Comparative molecular field analysis of anti-tubulin agents with indole ring binding at the colchicine binding site

I. Hung Lin, Cheng Chang Hsu, Shih Hong Wang, Hsing Pang Hsieh*, Ying Chieh Sun

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


A 3D-QSAR study using comparative molecular field analysis (CoMFA) was carried out on anti-tubulin agents with indole as a nucleus core. The structures of the compounds were obtained using docking calculations, and were then subjected to alignment procedures. CoMFA calculations for the 42 ligands that were examined as the training set gave a q2 value of 0.623 in correlation with experimental IC50 values for the inhibition of MKN-45 gastric cancer cells. Calculation for the test set of 17 ligands resulted in an r2 value of 0.714. The calculated results suggest that the R3 functional group site (see structure in Fig. 1) favored bulky groups while R1, R2, and R4 sites favored the opposite. At the R5 and R6 sites, parts of the region favored bulky groups while other parts favored the opposite. As for the electrostatic aspect, the R3 site was found to favor groups with a negative partial charge. At the R2 site, part of the region favored the group with a negative partial charge while other regions favored groups with a positive partial charge. The R4 and R5 sites favored groups with negative and positive partial charges, respectively, with a less favorable magnitude when compared with the R2 and R3 sites. The R1 and R6 sites did not exhibit significant electrostatic favor. Correlation of the results with IC50 values of ligands were analyzed and discussed.

Original languageEnglish
Pages (from-to)279-291
Number of pages13
JournalJournal of Theoretical and Computational Chemistry
Issue number1
Publication statusPublished - 2010 Feb


  • Anti-cancer
  • CoMFA
  • QSAR

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computational Theory and Mathematics


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