International Journal of Molecular Sciences Article Rational Design of CYP3A4 Inhibitors: A One-Atom Linker Elongation in Ritonavir-Like Compounds Leads to a Marked Improvement in the Binding Strength Eric R. Samuels 1 and Irina F. Sevrioukova 2,* 1 Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3900, USA;
[email protected] 2 Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA * Correspondence:
[email protected]; Tel.: +1-949-824-1953 Abstract: Inhibition of the major human drug-metabolizing cytochrome P450 3A4 (CYP3A4) by pharmaceuticals and other xenobiotics could lead to toxicity, drug–drug interactions and other adverse effects, as well as pharmacoenhancement. Despite serious clinical implications, the structural basis and attributes required for the potent inhibition of CYP3A4 remain to be established. We utilized a rational inhibitor design to investigate the structure–activity relationships in the analogues of ritonavir, the most potent CYP3A4 inhibitor in clinical use. This study elucidated the optimal length of the head-group spacer using eleven (series V) analogues with the R1/R2 side-groups as phenyls or R1–phenyl/R2–indole/naphthalene in various stereo configurations. Spectral, functional and structural characterization of the inhibitory complexes showed that a one-atom head-group linker elongation, from pyridyl–ethyl to pyridyl–propyl, was beneficial and markedly improved K , s IC50 and thermostability of CYP3A4. In contrast, a two-atom linker extension led to a multi-fold decrease in the binding and inhibitory strength, possibly due to spatial and/or conformational Citation: Samuels, E.R.; constraints. The lead compound, 3h, was among the best inhibitors designed so far and overall, the Sevrioukova, I.F.