Structure-Based Design, Synthesis, and Biological Evaluation of Irreversible Human Rhinovirus 3C Protease Inhibitors. 2. Peptide Structure−Activity Studies

The structure-based design, chemical synthesis, and biological evaluation of various peptide-derived human rhinovirus (HRV) 3C protease (3CP) inhibitors are described. These compounds are comprised of an ethyl propenoate Michael acceptor moiety and a tripeptidyl binding determinant. The systematic modification of each amino acid residue present in the binding determinant as well as the N-terminal functionality is described. Such modifications are shown to provide irreversible HRV-14 3CP inhibitors with anti-3CP activities (k<INF>obs</INF>/[I]) ranging from 60 to 280 000 M^-1 s^-1 and antiviral EC<INF>50</INF>'s which approach 0.15 μM. An optimized inhibitor which incorporates several improvements identified by the structure−activity studies is also described. This molecule displays very rapid irreversible inhibition of HRV-14 3CP (k<INF>obs</INF>/[I] = 800 000 M^-1 s^-1) and potent antiviral activity against HRV-14 in cell culture (EC<INF>50</INF> = 0.056 μM). A 1.9 Å crystal structure of an S-alkylthiocarbamate-containing inhibitor complexed with HRV-2 3CP is also detailed.