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Molecules 2009, 14(1), 102-121; doi:10.3390/molecules14010102

The Inhibitory Action of Kohamaic Acid A Derivatives on Mammalian DNA Polymerase β

1
Laboratory of Food & Nutritional Sciences, Department of Nutritional Science, Kobe-Gakuin University, Nishi-ku, Kobe, Hyogo 651-2180, Japan
2
Cooperative Research Center of Life Sciences, Kobe-Gakuin University, Nishi-ku, Kobe, Hyogo 651-2180, Japan
3
Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
4
Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo 162-8601, Japan
5
Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, Hyogo 657-8501, Japan
*
Author to whom correspondence should be addressed.
Received: 18 November 2008 / Revised: 22 December 2008 / Accepted: 29 December 2008 / Published: 29 December 2008
(This article belongs to the Special Issue Nucleic Acids)
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Abstract

We previously isolated a novel natural product, designated kohamaic acid A (KA-A, compound 1), as an inhibitor of the first cleavage of fertilized sea urchin eggs, and found that this compound could selectively inhibit the activities of mammalian DNA polymerases (pols). In this paper, we investigated the structure and bioactivity of KA-A and its chemically synthesized 11 derivatives (i.e., compounds 2–12), including KA-A - fatty acid conjugates. The pol inhibitory activity of compound 11 [(1S*,4aS*,8aS*)-17-(1,4,4a,5,6,7,8,8a-octahydro-2,5,5,8a-tetramethyl-naphthalen-1-yl)heptadecanoic acid] was the strongest among the synthesized compounds, and the range of IC50 values for mammalian pols was 3.22 to 8.76 µM; therefore, the length of the fatty acid side chain group of KA-A is important for pol inhibition. KA-A derivatives could prevent human cancer cell (promyelocytic leukemia cell line, HL-60) growth with the same tendency as the inhibition of mammalian pols. Since pol β is the smallest molecule, we used it to analyze the biochemical relationship with KA-A derivatives. From computer modeling analysis (i.e., docking simulation analysis), these compounds bound selectively to four amino acid residues (Leu11, Lys35, His51 and Thr79) of the N-terminal 8-kDa domain of pol β, and the binding energy between compound 11 and pol β was largest in the synthesized compounds. The relationship between the three-dimensional molecular structures of KA-A-related compounds and these inhibitory activities is discussed. View Full-Text
Keywords: Kohamaic acid A (KA-A); DNA polymerase (DNA-directed DNA polymerase [E.C. 2.7.7.7]; pol); Enzyme inhibitor; Cytotoxicity; Computer simulation Kohamaic acid A (KA-A); DNA polymerase (DNA-directed DNA polymerase [E.C. 2.7.7.7]; pol); Enzyme inhibitor; Cytotoxicity; Computer simulation
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MDPI and ACS Style

Mizushina, Y.; Manita, D.; Takeuchi, T.; Sugawara, F.; Kumamoto-Yonezawa, Y.; Matsui, Y.; Takemura, M.; Sasaki, M.; Yoshida, H.; Takikawa, H. The Inhibitory Action of Kohamaic Acid A Derivatives on Mammalian DNA Polymerase β. Molecules 2009, 14, 102-121.

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