Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors

A rational structure-based approach was employed to develop novel 3-amidinophenylalanine-derived matriptase inhibitors with improved selectivity against thrombin and factor Xa. Of all 23 new derivatives, several monobasic inhibitors exhibit high matriptase affinities and strong selectivity against thrombin. Some inhibitors also possess selectivity against factor Xa, although less pronounced as found for thrombin. A crystal structure of a selective monobasic matriptase inhibitor in complex with matriptase and three crystal structures of related compounds in trypsin and thrombin have been determined. The structures offer an explanation for the different selectivity profiles of these inhibitors and contribute to a more detailed understanding of the observed structure-activity relationship. Selected compounds were tested in vitro against a matriptase-dependent H9N2 influenza virus strain and demonstrated a concentration-dependent inhibition of virus replication in MDCK(II) cells. [Display omitted] •Synthesis of 23 new matriptase inhibitors of the 3-amidinophenylalanine type.•Matriptase inhibitors possess high selectivity against thrombin.•Crystal structure determination in complex with matriptase, thrombin, and trypsin.•Antiviral potency found against matriptase-dependent H9N2 influenza virus.