Theoretical studies on model reaction pathways of prostaglandin H2 isomerization to prostaglandin D2/E2 |
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| Authors: | Naoto Yamaguchi Tatsuya Naiki Takamitsu Kohzuma Toshikazu Takada Fumihiko Sakata Seiji Mori |
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| Affiliation: | (1) Graduate School of Science and Engineering, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Ibaraki, Japan;(2) VALWAY Technology Center, NEC Soft, Ltd, 1-18-7 Shinkiba, Koto-ku, Tokyo 136-8627, Japan;(3) Faculty of Science, Ibaraki University, 2-1-1 Bunkyo, Mito 310-8512, Ibaraki, Japan;(4) Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai 319-1106, Ibaraki, Japan;(5) NEC Corporation, 34 Miyukigaoka, Tsukuba 305-8501, Ibaraki, Japan;(6) Present address: National Security Solutions Division, NEC Corporation, 33-8 Shiba 5-chome Minato-ku, Tokyo 108-8424, Japan;(7) Present address: Research and Development Program for Next-Generation Computational Research, RIKEN, 2-1-1 Marunouchi, Chiyoda-ku, Tokyo 100-0005, Japan; |
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| Abstract: | ![]()
Model reaction mechanisms in the biosynthesis of prostaglandin D2 (PGD2) and prostaglandin E2 (PGE2) from prostaglandin H2 with PGD2/E2 synthase were examined using the ab initio second-order Møller–Plesset perturbation method and density functional theory. The reaction was modeled similar to the isomerization of 2,3-dioxabicyclo[2.2.1]heptane to 3-hydroxycyclopentanone in the presence of MeS?. An explicit solvation of two H2O molecules was also considered, and two probable types of reaction mechanisms were demonstrated. One mechanism starts with proton abstraction from an oxygen-bound carbon at the endoperoxide by a thiolate ion and the other is stepwise and involves attack of a thiolate anion on an oxygen of the endoperoxide group in the first step with protonation of the other oxygen, followed by deprotonation from a carbon-attached oxygen to break an O–S bond to yield PGD2 or PGE2. We also found that the mPW1LYP hybrid method was superior to the B3LYP functional for systems with respect to the state-of-the-art CCSD(T) energetics. |
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