Modeling of human M1 aminopeptidases for in silico screening of potential Plasmodium falciparum alanine aminopeptidase (PfA-M1) specific inhibitors

Abstract

Plasmodium falciparum alanine M1-aminopeptidase (PfA-M1) is a validated target for anti-malarial drug development. Presence of significant similarity between PfA-M1 and human M1-aminopeptidases, particularly within regions of enzyme active site leads to problem of non-specificity and off-target binding for known aminopeptidase inhibitors. Molecular docking based in silico screening approach for off-target binding has high potential but requires 3D-structure of all human M1-aminopeptidaes. Therefore, in the present study 3D structural models of seven human M1-aminopeptidases were developed. The robustness of docking parameters and quality of predicted human M1-aminopeptidases structural models was evaluated by stereochemical analysis and docking of their respective known inhibitors. The docking scores were in agreement with the inhibitory concentrations elucidated in enzyme assays of respective inhibitor enzyme combinations (r2≈0.70). Further docking analysis of fifteen potential PfA-M1 inhibitors (virtual screening identified) showed that three compounds had less docking affinity for human M1-aminopeptidases as compared to PfA-M1. These three identified potential lead compounds can be validated with enzyme assays and used as a scaffold for designing of new compounds with increased specificity towards PfA-M1.

Keywords: Drug designing; homology modeling; in silico screening; malaria; molecular docking.

Figure 1

Ribbon representation of predicted 3D structural models of seven human M1 aminopeptidases. All the proteins show same four domain architecture but differ in arrangement of helices and sheets leading to differences in volume and accessibility of active site.

Figure 2

Ligand interaction diagrams of bestatin docking in PfA-M1 (A) and human PSA (B). Bestatin shows formation of hydrogen bond with active site residues and metal ion in both PfA-M1 and human PSA.

Figure 3

Backbone superimposition of PfA-M1 (in dark blue) with PSA (in turquoise) with (A) and (B) APN (in brown). C Molecular structureof three PfA-M1 inhibitors that shows high affinity binding towards P. falciparum PfA-M1 than most of the human M1 aminopeptidases.

Figure 4

Ligand interaction diagrams of Compound 2 docking in PfA-M1 A) and human PSA; B) Compound 2 docking shows metal ion interaction with PfA-M1 but not with PSA. Number of hydrogen bonds formed by Compound 2 with PfA-M1 are more than with human PSA.