New compounds identified through in silico approaches reduce the α-synuclein expression by inhibiting prolyl oligopeptidase in vitro

Abstract

Prolyl oligopeptidase (POP) is a serine protease that is responsible for the maturation and degradation of short neuropeptides and peptide hormones. The inhibition of POP has been demonstrated in the treatment of α-synucleinopathies and several neurological conditions. Therefore, ligand-based and structure-based pharmacophore models were generated and validated in order to identify potent POP inhibitors. Pharmacophore-based and docking-based virtual screening of a drug-like database resulted in 20 compounds. The in vitro POP assays indicated that the top scoring compounds obtained from virtual screening, Hit 1 and Hit 2 inhibit POP activity at a wide range of concentrations from 0.1 to 10 µM. Moreover, treatment of the hit compounds significantly reduced the α-synuclein expression in SH-SY5Y human neuroblastoma cells, that is implicated in Parkinson’s disease. Binding modes of Hit 1 and Hit 2 compounds were explored through molecular dynamics simulations. A detailed investigation of the binding interactions revealed that the hit compounds exhibited hydrogen bond interactions with important active site residues and greater electrostatic and hydrophobic interactions compared to those of the reference inhibitors. Finally, our findings indicated the potential of the identified compounds for the treatment of synucleinopathies and CNS related disorders.

Computational Simulations Identified Two Candidate Inhibitors of Cdk5/p25 to Abrogate Tau-associated Neurological Disorders

“…Therefore, we argued that the resultant pharmacophore is a suitable choice to use as a 3D query in virtual screening of the drug-like database for the identification of candidate inhibitors of Cdk5. The selected pharmacophore obtained highest GH and EF scores of 0.88 and 7.23, respectively, which validates its suitability in virtual screening practices [ 34 , 35 ]. Since, drug-like molecules are restricted to certain chemical properties such as physiochemical and pharmacokinetics and pharmacodynamics properties.…”

“…Since, molecular docking does not provide simulated physiological environment and real-time behavior of the drug-receptor interaction; therefore, molecular dynamics (MD) simulation was employed to identify the true positive inhibitors of Cdk5/p25 [ 35 , 36 , 58 ]. The root mean square deviation (rmsd) analysis is a key factor to evaluate the stability and successful execution of MD simulation [ 34 , 35 , 58 ]. Our results suggested that the final candidate inhibitors showed stable rmsd of the alpha carbon atoms (C α ) of Cdk5/p25, the backbone atoms of Cdk5/p25, and the Cdk5/p25 in complex with candidate inhibitors.…”

“…Our results suggested that the final candidate inhibitors showed stable rmsd of the alpha carbon atoms (C α ) of Cdk5/p25, the backbone atoms of Cdk5/p25, and the Cdk5/p25 in complex with candidate inhibitors. Potential energy estimation is an essential component of molecular dynamics simulation analysis [ 34 , 35 ]. Our results estimated the lowest potential energy and confirmed that each simulation system behaved stable during the entire simulation period.…”

“…The enrichment factor (EF) determines the specificity and selectivity of the model to identify active compounds during the screening of decoy test set. The higher the EF value the higher will be the selectivity of the model [ [33] , [34] , [35] ].…”

Removal of prolyl oligopeptidase reduces alpha-synuclein toxicity in cells and in vivo

“…Studies with PREP have shown beneficial effects on aSyn aggregation and clearance after PREP inhibitor treatment 16 – 18 , 44 , 53 . However, information about aSyn toxicity in the total absence of PREP has not been reported.…”