Department of Biomolecular Science

Associate Professor Soichiro Watanabe

Organic chemistry of biomolecules

We believe that organic chemistry can play an important role in biological science, and have been studying methods to detect or control biological molecules.

Caged compounds, biologically inert molecules which can release bioactive compounds upon photolysis, are very useful tools to study on complicated biological pathways. We had been proposed the new concept of "dendritic caged compounds" having a caged moiety as a prodrug and a dendrimer skeleton with peripheral sugar units as a drug carrier.

We are now studying to develop new chemical tools that can detect interaction of biomolecules or can analyze topology of peptides. We are also interested in finding new bioactive molecules. Our current research interests include,
  Synthesis of new chemical tools to detect DNA-protein interaction
  Synthesis of new chemical tools to detect protein-protein interaction
  Synthesis of new chemical tools to analyze topology of peptide helix
  Survey for bioactive organic molecules that can control bacterial function


“Synthesis and Metal Complex Formation of a Bis(terpyridine) Derivative with a Phenylacetylene Framework”, T. Tokizaki, T. Toyoshima, S. Watanabe, Synth. Commun., 45, 127-136 (2015).

“Synthesis of nucleobase-caged peptide nucleic acids having improved photochemical properties”, T. Watanabe, T. Hoshida, J. Sakyo, M. Kishi, S. Tanabe, J. Matsuura, S. Akiyama, M. Nakata, Y. Tanabe, A. Z. Suzuki, S. Watanabe, T. Furuta, Org. Biomol. Chem., 12, 5089-5093 (2014).

“Preparation and affinity-based purification of caged linear DNA for light-controlled gene expression in mammalian cells”, A. Teraoka, K. Murakoshi, K. Fukamauchi, A. Z. Suzuki, S. Watanabe, T. Furuta , Chem. Commun., 50, 664-666 (2014).

“Synthesis of an alkylthio-substituted dibenz[a,j]anthracene with improved solubility via the oxidative photocyclization of 1,3-distyrylbenzene derivatives”, T. Toyoshima, S. Yoshida, S. Watanabe, Tetrahedron, 69, 1904-1911 (2013).

“Preparation and reaction of uracil substituted cyclen and cyclam: formation of tricyclic guanidinium and dihydroimidazolium salts”, S. Watanabe, A. Komori, M. Saito, A.Uchida, Tetrahedron, 66 , 1196-1201 (2010).

“Synthesis of fluorescent alkyl lactoside derivatives”, S. Watanabe, Carbohydr. Res., 2008, 343, 2325-2328.

"Effect of the Photolysis of Dendritic Caged Compound within the Vaterite Crystal on the Crystalline Phase Transformation", Y. Yanagimoto, Y. Takaguchi, S. Tsuboi, S. Watanabe, M. Iwamura, ITE Letters on Batteries, New Technologies & Medicine, 2007, 8, 277-282.

"1, 7-Bis(1, 3-dimethyuracil-6-yl)-1, 4, 7, 10-tetraazadodecane acetonitrile disolvate at 100 K", Uchida, A.; Komori, A.; Watanabe, S. Acta Cryst. 2007, E63, o648-o649.

"Modified DNA Analogues That Sense Light Exposure with Color Changes", J. Gao, S. Watanabe, and E. T. Kool, J. Am. Chem. Soc., 126, 12748-12749 (2004).

"Dendritic Caged Compounds", S. Watanabe, M. Iwamura, Journal of Photochemistry & Photobiology, A: Chemistry , 155, 57-62 (2003).

"Caged Compounds with a Steroid Skeleton: Synthesis, Liposome-formation and Photolysis.", S. Watanabe, R. Hiratsuka, Y. Kasai, K. Munakata, Y. Takahashi, M. Iwamura, Tetrahedron, 58, 1685-1691 (2002).

"Design, Synthesis, Photochemical Properties and Cytotoxic Activities of Water-soluble Caged L-Leucyl-L-Leucine Methyl Esters that Control Apoptosis of Immune Cells.", H. Mizuta, S. Watanabe, Y. Sakurai, K. Nishiyama, T. Furuta, Y. Kobayashi, M. Iwamura, Bioorg. Med. Chem., 10, 675-683 (2002).

"Reductive Ring Opening of o-Nitrobenzylidene Acetals of Monosaccharides: Synthesis and Photolysis of Some Photolabile Sugars", S. Watanabe, T. Sueyoshi, M. Ichihara, C. Uehara, M. Iwamura, Org. Lett., 3, 255-257 (2001).

"New Dendritic Caged Compounds: Synthesis, Mass Spectrometric Characterization and Photochemical Properties of Dendrimers with a-Carboxy-2-nitrobenzyl Caged Compounds at Their Periphery", S. Watanabe, M. Sato, S. Sakamoto, K. Yamaguchi, M. Iwamura, J. Am. Chem. Soc., 122, 12588-12589 (2000).

"Desilylation-triggered Isomerization of a Molecular Capsule from an Open-type to a Collapsed-type Isomer", S. Watanabe, K. Goto, T. Kawashima, R. Okazaki, Tetrahedron Lett., 40, 3569-3572 (1999).

"Caged Compounds of a 2-Deoxyglucose: Facile Synthesis and Their Photoreactivity", S. Watanabe, R. Hirokawa, M. Iwamura, Bioorg. Med. Chem. Lett., 8, 3375-3378 (1998).

"A Liposome-Forming Caged Compound: Synthesis and Photochemical Properties of a Caged L-Leucyl-L-leucine Methyl Ester with a Steroid Skeleton", S. Watanabe, M. Iwamura, J. Org. Chem., 62, 8616-8617 (1997).

"An Endohedral Simple Enol: The First Isolation of a b-Unsubstituted Simple Enol Utilizing a Lantern-shaped Molecular Framework", S. Watanabe, K. Goto, T. Kawashima, R. Okazaki, J. Am. Chem. Soc., 119, 3195-3196 (1997).

"Cycloaddition and Oxidation Reactions of a Stable Thioaldehyde, (2,4,6-Tri-t-butyl)thiobenzaldehyde", S. Watanabe, T. Yamamoto, T. Kawashima, N. Inamoto, and R. Okazaki, Bull. Chem. Soc. Jpn., 69, 719-724 (1996). "Synthesis of New Lantern-shaped Molecules Based on Resorcin[4]arene and m-Terphenyl Units", S. Watanabe, K. Goto, T. Kawashima, and R. Okazaki, Tetrahedron Lett., 36, 7677-7680 (1995).

"Reactions of (2,4,6-Tri-t-butyl)thiobenzaldehyde with Diazo Compounds. Synthesis and Reactions of Sterically Congested Thiiranes", S. Watanabe, T. Kawashima, and R. Okazaki, Bull. Chem. Soc. Jpn., 68, 1437-1448 (1995).

"Reaction of 2,4,6-Tri-t-butylselenobenzaldehyde with Sterically Crowded Diazo Compounds. Formation of Seleniranes", S. Watanabe, T. Kawashima, and R. Okazaki, Chem. Lett., 1994, 1289-1292.

"Synthesis and Unusual Photochemical Reaction of Highly Congested 2,4,6-Tri-t-butylstyrene Episulfides", T. Kawashima, S. Watanabe, and R. Okazaki, Chem. Lett., 1992, 1603-1606.