Structural Analysis of Prolyl Oligopeptidases Using Molecular Docking and Dynamics: Insights into Conformational Changes and Ligand Binding

Abstract

Prolyl oligopeptidase (POP) is considered as an important pharmaceutical target for the treatment of numerous diseases. Despite enormous studies on various aspects of POPs structure and function still some of the questions are intriguing like conformational dynamics of the protein and interplay between ligand entry/egress. Here, we have used molecular modeling and docking based approaches to unravel questions like differences in ligand binding affinities in three POP species (porcine, human and A. thaliana). Despite high sequence and structural similarity, they possess different affinities for the ligands. Interestingly, human POP was found to be more specific, selective and incapable of binding to a few planar ligands which showed extrapolation of porcine POP in human context is more complicated. Possible routes for substrate entry and product egress were also investigated by detailed analyses of molecular dynamics (MD) simulations for the three proteins. Trajectory analysis of bound and unbound forms of three species showed differences in conformational dynamics, especially variations in β-propeller pore size, which was found to be hidden by five lysine residues present on blades one and seven. During simulation, β-propeller pore size was increased by ∼2 Å in porcine ligand-bound form which might act as a passage for smaller product movement as free energy barrier was reduced, while there were no significant changes in human and A. thaliana POPs. We also suggest that these differences in pore size could lead to fundamental differences in mode of product egress among three species. This analysis also showed some functionally important residues which can be used further for in vitro mutagenesis and inhibitor design. This study can help us in better understanding of the etiology of POPs in several neurodegenerative diseases.

Parasite Prolyl Oligopeptidases and the Challenge of Designing Chemotherapeuticals for Chagas Disease, Leishmaniasis and African Trypanosomiasis

“…An insertion of a disulfide bridge between the two domains packed them together in a close structure and impaired the catalytic activity [20], reinforcing the concept that a physical step involving conformational change is the ratelimiting step, rather than chemical catalysis [36]. In addition, MD simulation and amino acid substitution also showed a loop (residues 193-209 in porcine POP) that detaches from the protein structure and may play a direct role in gating/recruiting substrates, as the channel through the loop region is both more flexible and wider, and thus, the more likely access pathway to the active site [23,24]. Data from both experimental and computational studies have revealed that although POPs from different species show similar three-dimensional structures, differences among their primary sequences confer some divergent features such as conformational behavior, susceptibility to in- hibitors and substrate specificity [23].…”

“…Structural data obtained by crystallization, threedimensional modeling, molecular dynamics (MD), spectroscopic analysis and site-directed mutagenesis of POP family members of different species [15][16][17][18][19][20][21][22][23][24] have facilitated the understanding of how these structurally similar enzymes can present different biochemical features. In this section, we describe an overview of the structural properties of POP and OPB.…”

“…In addition, the tunnel exit (4 Å in a resting state) is not wide enough to allow the passage of typical peptides (6-12 Å in diameter). On the other hand, a more recent MD and docking study suggested a role for the -propeller domain in the egress of small products, instead of substrate/inhibitor entry into POP with a larger pore size [24]. The fluctuations in the -propeller pore size among various species are due to the presence of lysine residues on the first and seventh blades (highly conserved in mammalian POPs) that hide the opening.…”

“…POPs in which lysine residues are replaced by smaller amino acids can present a bigger pore size. However, replacement of lysine residues by long amino acids such as arginine (e.g., as seen in Arabidopsis thaliana, T. brucei and T. cruzi POPs) result in decreasing the pore size or completely hiding the pore opening [24] (Fig. 2B).…”

Computational Analysis of the Domain Architecture and Substrate-Gating Mechanism of Prolyl Oligopeptidases from Shewanella woodyi and Identification of Probable Lead Molecules

“…The active site is hidden in a large cavity formed by the interface of propeller and hydrolase domain [5]. The molecular dynamics simulation studies have suggested that opening of two domains is the only possible pathway for the substrate entry in POPs [6].…”