Restriction of the Conformational Dynamics of the Cyclic Acyldepsipeptide Antibiotics Improves Their Antibacterial Activity

The cyclic acyldepsipeptide (ADEP)
antibiotics are a new class
of antibacterial agents that kill bacteria via a mechanism that is
distinct from all clinically used drugs. These molecules bind and
dysregulate the activity of the ClpP peptidase. The potential of these
antibiotics as antibacterial drugs has been enhanced by the elimination
of pharmacological liabilities through medicinal chemistry efforts.
Here, we demonstrate that the ADEP conformation observed in the ADEP–ClpP
crystal structure is fortified by transannular hydrogen bonding and
can be further stabilized by judicious replacement of constituent
amino acids within the peptidolactone core structure with more conformationally
constrained counterparts. Evidence supporting constraint of the molecule
into the bioactive conformer was obtained by measurements of deuterium-exchange
kinetics of hydrogens that were proposed to be engaged in transannular
hydrogen bonds. We show that the rigidified ADEP analogs bind and
activate ClpP at lower concentrations in vitro. Remarkably,
these compounds have up to 1200-fold enhanced antibacterial activity
when compared to those with the peptidolactone core structure common
to two ADEP natural products. This study compellingly demonstrates
how rational modulation of conformational dynamics may be used to
improve the bioactivities of natural products.