Macrocyclic Inhibitors of Penicillopepsin. 3. Design, Synthesis, and Evaluation of an Inhibitor Bridged between P2 and P1‘

Through application of a thorough design and modeling protocol, the macrocyclic peptidyl phosphonate 5 was derived from the bound structure of an acyclic inhibitor of penicillopepsin, 4, by linking the P1‘ and P2 side chains; the acyclic analogues 6 and 7 were also synthesized and evaluated for comparison. As observed for a related set of inhibitors, 1 − 3 [Meyer, J. H.; Bartlett, P. A. J. Am. Chem. Soc. 1998, 120, xxxx], the binding affinity at pH 4.5 was found to be inversely related to the degree of conformational flexibility across the series, 7 ( K i = 1300 nM), 6 ( K i = 42 nM), and 5 ( K i = 0.10 nM), although the differences are much greater. The structure of the macrocyclic ring of 5 in solution was determined by a combined NMR and molecular modeling method and found to correspond closely to the designed structure and to the backbone conformation of the original target, 4 . The binding enhancement conveyed by the macrocyclic constraint corresponds to 0.9−1.4 kcal/mol/deg of rotational freedom lost, indicating what can be gained from this structure-based design strategy.