Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches

Abstract

Background Fasciola hepatica is the causative agent of fascioliasis, a disease affecting grazing animals, causing economic losses in global agriculture and currently being an important human zoonosis. Overuse of chemotherapeutics against fascioliasis has increased the populations of drug resistant parasites. F. hepatica cathepsin L3 is a protease that plays important roles during the life cycle of fluke. Due to its particular collagenolytic activity it is considered an attractive target against the infective phase of F. hepatica.Methodology/Principal FindingsStarting with a three dimensional model of FhCL3 we performed a structure-based design of novel inhibitors through a computational study that combined virtual screening, molecular dynamics simulations, and binding free energy (ΔGbind) calculations. Virtual screening was carried out by docking inhibitors obtained from the MYBRIDGE-HitFinder database inside FhCL3 and human cathepsin L substrate-binding sites. On the basis of dock-scores, five compounds were predicted as selective inhibitors of FhCL3. Molecular dynamic simulations were performed and, subsequently, an end-point method was employed to predict ΔGbind values. Two compounds with the best ΔGbind values (-10.68 kcal/mol and -7.16 kcal/mol), comparable to that of the positive control (-10.55 kcal/mol), were identified. A similar approach was followed to structurally and energetically characterize the interface of FhCL3 in complex with a peptidic substrate. Finally, through pair-wise and per-residue free energy decomposition we identified residues that are critical for the substrate/ligand binding and for the enzyme specificity.Conclusions/SignificanceThe present study is the first computer-aided drug design approach against F. hepatica cathepsins. Here we predict the principal determinants of binding of FhCL3 in complex with a natural substrate by detailed energetic characterization of protease interaction surface. We also propose novel compounds as FhCL3 inhibitors. Overall, these results will foster the future rational design of new inhibitors against FhCL3, as well as other F. hepatica cathepsins.

Identification of Chalcones as Fasciola hepatica Cathepsin L Inhibitors Using a Comprehensive Experimental and Computational Approach

“…This residue is specific of Fh CL3 and when mutated for Leu as in Fh CL1 it renders the enzyme almost inactive highlighting its importance for substrate positioning for catalysis [ 39 ]. A recent in silico search for Fh CL3 inhibitors provides additional evidence that the non-polar side chain of Trp 69 establishes critical interaction with ligands and adopts variable conformations to accommodate different groups in the enzyme binding site [ 62 ]. Furthermore, it showed that aromatic moieties with high hydrophobicity can establish favorable interactions with non-polar residues from Fh CL3 binding cleft [ 62 ].…”

“…A recent in silico search for Fh CL3 inhibitors provides additional evidence that the non-polar side chain of Trp 69 establishes critical interaction with ligands and adopts variable conformations to accommodate different groups in the enzyme binding site [ 62 ]. Furthermore, it showed that aromatic moieties with high hydrophobicity can establish favorable interactions with non-polar residues from Fh CL3 binding cleft [ 62 ]. The greater number of interactions between inhibitor and residues from Fh CL3 sub-sites compared with Fh CL1, might explain its lower IC 50 ( Table 1 ), its behavior as a slowly reversible inhibitor ( Fig 2 ), and its highest percentage of inhibition reached after 120 min ( Table 1 ).…”

Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships

“…Three FP‐2 residues, that is, Q36, G83, and N173, were predicted to form hydrogen bonds with the backbone nitrogen and oxygen atoms at P2 to P1′ sites of the ligands with relatively high occupancies (Supporting Information, Table S2). Equivalent hydrogen bonds occur at the interfaces of crystal structures of C1 cysteine proteases in complex with peptide‐based inhibitors, and have been predicted for FP‐2 and other homologous enzymes complexed with nonpeptidic compounds . Remarkably, G83 and N173 each formed up to two hydrogen bonds with the inhibitors ((a–d), Fig.…”

Polar Desolvation and Position 226 of Pancreatic and Neutrophil Elastases Are Crucial to their Affinity for the Kunitz-Type Inhibitors ShPI-1 and ShPI-1/K13L

“…The MMPBSA.py program of Amber12 package was used for MM-GB(PB)SA free energy calculations [ 48 , 50 ] after converting the GROMACS trajectories into the Amber format by using VMD v1.9.1 as described elsewhere [ 51 ]. In all cases we followed the single trajectory (ST) approach, in which the trajectories for the free enzyme and the free ligand are extracted from that of the complex [ 48 , 50 ].…”