Figure 5
Molecular docking and molecular dynamics simulation reveal that CC-410 specifically inhibits NNMT by stably binding to its catalytic active site. (A) Best solutions of docking computations of CC-410 targeting hNNMT (top) and mNNMT (middle), and the complex between mNNMT and SAH (bottom) according to the X-ray diffraction model (PDB 5YJI). All the structures are based on the coordinates closest to the average of the last 70 ns of 100 ns molecular dynamics (MD) trajectories. Protein backbones are represented by Richardson’s ribbon diagram and the CC-410 molecule by sticks. Carbon atoms are in green, nitrogen in blue, oxygen in red and sulfur in yellow. Gray arrows point to the active-site cavity opening. (B) Statistics of MD computations. For each set of computations, the upper panel shows the Root Mean Square Deviation (RMSD) of protein main chain atoms with respect to the energy-minimized structure throughout trajectory calculations in the presence (red) and absence (black) of CC-410 ligand. The lower panels show radii of gyration (RG) of NNMT in the presence and absence of ligand. In red, RG of NNMT protein moiety in the presence of ligand, in green, RG of NNMT plus ligand, in black, RG of NNMT along the trajectory without ligand. (C) Atomic fluctuations and secondary structure analysis. Upper panels: Backbone fluctuations represented as per-residue root mean square fluctuations (RMSF) of atomic positions with respect to their average. Data corresponding to the apoprotein are in black, those for the bound protein in red. Lower panels: timeline of secondary structured as determined with Kabsh’s algorithm. Extended conformations are in blue, α-helices in dark red, 310 helices in orange, p helices are in red, turns are in beige, and bends in yellow. (D) Details of the structure closest to the MD average of CC-410 bound to mNNMT. Green lines represent hydrogen bonds. (E) Structural alignment of the MD-refined docking results of CC-410, in the B2 (mNNMT) and A1 (hNNMT) orientations, with SAH. Only the ligands are shown. (F) Structural alignments of bifunctional drugs MS2756 and compound 8 (cmpd8) docked to mNNMT with SAH and CC-410 docking solutions. The view has been rotated arbitrarily with respect to panel C to highlight the moiety of the bifunctional ligands that enter the nicotinamide (methyl-acceptor) pocket. * and # stand for R1 and R2 sidechains, respectively.
