Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Prediction of Chiral Discrimination by β-Cyclodextrins Using Grid-based Monte Carlo Docking Simulations

  • Choi, Young-Jin (Department of Microbial Engineering, Bio/Molecular Informatics Center, Konkuk University) ;
  • Kim, Dong-Wook (Electronics and Telecommunications Research Institute) ;
  • Park, Hyung-Woo (Korea Institute of Science and Technology Information) ;
  • Hwang, Sun-Tae (Department of Computer Science, Kookmin University) ;
  • Jeong, Karp-Joo (College of Information and Communication, Konkuk University) ;
  • Jung, Seun-Ho (Department of Microbial Engineering, Bio/Molecular Informatics Center, Konkuk University)
  • Published : 2005.05.20
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Abstract

An efficiency of Monte Carlo (MC) docking simulations was examined for the prediction of chiral discrimination by cyclodextrins. Docking simulations were performed with various computational parameters for the chiral discrimination of a series of 17 enantiomers by $\beta$-cyclodextrin ($\beta$-CD) or by 6-amino-6-deoxy-$\beta$-cyclodextrin (am-$\beta$-CD). A total of 30 sets of enantiomeric complexes were tested to find the optimal simulation parameters for accurate predictions. Rigid-body MC docking simulations gave more accurate predictions than flexible docking simulations. The accuracy was also affected by both the simulation temperature and the kind of force field. The prediction rate of chiral preference was improved by as much as 76.7% when rigid-body MC docking simulations were performed at low-temperatures (100 K) with a sugar22 parameter set in the CHARMM force field. Our approach for MC docking simulations suggested that the conformational rigidity of both the host and guest molecule, due to either the low-temperature or rigid-body docking condition, contributed greatly to the prediction of chiral discrimination.

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