Fig 1.
2D Chemical structures of 25 Btk inhibitors in the training set used for hypothesis generation along with their IC50 values.
Fig 2.
Chemical features of the best pharmacophore 'Hypo 1' with its distance constraints.
'Hypo 1' consists of one hydrogen bond acceptor lipid (HBAL: Green), one hydrogen bond donor (HBD: Magenta), three hydrophobic (HYP: Cyan) features.
Table 1.
Statistical data of ten pharmacophore hypotheses generated by HypoGen.
Table 2.
Experimental and estimated activity of training set compounds based on Hypo 1.
Fig 3.
The best pharmacophore model Hypo1 aligned to training set compounds: A) most active compound 1 (IC50 0.09 nmol/L) and B) least activity compound 20 (IC50 40570 nmol/L). The most active compound mapped to all four features in Hypo 1, whereas the least active compound mapped only two features.
Table 3.
Evaluation of estimated and experimental activity (IC50) values of test set compounds using Hypo 1.
Fig 4.
Correlation plot between Hypo1 predicted Btk inhibitory activities and experimental activities of 60 test set compounds and 25 training set compound.
Fig 5.
Comparison between the total cost of Hypo1 with the total costs of the 19 scrambled runs generated during the Fisher randomization run.
Table 4.
Comparison of Gold fitness score, Chemscore and average binding energy of Btk and reference inhibitor/hit1/hit2/hit3 complex.
Fig 6.
Hypo1 mapped onto the hit compounds.
A) Hit 1, (B) Hit 2, (C) Hit 3. The HBAL, HBD and HYP features are displayed in green magenta and cyan, respectively.
Fig 7.
The RMSD and potential energy graph for four complex systems.
(A) The RMSD profile for the backbone atoms of Btk protein. (B) The potential energy of the system. These graphs were calculated during 20 ns MD simulations for each complex. Blue, cyan, pink, and green lines represent Hit1, Hit2, Hit3, and Inhibitor respectively.
Fig 8.
The binding mode of the three hit compounds and reference inhibitor in the active site of Btk.
All compounds in their representative structures were superimposed (left) and enlarged (right). The Btk protein is shown in gray color solid ribbon while the compounds are depicted by sticks. Blue, cyan, pink, and green sticks represent Hit1, Hit2, Hit3, and Inhibitor respectively.
Fig 9.
The binding conformation and hydrogen bonding interactions of the three hit compounds and reference inhibitor in the active site of Btk.
(A) Hit1: blue (B) Hit2: cyan (C) Hit3: pink and (D) Inhibitor: Green. Hydrogen bond interactions between proteins and compounds are shown as black dotted line. Only polar hydrogen atoms are shown for clarity.
Table 5.
The molecular interactions between the compounds and Btk protein.
Fig 10.
The number of intermolecular hydrogen bonds between protein and compound during 20 ns MD simulations.
Blue, cyan, pink, and green colors represent Hit1, Hit2, Hit3, and Inhibitor respectively.
Fig 11.
2D structures of the hit compounds.
Fig 12.
MM/PBSA estimated binding free energy of Btk and hit 1/hit 2/hit 3/ reference inhibitor complex throughout simulation time.
Color coding; Hit 1: Blue, Hit 2: cyan, Hit 3: pink and Inhibitor: green.