Mechanism-Based Macrocyclic Inhibitors of Serine Proteases

Protease inhibitor drug discovery is challenged by the
lack of
cellular and oral permeability, selectivity, metabolic stability,
and rapid clearance of peptides. Here, we describe the rational design,
synthesis, and evaluation of peptidomimetic side-chain-cyclized macrocycles
which we converted into covalent serine protease inhibitors with the
addition of an electrophilic ketone warhead. We have identified potent
and selective inhibitors of TMPRSS2, matriptase, hepsin, and HGFA
and demonstrated their improved protease selectivity, metabolic stability,
and pharmacokinetic (PK) properties. We obtained an X-ray crystal
structure of phenyl ether-cyclized tripeptide VD4162 (8b) bound to matriptase, revealing an unexpected binding conformation.
Cyclic biphenyl ether VD5123 (11) displayed the best
PK properties in mice with a half-life of 4.5 h and compound exposure
beyond 24 h. These new cyclic tripeptide scaffolds can be used as
easily modifiable templates providing a new strategy to overcoming
the obstacles presented by linear acyclic peptides in protease inhibitor
drug discovery.