Force field design and molecular dynamics simulations of factor-inhibiting HIF-1 and its complex with known inhibitors: Implications for rational inhibitor design

Based on molecular dynamics simulations in aqueous solution, we investigate the dynamic properties of factor-inhibiting HIF-1 (FIH1) and its complexes with the substrate 2-oxoglutarate (2OG) and the two known inhibitors, N-oxalylglycine (NOG) and N-oxalyl-d-phenylalanine (NODP). The results obtained with the newly developed force field parameters for the coordination environment of the active-site ferrous ion show that FIH1 undergoes a significant conformational stabilization with a decrease in motional amplitude upon binding of the substrate or the inhibitors. Two loop structures around the active-site reveal a high flexibility in the resting form of FIH1 with the high B-factor values. These high-amplitude motions of the flexible loops are found to be weakened significantly in the presence of the substrate or a weak inhibitor (NOG), and damped out upon binding of a potent and selective inhibitor (NODP) in the active site. A characteristic feature that discriminates the coordination structures of the active-site ferrous ion in complex with 2OG and NOG in solution from those in the X-ray crystal structures lies in the presence of a structural water molecule from bulk solvent at the sixth coordination position, which leads to the formation of a stable octahedral coordination geometry. However, the approach of such a structural water molecule to the active-site ferrous ion is prohibited in the FIH1–NODP complex, which should be attributed to the formation of hydrophobic contacts between the phenyl ring of the inhibitor and the side chains of Tyr102, Leu186, and Trp296 at the entrance of the active site. This indicates that the d-enantiomeric side-chain phenyl group of NODP should play an essential role in potent and selective inhibition of FIH1.

Figure optionsDownload high-quality image (86 K)Download as PowerPoint slideResearch highlights▶ Force field parameters for the active-site Fe(II) cluster are developed. ▶ FIH1 undergoes a decrease in motional amplitude upon binding of the ligands. ▶ A potent inhibitor immobilizes the two flexible loop structures around the active site. ▶ A water molecule from bulk solvent occupies the sixth coordination position of Fe(II).