De Novo Design, Synthesis, and In Vitro Evaluation of Inhibitors for Prokaryotic tRNA-Guanine Transglycosylase: A Dramatic Sulfur Effect on Binding Affinity

A lipophilic pocket at the tRNA-guanine transglycosylase (TGT) enzyme active site was discovered and a substantial contribution to the substrate binding free energy was observed when this pocket was filled by apolar side chains. A family of new inhibitors of TGT was developed by employing the principles of molecular recognition and structure-based de novo design, and shown to display up to submicromolar binding affinity. Two X-ray structures of TGT–inhibitor complexes confirmed the binding mode predicted in the design stage. An exceptional ”point mutation” effect on binding affinity was observed upon substitution of X=CH2 in 1 with O or S.