Binding to Large Enzyme Pockets: Small‐Molecule Inhibitors of Trypanothione Reductase

Abstract

The causative agents of the parasitic disease human African trypanosomiasis belong to the family of trypanosomatids. These parasitic protozoa exhibit a unique thiol redox metabolism that is based on the flavoenzyme trypanothione reductase (TR). TR was identified as a potential drug target and features a large active site that allows a multitude of possible ligand orientations, which renders rational structure-based inhibitor design highly challenging. Herein we describe the synthesis, binding properties, and kinetic analysis of a new series of small-molecule inhibitors of TR. The conjunction of biological activities, mutation studies, and virtual ligand docking simulations led to the prediction of a binding mode that was confirmed by crystal structure analysis. The crystal structures revealed that the ligands bind to the hydrophobic wall of the so-called "mepacrine binding site". The binding conformation and potency of the inhibitors varied for TR from Trypanosoma brucei and T. cruzi.

Targeting a Large Active Site: Structure‐Based Design of Nanomolar Inhibitors of Trypanosoma brucei Trypanothione Reductase

“…We have recently reported on a known class of TR ligands providing a novel lead 1 with improved potency (competitive inhibition constant ( K ic )=6.1 μ m ) and physicochemical properties (Figure ). The crystal structure of 1 in complex with Trypanosoma ( T .)…”

Dibenzosuberyl substituted polyamines and analogs of clomipramine as effective inhibitors of trypanothione reductase; molecular docking, and assessment of trypanocidal activities

“…Several crystal structures show aromatic moieties of inhibitors bound at the "hydrophobic wall" of TR, and interacting with Trp22 and Met114 (corresponding to BR 4), and often the inhibitor molecule extends into the region near Tyr111 (BR 3). For example, crystal structures locate in the region of Trp21/22 and Met113/114: the acridine rings of mepacrine (quinacrine) 42 and quinacrine mustard; 43 the dihydroquinazoline ring of T. brucei TR inhibitors (with groups also being close to Tyr110 and also in a conformationally induced sub-pocket); 34 also biaryl inhibitors 96 and a diarylpyrrole 32 (both of which also extended into region near Tyr110). Representative ligand poses compiled from all protonated versions and DBS/DBA configurations of compounds (1) to (7) …”

“…1). The active site has several locations where ligands can bind 40,96 and for some inhibitors is large enough to accommodate two molecules. 32 The residues directly involved in catalysis (including the redox active Cys53 and Cys58, along with His461') are positioned at the deepest part of the cleft, and close to the dimer interface (note, in one subunit the residues are labeled with primed numbers).…”

Synthesis, biological profiling and mechanistic studies of 4-aminoquinoline-based heterodimeric compounds with dual trypanocidal–antiplasmodial activity

“…new non toxic and inexpensive chemical entities that are effective against resistant parasite strains and are brain permeable, so that they may be useful for both disease stages in the case of HAT and for cerebral malaria, as well. Intensive research efforts involving phenotypic whole-cell screening of chemical libraries or newly synthesized compounds, [13][14][15][16] identification of novel key biological targets and subsequent target-based screening or rational design campaigns, [17][18][19][20][21] development of multitarget-directed ligands, [22][23][24] or drug repurposing programs 1 are being carried out in the pursuit of novel antiprotozoal compounds.…”