Intramolecular interactions enhance the potency of gallinamide A analogs againstTrypanosoma cruzi

Abstract

Gallinamide A, a metabolite of the marine cyanobacterium Schizothrix sp., selectively inhibits cathepsin L-like cysteine proteases. We evaluated potency of gallinamide A and 23 synthetic analogs against intracellular Trypanosoma cruzi amastigotes and the cysteine protease, cruzain. We determined the co-crystal structures of cruzain with gallinamide A and two synthetic analogs at ~2Å. 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 ~5-fold, likely due to an increase in solubility/permeability of the analogs.

Covalent Inhibitors for Neglected Diseases: An Exploration of Novel Therapeutic Options

“…In this instance, one of the compounds was shown to have a LD 50 of 5.1 ± 1.4 nM, while compound 90 had a LD 50 of 14.7 nM against Trypanosoma cruzi . Following this, Silva et al found compounds 92 , 93 and 94 , whose activities exceeded 90 by 15 times [ 74 ]. The structural difference between 92 and 93, in comparison with 94, was the lack of CH 2 -CH 2 -Ph in P1, which excludes the stabilizer effect of intramolecular interactions between indole and CH 2 -CH 2 -Ph.…”

“…Similarly to [ 73 ], Silva et al approached the CZ inhibitory potential of these compounds [ 74 ]. As a result, they explored P4 to module pharmacokinetics properties.…”

“… Representative compounds synthesized Silva et al [ 65 ] and gallinamide A ( 90 ) and derived compounds alongside SAR studies [ 73 , 74 ]. …”

“…Rhodesain (RD) Trypanothione Reductase (TR) [32][33][34][35][36][37] Trypanothione Synthetase (TryS) [38] Tryparedoxin (Tpx) [39] Human African Trypanosomiasis (HAT) CATL [40] Pterine Reductase I [41,42] CLK1 [43,44] GAPDH [30] Non-specific [45][46][47][48] Cruzain (CZ) [49][50][51][52][53][54][55][56][57][58][59][60][61][62][63][64][65] Chagas Disease (CD) Proline Racemase (PRAC) [66][67][68][69][70] Trypanothione Reductase (TR) [37,71,72] Non-Specific [73,74] Falcipain (FP) [15,[75][76][77]] Proteasome…”

“…This compound might undergo a nucleophilic attack by Cys25 residue through a C3-Michael addition, as demonstrated by covalent molecular docking and DFT simulations. To assess the reversibility of such molecules, they performed a dilution experiment in which they observed the remaining enzyme inhibition upon dilution for a known irreversible cysteine protease Similarly to [73], Silva et al approached the CZ inhibitory potential of these compounds [74]. As a result, they explored P4 to module pharmacokinetics properties.…”