Fig. 5: Co-crystallization of PDE6D and DW0254 confirms compound binding to hydrophobic pocket and evidences different binding modes between this inhibitor and Deltarasin.

A Binding affinity (Kd) and thermodynamics parameters for ligand binding to PDE6D determined by Isothermal Titration Calorimetry (ITC). B The crystal structure of compound DW0254 in the PDE6D-binding pocket; Q88, R61, and Y149 are shown in sticks to highlight the hydrogen bind interactions. C The crystal structure of Deltarasin in the PDE6D-binding pocket; C56, R61, and Y149 are shown in sticks to highlight the hydrogen bind interactions. D Experimental binding mode of DW-0254 (cyan) in wild type PDE6D. The superposed 3D coordinates of Deltarasin (orange) are also shown. Several binding site residues, including V49, are shown for reference. E Docking results in wild type apo structure of PDE6D and R48delV49del mutant; Root mean square deviation (RMSD) with respect to 3D coordinates of the ligands in the superposed X-ray complex of the wild type protein are reported. F Drug dosage curves for P12-ICHIKAWA cells treated with DW0254 alone, Deltarasin alone, or various combinations of both obtained from a full matrix using the “Fixed Ratio” Method; data show mean ± SD of n = 3 samples for each condition, and combination indexes for each combo calculated using the Chou-Talalay theorem. G Drug dosage curves for P12-ICHIKAWA cells treated with DW0254 alone, Deltarasin alone, or the combination of both at a 1:2 ratio; data show mean ± SD of n = 3 samples for each condition. H Colony counts of healthy human CD34⁺ cells after 14 days culture in MethoCult H4435 enriched medium in presence of DMSO or increasing concentrations of DW0254 or Deltarasin. CFU-GEMM: Colony-forming unit—granulocyte, erythroid, macrophage, megakaryocyte; CFU-GM: Colony-forming unit—granulocyte, macrophage; BFUE: Burst-forming unit—erythroid. Data represent mean ± SD, n = 3 samples for each condition. *p < 0.05; ***p < 0.001.