Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi

Gallinamide A, a metabolite of the
marine cyanobacterium Schizothrix sp.,
selectively inhibits cathepsin L-like
cysteine proteases. We evaluated the potency of gallinamide A and
23 synthetic analogues against intracellular Trypanosoma
cruzi amastigotes and the cysteine protease, cruzain.
We determined the co-crystal structures of cruzain with gallinamide
A and two synthetic analogues at ∼2 Å. SAR data revealed
that the N-terminal end of gallinamide A is loosely bound and weakly
contributes in drug–target interactions. At the C-terminus,
the intramolecular π–π stacking interactions between
the aromatic substituents at P1′ and P1 restrict the bioactive
conformation of the inhibitors, thus minimizing the entropic loss
associated with target binding. Molecular dynamics simulations showed
that in the absence of an aromatic group at P1, the substituent at
P1′ interacts with tryptophan-184. The P1–P1′
interactions had no effect on anti-cruzain activity, whereas anti-T. cruzi potency increased by ∼fivefold, likely
due to an increase in solubility/permeability of the analogues.