Integration of an Inhibitor-like Rule and Structure-based Virtual Screening for the Discovery of Novel Myeloperoxidase Inhibitors

Abstract

Myeloperoxidase (MPO) is an attractive therapeutic target against inflammation. Herein, we developed an inhibitor-like rule, based on known MPO inhibitors, and generated a target database containing 6546 molecules with privileged inhibitory properties. Using a structure-based approach validated by decoys, robust statistical metrics, redocking, and cross-docking, we selected 10 putative MPO inhibitors with high chemical diversity. At 20 μM, six of these 10 compounds (i.e., 60% success rate) inhibited more than 20% of the chlorinating activity of the enzyme. Additionally, we found that compound ZINC9089086 forms hydrogen bonds with Arg233 and with the hemic carboxylate. It makes a π-stacking interaction with the heme group and displays a high affinity for the enzyme active site. When incubated with purified MPO, ZINC9089086 inhibited the chlorinating activity of the enzyme with an IC50 of 2.2 ± 0.1 μM in a reversible manner. Subsequent experiments revealed that ZINC9089086 inhibited hypochlorous acid production in dHL-60 cells and human neutrophils. Furthermore, the theoretical ADME/Tox profile indicated that this compound exhibits low toxicity risks and adequate pharmacokinetic parameters, thus making ZINC9089086 a very promising candidate for preclinical anti-inflammatory studies. Overall, our study shows that integrating an inhibitor-like rule with a validated structure-based methodology is an excellent approach for improving the success rate and molecular diversity of novel MPO inhibitors with good pharmacokinetics and toxicological profiles. By combining these tools, it was possible to increase the assurance rate, which ultimately diminishes the costs and time needed for the acquisition, synthesis, and evaluation of new compounds.

Development of methyl 5-((cinnamoyloxy)methyl)picolinate, exploring its bio-target potential aiming at CVD mediated by multiple proteins through surface and physiochemical analysis

“…It oxidizes the HDL protein; this Ox-HDL leads to critical cardiovascular events 39 , 40 . It is also linked with various diseases, including Parkinson’s and rheumatoid arthritis 41 . The MPO protein is docked with Compound 5 , with the best binding interaction of − 6.17 kcal mol −1 , and the estimated inhibition is 29.99 µM.…”

Targeting Myeloperoxidase Ameliorates Gouty Arthritis: A Virtual Screening Success Story

“…A new virtual screening of the previously identified 242 computational hits that met the MPO inhibitor-like rule and exhibited a favorable binding mode in molecular docking was carried out . Initially, we conducted a comprehensive re-evaluation of the molecular docking protocol.…”

“…We investigated the effects of cell-active compounds, RL6 and RL7, along with the previously tested compound ZINC9089086, on the release of NETs. MSU crystals represent a classical inducer of aseptic NETosis, and MPO inhibitors are considered potential anti-NETotic agents .…”

“…The combination of these methods led to a high hit ratio and the identification of chemically diverse molecules. 31 The inhibitor-like rule was developed using descriptors traditionally used to predict the permeability/bioavailability of molecules. The rule states that MPO inhibition and the respective bioavailability of inhibitors are more likely for molecules that meet the following criteria: (1) molecular mass between 174 and 396 Da; (2) ACD/logP between 0.1 and 4.37; (3) hydrogen-bond donors up to 7 and hydrogen bond receptors between 2 and 9; (4) rotatable bond count up to 9; and (5) topological surface area (TPSA) between 18 and 122 Å 2 .…”

“…These were then docked to MPO using a validated protocol using AutoDock and visual inspection, leading to the selection of 10 compounds for testing against MPO activity. Among them, six compounds inhibited enzyme activity, resulting in 60% success rate of this strategy …”