Why Are We Targeting DapE?

DapE is part of the succinylase biosynthetic pathway, which is critical to the production of lysine and meso-diaminopimelate (mDap) which are essential in protein synthesis and bacterial peptidoglycan cell wall remodeling. The deletion of the dapE gene is lethal to bacteria, so inhibition of the enzymatic activity of DapE provides an avenue toward new antibiotics with a new mechanism of action, which is critical now that society is faced with increasing bacterial resistance. DapE is a particularly appealing antibiotic target since there is no enzyme in mammals similar to DapE. Thus inhibitors of DapE could potentially provide selective toxicity against bacteria with no mechanism-based toxicity in humans.

As a part of the M20 family of dinuclear Zn(II)- dependent metalloproteases, DapE forms dimers as the quarternary structure where each subunit consists of two functional peptide domains. These domains consist of one larger catalytic domain that houses the active site and one dimerization domain that forms the dimer interface. One challenge of inhibiting this class of dimetalloprotease enzymes is the ability of the enzyme to function with different metals in the active site, including manganese in place of zinc.  Taking advantage of potent binding to zinc with thiol moieties in particular may be unsuccessful where bacteria may simply exchange metal ions from the environment, thus we are moving away from an earlier generation of captopril-based inhibitors that we reported previously.

Design and Synthesis of Inhibitors

A High-Throughput Screening (HiTS) was used to identify inhibitors among a library of over 33,000 compounds which identified several promising inhibitors including the two indoline sulfonamides shown. Our present focus is to synthesize analogs of these two lead indolines and test their inhibitory potency against DapE.