In vitro screening of Schistosoma mansoni JNK against a prioritized library of predicted type II-kinase inhibitors

Abstract text

Introduction

Chemotherapy of schistosomiasis relies on a single drug, praziquantel, which efficiently reduces morbidity and mortality due to the disease. The emergence of resistant parasite strains together with the lack of efficiency in killing larval stages transiting through the body substantiate the pursuit for a new drug. Immense efforts have been invested in the discovery of protein kinase (PK) inhibitors; however, given that the majority of PKs are still not targeted by an inhibitor with a useful level of selectivity, there is a compelling need to expand the chemical space available for synthesizing new, potent and selective PKI.

Objective

Small-molecule inhibitors targeting the ATP pocket of the catalytic domain of PKs have potential to become drugs devoid of (major) side effects, particularly if they bind selectively. This is the case for type II PK inhibitors, which cause PKs to adopt the so-called DFG-out conformation, which corresponds to the inactive state of the enzyme. In this conformation, the ligand occupies at the same time the ATP-pocket and an additional space in the cleft between the two lobes of the kinase. Therefore, the goal was to perform a virtual screen against the ATP pocket of S. mansoni JNK in a state where selectivity has more often been observed, to help with potential kinase selectivity issues.

Materials & Methods

Here, we selected the human JNK2 (PDBID: 3NPC) as a template model for the ATP pocket of SmJNK, because it has high sequence identity, great coverage of the protein sequence and was solved with a type II inhibitor. Atomwise performed the screen of a molecular library of several million compounds at the selected target site using AtomNet®, the first deep learning neural network for structure-based drug design and discovery. Its speed and accuracy make it the most advanced technology for small molecule binding affinity prediction.

Results

Top scoring compounds were clustered and filtered to arrive at a final subset of 85 deliverable compounds. These drugs will be screened in vitro against larval and adult stages of S. mansoni, with additional confocal microscopy analysis of adult worms in order to assess morphological alterations. Moreover, positive hits will be used in our developed fluorescence polarization assay to show the target-ligand interaction.

Conclusion

This study will possibly provide information on novel candidates targeting JNK that can be developed for therapeutic use against schistosomiasis.