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Kim, Kim, Sohn, Yim, and Im: Cytotoxic Activity and Structure Activity Relationship of Ceramide Analogues in Caki-2 and HL-60 Cells
Original Article

Korean J Physiol Pharmacol 2010;14(6):441-447.

Published online: 18 February 2010

DOI: https://doi.org/10.4196/kjpp.2010.14.6.441

Cytotoxic Activity and Structure Activity Relationship of Ceramide Analogues in Caki-2 and HL-60 Cells

Yong Jin Kim, Eun Ae Kim, Uy Dong Sohn, Chul Bu Yim, Chaeuk Im

College of Pharmacy, Chung-Ang University, Seoul 156-756, Korea

Corresponding to: Chaeuk Im, College of Pharmacy, Chung-Ang University, Heuksuk-dong, Dongjak-gu, Seoul 156-756, Korea. (Tel) 82-2-820-5603, (Fax) 82-2-816-7338, (E-mail) Chaeukim@cau.ac.kr

Received 19 November 2010       Revised 3 December 2010       Accepted 10 December 2010

Copyright © 2010 Korean J Physiol Pharmacol

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

B13, a ceramide analogue, is a ceramidase inhibitor and induces apoptosis to give potent anticancer activity. A series of thiourea B13 analogues was evaluated for their in vitro cytotoxic activities against human renal cancer Caki-2 and leukemic cancer HL-60 in the MTT assay. Some compounds (12, 15, and 16) showed stronger cytotoxicity than B13 and C6-ceramide against both tumor cell lines, and compound (12) gave the most potent activity with IC50 values of 36 and 9 μM, respectively. Molecular modeling of thiourea B13 analogues was carried out by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). We obtained highly reliable and predictive CoMSIA models with cross-validated q2 values of 0.707 and 0.753 and CoMSIA contour maps to show the structural requirements for potent activity. These data suggest that the amide group of B13 could be replaced by thiourea, that the stereochemistry of 1,3-propandiol may not be essential for activity and that long alkyl chains increase cytotoxicity.

Keywords: B13, CoMFA, CoMSIA, Cytotoxicity, Ceramide

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Fig. 1.
Structures of ceramide analogues.
kjpp-14-441f1.tif
Fig. 2.
Plot of the actual versus predicted activities against tumor cell lines. (A) Renal cancer Caki-2 cells. (B) Leukemic cancer HL-60 cells. The IC50 values were converted into pIC50 (–log IC50) values (: training set molecules, ▴: test set molecules).
kjpp-14-441f2.tif
Fig. 3.
3D-contour maps of CoMSIA models. (A) CoMSIA model with steric and hydrogen bond donor fields for renal cancer Caki-2 cells. (B) CoMSIA model with steric and electrostatic fields for leukemic cancer HL-60 cells. Compound 12 is shown inside fields (green: sterically favorable; yellow: sterically unfavorable; cyan: hydrogen bond donor favorable; purple: hydrogen bond donor unfavorable; blue: positive charge favorable; red: negative charge favorable).
kjpp-14-441f3.tif
Table 1.
Structures and in vitro cytotoxic activities of the ceramide analogues
kjpp-14-441f4.tif
Table 2.
Statistical data for CoMFA and CoMSIA models
Fielda q2b Nc SEPd r2ncve SEEf Fg r2predh Contributionsa
S E D A
Renal cancer Caki-2 cells                      
 CoMFA                      
  S 0.430 3 0.268 0.992 0.031 592.153   1      
  E 0.299 3 0.297 0.919 0.101 53.162     1    
  SE 0.556 2 0.228 0.958 0.070 170.692   0.550 0.450    
 CoMSIA                      
  S 0.465 3 0.260 0.978 0.053 204.852   1      
  E 0.479 5 0.277 0.996 0.026 533.148     1    
  D 0.312 4 0.306 0.900 0.116 29.402       1  
  A -0.127 1 0.353 0.510 0.232 16.681         1
  SE 0.522 2 0.237 0.963 0.066 197.916   0.444 0.556    
  SD 0.707 4 0.200 0.999 0.014 2377.228 0.975 0.581   0.419  
  DA 0.269 3 0.303 0.935 0.090 67.381       0.429 0.571
Leukemia HL-60 cells                      
 CoMFA                      
  S 0.555 2 0.297 0.961 0.087 186.554   1      
  E 0.414 4 0.366 0.984 0.061 199.632     1    
  SE 0.602 3 0.291 0.990 0.047 452.730   0.505 0.495    
 CoMSIA                      
  S 0.606 2 0.280 0.941 0.108 120.378   1      
  E 0.579 2 0.289 0.897 0.143 65.338     1    
  D 0.485 1 0.309 0.688 0.241 35.279       1  
  A 0.232 1 0.378 0.619 0.266 25.978          
  SE 0.753 2 0.221 0.982 0.060 411.615 0.965 0.395 0.605    
  SD 0.562 1 0.285 0.787 0.199 59.254   0.430   0.570  
  DA 0.466 1 0.315 0.729 0.224 43.026       0.487 0.513

a Fields used (S, steric; E, electrostatic; D, H-bond donor); A, H-bond acceptor;

b q2, cross-validated correlation coefficient from leave-one-out (LOO);

c N, optimum number of components;

d SEP, standard error of prediction;

e r2ncv, non-cross-validated correlation coefficient;

f SEE, standard error of estimate;

g F, F-test value;

h r2pred, predicted correlation coefficient.

Table 3.
Actual and predicted activities (pIC50) of the training set
Compounds Caki-2 cells HL-60 cells
Actuala Predictedb Residualc Actuala Predictedd Residualc
1 4.02 4.01 0.01 4.06 3.98 0.08
2 4.33 4.35 -0.02 4.13 4.16 –0.03
3 3.53 3.54 -0.01 3.55 3.53 0.02
4 4.00 4.00 0 4.02 3.96 0.06
5 4.11 4.13 -0.02 4.28 4.21 0.07
6 4.41 4.40 0.01 4.52 4.49 0.03
7 4.38 4.38 0 4.49 4.48 0.01
8 3.53 3.54 -0.01 3.56 3.67 -0.11
9 3.96 3.95 0.01 4.40 4.46 -0.06
10 4.33 4.33 0 4.33 4.40 -0.07
11 4.20 4.21 -0.01 4.62 4.59 0.03
12 4.44 4.45 -0.01 5.03 4.99 0.04
13 3.68 3.67 0.01 3.94 3.96 -0.02
14 4.16 4.14 0.02 4.42 4.52 -0.1
15 4.41 4.42 -0.01 4.76 4.80 -0.04
16 4.42 4.41 0.01 4.96 4.93 0.03
17 3.64 3.63 0.01 3.98 3.94 0.04
18 4.37 4.37 0 4.58 4.57 0.01
  Average   0.01     0.05

a Actualcytotoxic activity;

b predicted activity by the CoMSIA model with steric and hydrogen bond donor fields;

c difference between the actual and predicted activity;

d predictedactivity by the CoMSIA model with steric and electrostatic fields. The pIC50 (–log IC50) values were converted from IC50 values.

Table 4.
Actual and predicted activities (pIC50) of the test set
Compounds Caki-2 cells HL-60 cells
Actuala Predictedb Residualc Actuala Predictedd Residualc
T1 4.37 4.17 0.2 4.26 4.14 0.12
T2 4.16 4.10 0.06 4.32 4.18 0.14
T3 4.23 4.25 -0.02 4.30 4.45 -0.15
T4 3.96 3.96 0 4.55 4.53 0.02
  Average   0.07     0.11

a Actualcytotoxic activity;

b predicted activity by the CoMSIA model with steric and hydrogen bond donor fields;

c difference between the actual and predicted activity;

d predictedactivity by the CoMSIA model with steric and electrostatic fields. The pIC50 (–log IC50) values were converted from IC50 values.

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