Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors

ACS Med Chem Lett. 2016 Sep 13;7(12):1092-1096. doi: 10.1021/acsmedchemlett.6b00299. eCollection 2016 Dec 8.


Aberrant activation of the complement system is associated with diseases, including paroxysmal nocturnal hemoglobinuria and age-related macular degeneration. Complement factor D is the rate-limiting enzyme for activating the alternative pathway in the complement system. Recent development led to a class of potent amide containing pyrrolidine derived factor D inhibitors. Here, we used biochemical enzymatic and biolayer interferometry assays to demonstrate that the amide group improves the inhibitor potency by more than 80-fold. Our crystal structures revealed buried hydrogen bond interactions are important. Molecular orbital analysis from quantum chemistry calculations dissects the chemical groups participating in these interactions. Free energy calculation supports the differential contributions of the amide group to the binding affinities of these inhibitors. Cell-based hemolysis assay confirmed these compounds inhibit factor D mediated complement activation via the alternative pathway. Our study highlights the important interactions contributing to the high potency of factor D inhibitors reported recently.

Keywords: Paroxysmal nocturnal hemoglobinuria; age-related macular degeneration; biolayer interferometry assay; complement factor D inhibitors; complement system; computational docking; crystal structure; enzyme inhibition assay; hemolysis assay; molecular dynamics simulations; quantum chemistry calculations; serine protease; thermodynamic integration method.