Repurposing of Kinase Inhibitors to Target c-Abl as Potential Therapeutics for Alzheimer’s Disease

In silico-in vitro discovery of untargeted kinase-inhibitor interactions from kinase-targeted therapies: A case study on the cancer MAPK signaling pathway

Protein kinase inhibitors have been widely used as therapeutic agents to treat a variety of diseases, but many of them may cause off-target effects by unexpectedly targeting other noncognate kinases due to high conversion across the protein kinase family. The mitogen-activated protein kinase (MAPK) signaling pathway plays an essential role in tumorigenesis, which has been recognized as a high priority in the druggable target candidates of anticancer therapy. Here, we attempt to investigate the untargeted kinase-inhibitor interactions (UKIIs) of kinase-targeted therapies for the cancer MAPK signaling cascade via an integration of biomolecular modeling, cell viability assay and kinase inhibition analysis. A systematic kinase-inhibitor interaction profile is created for 28 FDA-approved kinase inhibitor drugs across 9 caner-related MAPK kinases. The created profile is analyzed at structural, energetic and dynamic levels and, consequently, totally 18 promising UKII pairs with high theoretical affinity are derived, from which the noncognate inhibitors Cabozantinib, Regorafenib and Crizotinib are selected to test their cytotoxic effects on human epithelial colorectal adenocarcinoma Caco-2 cell line and inhibition activity against the recombinant protein of human p38α kinase domain. The obtained results are compared with two cognate MAPK inhibitors JNK-IN-8 and BIRB796. As might be expected, the Regorafenib, Crizotinib and Cabozantinib exhibit high, moderate and low cytotoxicities, respectively. In addition, the Regorafenib is determined to have a potent p38α-inhibitory activity. This is basically in line with the test results of positive controls JNK-IN-8 and BIRB796 and can be well confirmed by computational modeling.

Identification of abelson tyrosine kinase inhibitors as potential therapeutics for Alzheimer's disease using multiple e-pharmacophore modeling and molecular dynamics

Efforts to combat Alzheimer's disease are focused predominantly on inhibiting the activity of the enzyme(s) that have been identified to be responsible for the production of the amyloid-forming peptide. However, the inherent complexity associated with the network of pathways leading to the disease may involve additional targets for designing effective therapies. Recent experimental findings have identified abelson tyrosine kinase, a non-receptor kinase as a new target for Alzheimer's. In this work, we employed energy optimized multiple pharmacophore modeling strategy from multiple c-Abl structures bound with ligands in the inactive ATP binding conformation (DFG-out). Virtual screening followed by docking of molecules from ChemBridge resulted in the identification of 10 best scoring molecules. MD simulations of the top three complexes revealed that Compound A, C are the most stable complexes with the most persistent protein-ligand interactions consistent with the calculated binding affinities for the top three compounds. Given the implied role of c-Abl not only in AD but in Parkinson's disease, the identified compounds may serve as leads for effective neurotherapeutics.

Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation

To explore the inhibitory mechanism of catechins for digestive enzymes, we investigated the binding mode of catechins to a typical digestive enzyme-trypsin and analyzed the structure-activity relationship of catechins, using an integration of molecular docking, molecular dynamics simulation and binding free energy calculation. We found that catechins with different structures bound to a conservative pocket S1 of trypsin, which is comprised of residues 189–195, 214–220 and 225–228. In the trypsin-catechin complexes, Asp189 by forming strong hydrogen bonding, and Gln192, Trp215 and Gly216 through hydrophobic interactions, all significantly contribute to the binding of catechins. The number and the position of hydroxyl and aromatic groups, the structure of stereoisomers, and the orientation of catechins in the binding pocket S1 of trypsin all affect the binding affinity. The binding affinity is in the order of Epigallocatechin gallate (EGCG) > Epicatechin gallate (ECG) > Epicatechin (EC) > Epigallocatechin (EGC), and 2R-3R EGCG shows the strongest binding affinity out of other stereoisomers. Meanwhile, the synergic conformational changes of residues and catechins were also analyzed. These findings will be helpful in understanding the knowledge of interactions between catechins and trypsin and referable for the design of novel polyphenol based functional food and nutriceutical formulas.