Charge density as a molecular descriptor to reveal differences on high active cruzain inhibitors

Abstract

Available chemotherapy for Chagas disease (CD) involves severe side effects and drug- resistance has been observed in some trypanosome strains. Thus, the discovery of new, safer and more effective drugs to treat CD is required [1]. Cruzain (Cz), a cysteine protease of the papain-like family, plays a vital role at every stage of the parasite’s life cycle. The active-site region of enzyme is similar to those of other members of the papain superfamily with seven substrate-binding subsites, four (S4, S3, S2, S1) on the acyl side and three (S1′, S2′, S3′) on the amino side of the cleaved substrate bond [2]. Currently, 25 inputs associated to this molecular target are registered in the Protein Data Bank (rcsb.org), where Cz has been co-crystallized with reversible and irreversible inhibitors. Thereby, Cz presents itself as an interesting target for development of potential therapeutics for the treatment of the disease by employing a structure-based approach. Among Cz inhibitors, those containing a vinyl sulfone warhead can exhibit good selectivity and a favorable in vivo safety profile despite the irreversible nature of inhibition [1]. Jaishankar et al. synthesized and determined the inhibition constant (and binding energies, ΔG) of a series of vinyl sulfone analogs. However, the analysis of key interactions among sub-pockets, that might explain the activity differences between the ligands, is not available yet [3]. The quantum theory of atoms in molecules (QTAIM) provides an important insight into the molecular interactions in ligand-receptor (L-R) complexes [4]. Through the mapping of the gradient vector field onto the complex charge density, a series of topological elements arise. Among these topological elements, the bond critical point (BCP) and, in particular, the charge density value (ρb) at an interaction BCP is considered as a measure of that interaction strength. Unlike ΔG that is a global property of the entire system, ρb is a local property measured at each interaction BCP. This means that ρb can be used to decompose the binding energy in contributions by groups of atoms [5]. Accordingly, the aim of this work was to exploit charge density to decompose total binding energy in contributions by sub-pockets of Cz. In other words, we want to know how strong is the anchoring of known inhibitors to each Cz sub-pocket. This analysis allowed us to identify easily the anchoring points that could be improved (by optimizing inhibitors structure) in order to increase inhibitor affinity to Cz.