Evaluation of Larger Side-Group Functionalities and the Side/End-Group Interplay in Ritonavir-Like Inhibitors of CYP3A4

A new series of 13 ritonavir-like inhibitors of human drug-metabolizing CYP3A4 was rationally designed to study the R side-group and R end-group interplay when the R side-group is represented by phenyl. Spectral, functional, and structural characterization showed no improvement in the binding affinity and inhibitory potency of R/R-phenyl inhibitors upon elongation and/or fluorination of R-Boc (tert-butyloxycarbonyl) or its replacement with benzenesulfonyl. When R is pyridine, the impact of R-phenyl-to-indole/naphthalene substitution was multidirectional and highly dependent on side-group stereo configuration. Overall, the R-naphthalene/R-pyridine containing 2f (R/S) was the series lead compound and one of the strongest binders/inhibitors designed thus far (K = 0.009 μM; IC = 0.10 μM). Introduction of a larger biphenyl or fluorene as R did not lead to any improvements. Contrarily, fluorene-containing 13 was the series weakest binder and inhibitor (K = 0.734 μM; IC = 1.32 μM), implying that the fluorene moiety is too large to allow unrestricted access to the active site. The R-biphenyl, however, can switch positions with R-Boc to enable heme ligation. Thus, for small and chemically simple end-groups such as Boc and pyridine, the R/R interplay could lead to conformational rearrangement that would be difficult to foresee without structural information.