wadgaonkar, R. Sphingomyelin synthase 2 (SMS2) deficiency attenuates LPS-induced lung injury. Am. J. Physiol. Lung C., 2011, 300(3), L430-L440.
Liu, J.; Huan, C.M.; Chakraborty, M.; Zhang, H.Q.; Lu, D.; Kuo, M.S.; Cao, G.Q.; Jiang, X.C. Macrophage sphingomyelin synthase 2 deficiency decreases atherosclerosis in mice. Circ. Res., 2009, 105(3), 295-U205.
Li, Z.; Zhang, H.; Liu, J.; Liang, C.P.; Li, Y.; Li, Y.; Teitelman, G.; Beyer, T.; Bui, H.H.; Peake, D.A.; Zhang, Y.; Sanders, P.E.; Kuo, M.S.; Park, T.S.; Cao, G.; Jiang, X.C. Reducing plasma membrane sphingomyelin increases insulin sensitivity. Mol. Cell. Biol., 2011, 31(20), 4205-4218.
Zhou, H.; Gong, Y.; Yang, P.; Ma, Y.; Fu, Z.; Zhou, Y.; Fu, J.; Zhu, X.; Yang, T. Sphingomyelin synthase 2 deficiency impairs insulin secretion in pancreatic beta cells. Diabetologia, 2017, 60, S221-S222.
Hayashi, Y.; Nemoto-Sasaki, Y.; Tanikawa, T.; Oka, S.; Tsuchiya, K.; Zama, K.; Mitsutake, S.; Sugiura, T.; Yamashita, A. Sphingomyelin synthase 2, but not sphingomyelin synthase 1, is involved in HIV-1 envelope-mediated membrane fusion. J. Biol. Chem., 2014, 289(44), 30842-30856.
Ohnishi, T.; Hashizume, C.; Taniguchi, M.; Furumoto, H.; Han, J.; Gao, R.F.; Kinami, S.; Kosaka, T.; Okazaki, T. Sphingomyelin synthase 2 deficiency inhibits the induction of murine colitis-associated colon cancer. FASEB J., 2017, 31(9), 3816-3830.
Deng, X.; Lin, F.; Zhang, Y.; Li, Y.; Zhou, L.; Lou, B.; Li, Y.; Dong, J.; Ding, T.; Jiang, X.; Wang, R.; Ye, D. Identification of small molecule sphingomyelin synthase inhibitors. Eur. J. Med. Chem., 2014, 73, 1-7.
Qi, X.Y.; Cao, Y.; Li, Y.L.; Mo, M.G.; Zhou, L.; Ye, D.Y. Discovery of the selective sphingomyelin synthase 2 inhibitors with the novel structure of oxazolopyridine. Bioorg. Med. Chem. Lett., 2017, 27(15), 3511-3515.
Adachi, R.; Ogawa, K.; Matsumoto, S.; Satou, T.; Tanaka, Y.; Sakamoto, J.; Nakahata, T.; Okamoto, R.; Kamaura, M.; Kawamoto, T. Discovery and characterization of selective human sphingomyelin synthase 2 inhibitors. Eur. J. Med. Chem., 2017, 136, 283-293.
Huitema, K.; van den Dikkenberg, J.; Brouwers, J.F.H.M.; Holthuis, J.C.M. Identification of a family of animal sphingomyelin synthases. EMBO J., 2004, 23(1), 33-44.
Zhang, Y.; Lin, F.; Deng, X.D.; Wang, R.X.; Ye, D.Y. Molecular modeling of the three-dimensional structure of human sphingomyelin synthase. Chin. J. Chem., 2011, 29(8), 1567-1575.
Hatanaka, Y.; Sadakane, Y. Photoaffinity labeling in drug discovery and developments: Chemical gateway for entering proteomic frontier. Curr. Top. Med. Chem., 2002, 2(3), 271-288.
Vodovozova, E.L. Photoaffinity labeling and its application in structural biology. Biochem. Moscow., 2007, 72(1), 1-20.
Sumranjit, J.; Chung, S.J. Recent advances in target characterization and identification by photoaffinity probes. Molecules, 2013, 18(9), 10425-10451.
Smith, E.; Collins, I. Photoaffinity labeling in target- and binding-site identification. Future Med. Chem., 2015, 7(2), 159-183.
Lapinsky, D.J.; Johnson, D.S. Recent developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. Future Med. Chem., 2015, 7(16), 2143-2171.
Murale, D.P.; Hong, S.C.; Haque, M.M.; Lee, J.S. Photo-affinity labeling (PAL) in chemical proteomics: A handy tool to investigate protein-protein interactions (PPIs). Proteome Sci., 2017, 15, 14.
Muranaka, H.; Momose, T.; Handa, C.; Ozawa, T. Photoaffinity labeling in drug discovery research In Photoaffinity Labeling for Structural Probing Within Protein; Hatanaka, Y.; Hashimoto, M., Eds.; Springer Japan: Tokyo, 2017, pp. 241-265.
Li, Z.Q.; Hao, P.L.; Li, L.; Tan, C.Y.J.; Cheng, X.M.; Chen, G.Y.J.; Sze, S.K.; Shen, H.M.; Yao, S.Q. Design and synthesis of minimalist terminal alkyne-containing diazirine photo-crosslinkers and their incorporation into kinase inhibitors for cell- and tissue-based proteome profiling. Angew. Chem. Int. Ed., 2013, 52(33), 8551-8556.
Deng, X.D.; Sun, H.; Gao, X.; Gong, H.J.; Lu, W.B.; Chu, Y.; Zhou, L.; Ye, D.Y. Development, validation, and application of a novel method for mammalian sphingomyelin synthase activity measurement. Anal. Lett., 2012, 45(12), 1581-1589.
Yestrepsky, B.D.; Kretz, C.A.; Xu, Y.X.; Holmes, A.; Sun, H.M.; Ginsburg, D.; Larsen, S.D. Development of tag-free photoprobes for studies aimed at identifying the target of novel Group A Streptococcus antivirulence agents. Bioorg. Med. Chem. Lett., 2014, 24(6), 1538-1544.
Seifert, T.; Malo, M.; Lengqvist, J.; Sihlbom, C.; Jarho, E.M.; Luthman, K. Identification of the binding site of chroman-4-one-based sirtuin 2-selective inhibitors using photoaffinity labeling in combination with tandem mass spectrometry. J. Med. Chem., 2016, 59(23), 10794-10799.

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