Computational insights into synergistic mechanisms of PD-901 and 5-azacitidine targeting PTPN11 (SHP2) E76K mutation in juvenile myelomonocytic leukemia

Introduction Juvenile Myelomonocytic Leukemia (JMML) is an aggressive pediatric hematological cancer categorized by aberrant activation of the RAS/MAPK pathway. It is commonly caused by gain-of-function mutations, such as E76K in the PTPN11 protein. While 5-azacitidine (5-Aza) and the MEK inhibitor PD0325901 (PD-901) are not known direct inhibitors of SHP2/PTPN11, the reported activity of 5-Aza combined with MEK inhibition in PTPN11-mutated JMML offered a biological rationale for examining their potential structural interactions with SHP2. Methods This study used a computational approach that included molecular docking, molecular dynamics (MD) simulations, and binding free-energy calculations using the MM-PBSA method to exploratively investigate interactions between 5-azacitidine (5-Aza) and the MEK inhibitor PD0325901 (PD-901) with wild-type and E76K-mutant PTPN11 proteins. Results In the molecular docking study, 5-Aza was observed to bind within the active site, whereas PD-901 bound preferentially to the allosteric site. The dual-ligand simulations were used to investigate whether occupancy of these distant regions was associated with changes in PTPN11's structural and dynamic characteristics. MD simulations showed that the structures of all complexes remained stable throughout, and that the combined structure exhibited lower deviations, less residue flexibility, compactness, and more intermolecular hydrogen-bond interactions. Principal component analysis also revealed differences in the dominant conformational motions of the ligand-bound systems. MM-PBSA calculations provided comparative estimates of binding energetics and revealed promising interaction energies for all complexes, particularly in the E76K mutant system. Discussion Overall, these computational findings suggest that the association of 5-Aza and PD-901 with distinct regions of PTPN11 may influence its structural and dynamic properties. These findings should therefore be considered exploratory and do not establish direct SHP2 binding or inhibition by either compound. Further biochemical, biophysical, and cellular studies are needed to validate these predicted interactions and determine their potential biological or therapeutic relevance in JMML.