Graph for actual and predicted pKi values for training and test set of CoMFA and CoMSIA studies are shown in Fig. 2. To visualize the content of derived 3D QSAR models, CoMFA and CoMSIA contour maps were generated. Molecular fields define the favorable or unfavorable interaction energies of aligned molecules with a probe atom traversing across the lattice plots Tyrosine Kinase Inhibitor Library manufacturer suggesting the modification required to design new molecules. The contour maps CoMFA denote the region in the space were the molecules would favorably or unfavorably interact with the receptor, while CoMSIA contour maps denote

areas within the specified region where the presence of the group with a particular physicochemical property binds to the receptor. The CoMFA and CoMSIA results were graphically interpret by

field contribution maps using the ‘STDEV*COEFF’ field type. Compound 42 the most LY2157299 chemical structure potent inhibitor among the series was embedded with the maps for visualization. All the contours represented the default 80 and 20% level contributions for favored and disfavored respectively. Fig. 3(a, b) shows the steric contour maps derived from the CoMFA and CoMSIA PLS models. The most potent analog, molecule 42, was embedded in the maps to demonstrate its affinity for the steric regions of inhibitors. The areas of yellow indicate regions of steric hindrance to activity, while green areas indicate a steric contribution to potency. Both the maps show a green contour near methyl substituent on the phenyl ring of benzimidazole ring and ortho position of phenyl ring attached to the NH of urea also has a green contour suggesting substitution with a bulky group will increase the potency. Fig. 4(a, b) shows the CoMFA and CoMSIA electrostatic contour maps respectively. The blue and red

contours depict the positions where positively charged groups and negatively charged groups would be beneficial for inhibitory activity. In CoMFA map a red region is seen near methyl substituent on the phenyl ring of benzimidazole Thymidine kinase ring, on NH of benzimidazole, ortho position of phenyl ring attached to the NH of urea and carbonyl group of urea, where electronegative groups will increase the activity. The hydrophobic fields are presented in Fig. 5, yellow and white contours highlight areas where hydrophobic and hydrophilic groups are preferred respectively. White hydrophilic favored contour is observed on the amide group of urea and on ortho position of phenyl ring attached to the NH of urea, suggesting group having hydrogen bond forming ability at these positions will be beneficial. Hydrogen bond donor and acceptor field contour maps are shown in Fig. 6 using the same template 42 cyan and purple contours represent favorable and disfavorable hydrogen bond donor groups and magenta and red contours represent favorable and disfavorable hydrogen bond acceptor groups respectively.