Fig 1.
The representative structure of αβ-tubulin dimer and indanocine.
(A) α/β-tubulin subunits. α subunit is shown in blue color and β subunit is shown in olive green color. Indanocine binding site i.e. ‘colchicine site’ is at the interface of α-tubulin and β-tubulin heterodimer (red dotted circle); while the ‘taxol site’ is present on only β-tubulin over the H7 helix (blue dotted circle). The indanocine binding pocket consists of H7 helix (shown in orange), T7 loop (shown in cyan), H8 helix (shown in magenta) and T5 loop of α-tubulin (shown in cyan). Here, H7 denotes the α-helix number 7, T7 stands for T loop number 7, and B9 implies the β-sheet number 9. The GTP in α-tubulin, GDP in β-tubulin are shown using space-fill models. The white, grey, red, blue and golden yellow colors represent carbon, hydrogen, oxygen, nitrogen and phosphorous atoms, respectively. (B) The structure of indanocine has a dimethoxyaniline group (labeled as X ring) and a dimethylphenol group (labeled as Y ring). The carbon, oxygen, nitrogen, and hydrogen atoms of indanocine are shown in green, red, blue and white color, respectively.
Fig 2.
Multiple sequence alignment of human β-tubulin isotypes.
The isotype βI shows variations of residues Val236-Ile, Cys239-Ser, Ala315-Cys, Val316-Ile and Thr351-Val, βIIa shows a change of Val316-Ile, βIII and βVI shows a change of Cys239-Ser, Ala315-Thr, and Thr351-Val at the indanocine binding pocket. Residue variations in the indanocine binding pocket are shown in red. Symbol ‘ * ‘ denotes positions of amino acid which have a single, fully conserved amino acid residue; the symbol ‘: ‘ denotes conservation between groups of strongly similar properties of amino acid; the symbol ‘.’ denotes the conservation between groups of weakly similar properties of amino acids, and the symbol ‘—‘ denotes gaps inserted to maximize sequence alignment [22].
Fig 3.
Docked conformations of indanocine with αβ-tubulin isotypes.
The color for α-tubulin is blue in all αβ-tubulin heterodimers while color of different β-tubulin isotypes is different in all αβ-tubulin heterodimers. The color code for β-tubulin is yellow for tubulin 1SA0, red for isotype βI, light brown for isotype βIIa, violet for isotype βIII, chocolate for isotype βIVa, orange for isotype βIVb, grey for isotype βV and light_green for isotype βVI. Here, indanocine and GTP is shown in stick model and the color code for indanocine and GTP is same as shown in Fig 1.(A) tubulin 1SA0-indanocine complex (B) αβI tubulin isotype-indanocine complex. (C) αβIIa tubulin isotype-indanocine complex (D) αβIII tubulin isotype-indanocine complex (E) αβIVa tubulin isotype-indanocine complex (F) αβIVb tubulin isotype-indanocine complex (G) αβV tubulin isotype-indanocine complex. (H) αβVI tubulin isotype-indanocine complex. Indanocine prefers the αβ-tubulin interface binding pocket in all human αβ-tubulin isotypes.
Table 1.
Binding energy as well as interactions of indanocine with tubulin 1SA0 and different human αβ tubulin isotypes after molecular docking.
Fig 4.
Root mean square deviations (RMSD) corresponding to tubulin 1SA0 and αβ-tubulin isotypes.
RMSD correspond to tubulin 1SA0 (black color), αβI(red color), αβIIa (green color), αβIII(blue color), αβIVa (yellow color), αβIVb (orange color), αβV(maroon color), and αβVI (violet color) tubulin heterodimer for 25ns molecular dynamics simulations.
Fig 5.
Molecular dynamics simulated structures of αβ tubulin isotypes-indanocine complex.
The position of indanocine before and after the simulation is shown for comparison. The color scheme for αβ-tubulin is same as shown in Fig 3. The color scheme for initial docked conformation of indanocine (before MD simulation) shown in green color while indanocine after MD simulation is shown in magenta color. (A) Tubulin1SA0-indanocine complex (B) αβI tubulin isotype-indanocine complex. (C) αβIIa tubulin isotype-indanocine complex (D) αβIII tubulin isotype-indanocine complex (E) αβIVa tubulin isotype-indanocine complex (F) αβIVb tubulin isotype-indanocine complex (G) αβV tubulin isotype-indanocine complex. (H) αβVI tubulin isotype-indanocine complex.
Table 2.
RMSD and hydrogen bonding interactions of different αβ-tubulin isotypes with indanocine after molecular dynamics simulation.
Table 3.
Binding energy of different αβ-tubulin isotypes with indanocine.