B. Kupcewicz et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4102–4106
4105
Figure 5. Williams plot, plot of standardized residuals versus leverages for each
compound in training and test set for WM-115 cancer cell line.
Figure 4. MLR model for cytotoxicity against WM-115 cancer cell line for training
set and test set.
partial charge on carbonyl oxygen (dO2). Electronic descriptor
in Supplementary data (Tables S3 and S4). Moreover, experimen-
tally (with the use of HPLC method) obtained logP values were
added to computational descriptors (Table S4).
(ELUMO) and hydrophobicity/lipophilicity (logP) are important
descriptors in the modelling of different (covalent and non-
covalent) mechanisms of toxicity.20–22 Covalent mechanism of
cytotoxicity requires electrophilic properties of active compounds.
The correlation between cytotoxic activity and structural prop-
erties was obtained using the multiple linear regression method
(MLR). Genetic algorithms (GA) was applied for modeling descrip-
Electrophilicity (x) of a molecule can be derived from energies of
frontier orbitals (HOMO, LUMO) as follows:
x
= (ELUMO + EHOMO)2/
x for tested compounds
Ò
tors subset selection. The calculation were made with the MATLAB
4 (ELUMO ꢀ EHOMO).22 The high values of
software.
correlated with the high cytotoxic activity. On the other hand
the efficient cytotoxic agent needs optimal lipophilicity that
allows it to get the reactive site (DNA, protein). Increase of logP
value of tested compounds leads to a reduction of cytotoxic
activity. The both isomers of 1a are characterized by relatively
low logPexp (2.85 and 2.98) and relatively high electrophilicity
which result in very good potential as cytotoxic agent. Whereas,
the loss of cytotoxic activity of Z-isomers of 1d, 1e and 1f might
be partially explained by concurrent factors, very high lipophilicity
(logPexp >4.4) and low electrophilicity.
A set of 17 compounds was used as a training set for a QSAR
modeling. Then the model was applied to a set of four new com-
pounds. The goodness of fit of each model, for both internal and
external validation was checked by determination coefficient (R2)
and root mean square errors of: calibration (RMSEC), cross-valida-
tion (RMSECV) and prediction (RMSEP). The results of statistical
parameters obtained for GA-MLR modeling of cytotoxic activity
can be found in Table 4.
As it can be seen the proposed models have potential for predic-
tive application (R2 test >0.84) although the fitting power verified
by R2 model not exceed 0.8. It might be related with relatively
small training set (17 compounds). In further study some new
compounds would have been helpful for the better validation of
the models. The predicted values of logIC50 for WM-115 cancer cell
line for the compounds in the training and test sets are plotted
against the measured values in Figure 4.
QSAR models are generally limited to query chemicals structur-
ally similar to the training compounds, therefore the chemical
applicability domain (AD), defined as theoretical space of the data
set of the model, was verified by the Williams plot. From plot in
Figure 5, the applicability domain was established inside an area
within
2 standard deviations and a
leverage threshold h⁄
(h⁄ = 3(p + 1)/n, where p is the number of model parameters and
n the number of compounds in training set).19 The plot indicate
that leverage values for the compounds from training and test sets
are lower than the critical value (the dotted line) and the residuals
are not greater than two standard deviation units. For the future,
predicted cytotoxic activity data must be considered reliable only
for those chemicals that fall within the applicability domain on
which the model was constructed.
The equations of GA-MLR models were obtained as follows:
log IC50ðHL60Þ ¼ 7:33 ꢀ 7:37 log Pexp ꢀ 31:91ELUMO
2
þ 0:80ðlog PexpÞ ꢀ 40:95E2
LUMO
ꢀ 2:39log Pexp ELUMO
log IC50 ðNALM6Þ ¼ ꢀ54:33 þ 15:8 log Pexp þ 4:8ELUMO
ꢀ 184:56dO2 þ 50:27log PexpdO2
In summary, the study of the relationship between the configu-
ration and cytotoxic activity against cancer cell lines of flavanone
derivatives, revealed that either both isomers exhibit very similar
cytotoxic activity or only Z-isomer is cytotoxic whilst E-isomer is
entirely inactive. The most promising compound is 1a, due to the
very high and independent of isomeric form cytotoxic activity
especially against human leukaemia cancer cell lines. Both leukae-
mia cancer cells are more sensitive than normal cells to the toxic
effect of 1a, therefore it is good candidate for anticancer lead com-
pound. However, further experiments are needed to understand
mechanism of cytotoxic action of these compounds.
log IC50 ðWM115Þ ¼ ꢀ29:12 þ 6:53 log Pexp þ 2:91ELUMO
2
ꢀ 89:39dO2 ꢀ 0:20ðlog Pexp
þ 14:54log PexpdO2
Þ
For HL-60 and WM-115 polynomial regression models with
interaction effect of the two variables were performed. All models
include two the same descriptors: energy of LUMO and logPexp
,
additionally equations for NALM-6 and WM-115 cell lines contain