FULL PAPER * E-mail: hliao2012@163.com; Fax: 0086-028-87603202 Received April 21, 2012; accepted July 1, 2012; published online XXXX, 2012. Chin. J. Chem. 2012, XX, 1—6 © 2012 SIOC, CAS, Shanghai, & WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim 1 DOI: 10.1002/cjoc.201200384 Homology Modeling and Molecular Docking Studies of (S)-Scoulerine 9-O-Methyltransferase from Coptis chinensis Zhu, Qiankun(朱乾坤) Zhou, Jiayu(周嘉裕) Zhang, Gan(张赶) Liao, Hai*(廖海) School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, China (S)-Scoulerine 9-O-methyltransferase (SMT), belonging to the S-adenosyl-L-methionine (SAM)-dependent O-methyltransferase family, is an essential enzyme in the berberine biosynthetic pathways. In order to study the in- teractions of SMT with its substrate and further to understand the catalytic mechanism and substrate specificity, a three dimensional model of SMT from Coptis chinensis was constructed by homology modeling using the crystal structure of caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase (COMT) as a template. The three dimen- sional structure of SMT, which was mainly composed of α-helices and some β-sheets, was similar to that of COMT. In contrast with COMT, the non-conserved residues in the substrate binding pocket of SMT might be responsible for their differences in the substrate specificity. Val119 and Asp254 in SMT were the key residues for orienting substrate for methylation as both residues had H-bonds with (S)-scoulerine. The methylation of (S)-scoulerine in- volved deprotonation of the 9-hydroxyl group by His253 and Asp254 in SMT followed by a nucleophilic attack on the SAM-methyl resulting in the product, (S)-tetrahydrocolumbamine. Keywords (S)-scoulerine 9-O-methyltransferase, homology modeling, molecular docking, Coptis chinensis Introduction Berberine, a benzylisoquinoline alkaloid obtained from Coptis species, is an important pharmaceutical alkaloid with anti-bacterial, anti-inflammatory, hy- potensive, hypoglycemic and anti-tumor activities. [1] Both medical importance of berberine and interests in elucidating its biosynthesis have led to the complete characterization of the pathway. [2,3] ( S)-Scoulerine 9-O- methyltransferase (SMT) [4] , belonging to the S-adenosyl-L-methionine (SAM)-dependent O-methyl- transferase family, [5,6] is an essential enzyme in the ber- berine biosynthetic pathways. [7] SMT possesses a high stereo specificity to catalyze the methylation of 9-hy- droxyl group in (S)-scoulerine to produce S-adenosyl- L-homocysteine (SAH) and (S)-tetrahydrocolumbamine (Figure 1). [8] Furthermore, the expression of an SMT gene with high catalytic activity in a heterologous host is a challenging task that will lead to efficient biotrans- formation. Thus, one goal in SMT research is to under- stand the specificity of that enzyme in stereoselective OH O O HO N H 3 C CH 3 H S O OH HO O O N N N NH 2 N H 2 N H 3 C S O OH HO O O N N N NH 2 N H 2 N O O O HO N H 3 C CH 3 H CH 3 SMT SAH SAM (S)-scoulerine (S)-tetrahydrocolumbamine 2 9 2 9 + - - Figure 1 The methylation of (S)-scoulerine catalyzed by SMT.