Journal of Natural Products
ARTICLE
Docking of r-Glucosidase Inhibitor. Blind docking was car-
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using the default parameters, except for the number of GA runs (100)
and the Lamarkian genetic algorithm with local search and 25 million
energy evaluations (Long. Evals.) per run, on a parallel supercomputer of
distributed memory; it contains 1368 processors AMD Opteron, around
unam.mx/). The target in each docking run was obtained from homol-
ogy modeling of R-glucosidase. The starting conformation of the ligand
was an energy-minimized form with geometric optimization using the
program HyperChem 8 release. Acarbose and 3-(Z)-butylidenephtha-
lide (3) molecules were first prepared by AutoDockTools 1.5.4 (http://
mgltools.scripps.edu/), adding polar hydrogen atoms and Kollman
charges to R-glucosidase and computing Gasteiger charges for acarbose
and 3-(Z)-butylidenephthalide (3). The protein was held rigid during
the docking process while the ligands were allowed to be flexible. The
grid box size was 126 Å ꢀ 126 Å ꢀ 126 Å in the x, y, and z dimensions,
with the center of the grid corresponding to the protein.
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’ ASSOCIATED CONTENT
S
Supporting Information. Figure S1 and the Tables
b
S1-S5 are available free of charge via the Internet at http://
pubs.acs.org.
’ AUTHOR INFORMATION
Corresponding Author
*Tel: 525-556225289. Fax: 525-556225329. E-mail: rachel@
servidor.unam.mx.
Notes
§This paper is taken in part from the Ph.D. thesis of F.B.
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’ ACKNOWLEDGMENT
This work was supported by grants from DGAPA-UNAM
(IN218110-3) and CONACyT (99395). We thank G. Duarte,
M. Guzmꢀan, N. Esturau, M. Gutierrez, I. Rivero, and A. Pꢀerez for
their valuable technical assistance. F.B. acknowledges a fellow-
ship from CONACYT; M.G.-A. acknowledges a postdoctoral
fellowship by DGAPA-UNAM. We are indebted to Direcciꢀon
General de Servicios de Cꢀomputo Acadꢀemico (DGSCA), UNAM,
for providing the resources to carry out computational calcula-
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’ DEDICATION
This paper is dedicated to Dr. Koji Nakanishi from Columbia
University for his pioneering work on bioactive natural products.
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