Quantitative analysis of the effect of tubulin isotype expression on sensitivity of cancer cell lines to a set of novel colchicine derivatives

Abstract

Background: A maximum entropy approach is proposed to predict the cytotoxic effects of a panel of colchicine derivatives in several human cancer cell lines. Data was obtained from cytotoxicity assays performed with 21 drug molecules from the same family of colchicine compounds and correlate these results with independent tubulin isoform expression measurements for several cancer cell lines. The maximum entropy method is then used in conjunction with computed relative binding energy values for each of the drug molecules against tubulin isotypes to which these compounds bind with different affinities.

Results: We have found by using our analysis that alphabetaI and alphabetaIII tubulin isoforms are the most important isoforms in establishing predictive response of cancer cell sensitivity to colchicine derivatives. However, since alphabetaI tubulin is widely distributed in the human body, targeting it would lead to severe adverse side effects. Consequently, we have identified tubulin isotype alphabetaIII as the most important molecular target for inhibition of microtubule polymerization and hence cancer cell cytotoxicity. Tubulin isotypes alphabetaI and alphabetaII are concluded to be secondary targets.

Conclusions: The benefit of being able to correlate expression levels of specific tubulin isotypes and the resultant cell death effect is that it will enable us to better understand the origin of drug resistance and hence design optimal structures for the elimination of cancer cells. The conclusion of the study described herein identifies tubulin isotype alphabetaIII as a target for optimized chemotherapy drug design.

Figure 1

The structures of the first class of colchicines. The structures of the first class of colchicine analogs and the corresponding X-side groups.

Figure 2

The structures of the second class of colchicines. The structures of the second class of colchicine analogs and the corresponding Y-side groups.

Figure 3

Thermodynamic cycle approach. The schematic plot of thermodynamic circle approach used for calculating relative binding free energy.

Figure 4

The ME expression levels with the consideration of a uniform prior The ME expression levels of four tubulin isotypes in five cell lines exposed to D20 with the consideration of a uniform prior. The hollow square denotes the ME expression level calculated based on mean relative binding free energy ΔΔG_{bind_i}. The black and gray bar are the ME expression level calculated based on mean ΔΔG_{bind_i} ± its standard deviation (SD). The histogram with sparse oblique strips denotes experimental expression level data.

Figure 5

The ME expression levels with the consideration of prior estimated from colchicine data. ME expression levels of four tubulin isotypes in five cell lines exposed to D20 with the consideration of prior estimated from experimental data for colchicine. The hollow square denotes the ME expression level calculated based on mean relative binding free energy ΔΔG_{bind_i}. The black and gray bar are the ME expression level calculated based on mean ΔΔG_{bind_i} ± its standard deviation (SD). The histogram with sparse oblique strips denotes experimental expression level data.

Figure 6

The ME expression levels with the consideration of prior estimated from colchicine data. The ME expression levels of four tubulin isotypes in six cell lines exposed to twenty colchicine derivatives. Color labels the cell lines. Note that D14 is removed since there is no sufficient data for the calculations.

Figure 7

Plot of colchicine derivatives vs. cell lines. The distribution of tubulin isotypes with the highest expression levels in six cell lines, where they are exposed to 20 colchicine derivatives. The color map level 1 to 5 indicates the types of tubulin isotypes. Label "U" denotes that there are multiple isotypes that have the same highest expression level. Label "0" denotes no ME prediction can be made. All the colchicine derivatives are sorted in the order of potency (logIC₅₀ value).

Figure 8

The ME expression levels in A549 with Tubulin isotypes IVa and IVb are distinguishable. The ME predictions for the expression levels of the five tubulin isotypes in the cell line A549 exposed to twenty colchicine derivatives. Tubulin isotypes IVa and IVb are assumed to be distinguishable. Note that N/A indicates no solution can be found.

Figure 9

The ME expression levels in A549 with all Tubulin isotypes are distinguishable. The ME expression levels of five tubulin isotypes in cell line A549 exposed to twenty colchicine derivatives. All Tubulin isotype are considered to be distinguishable. Note that N/A indicates no solution can be found.