In silico studies on 2-substituted phenol quinazoline derivatives as RET receptor tyrosine kinase antagonists

Investigating natural compounds against oncogenic RET tyrosine kinase using pharmacoinformatic approaches for cancer therapeutics

Rearranged during transfection (RET) tyrosine kinase is a transmembrane receptor tyrosine kinase regulating vital aspects of cellular proliferation, differentiation, and survival. An outstanding challenge in designing protein kinase inhibitors is due to the development of drug resistance. The “gain of function” mutations in the RET gate-keeper residue, Val804, confers resistance to the majority of known RET inhibitors, including vandetanib. To curtail this resistance, researchers developed selpercatinib (LOXO-292) against the RET gate-keeper mutant forms – V804M and V804L. In the present in silico investigation, a receptor–ligand pharmacophore model was generated to identify small molecule inhibitors effective for wild-type (WT) as well as mutant RET kinase variants. The generated model was employed to screen 144 766 natural products (NPs) available in the ZINC database and the retrieved NPs were filtered for their drug-likeness. The resulting 2696 drug-like NPs were subjected to molecular docking with the RET WT kinase domain and a total of 27 molecules displayed better dock scores than the reference inhibitors – vandetanib and selpercatinib. From 27 NPs, an aggregate of 12 compounds demonstrated better binding free energy (BFE) scores than the reference inhibitors, towards RET. Thus, the 12 NPs were also subjected to docking, simulation, and BFE estimation towards the constructed gate-keeper RET mutant structures. The BFE calculations revealed 3 hits with better BFE scores than the reference inhibitors towards WT, V804M, and V804L RET variants. Thus, the scaffolds of hit compounds presented in this study could act as potent RET inhibitors and further provide insights for drug optimization targeting aberrant activation of RET signaling, specifically the mutation of gate-keeper residue – Val804.

Identification of natural product inhibitors against rearranged during transfection (RET) tyrosine kinase as cancer therapeutics using combination of in silico techniques.

Docking and 3D-QSAR Studies of Hydrazone and Triazole Derivatives for Selective Inhibition of GRK2 over ROCK2

Introduction:

G protein-coupled receptor kinase 2 (GRK2) is known to be implicated in heart failure, and therefore serves as an important drug target. GRK2 belongs to the protein kinase A, G, and C family and shares high sequence similarity with its closely related protein, the Rhoassociated coiled-coil protein kinase 2 (ROCK2). Therefore, selective inhibition of GRK2 over ROCK2 is considered crucial for heart failure therapy.

Objective:

To understand the structural factors for enhancing the inhibitory activity for GRK2 and selectivity over ROCK2, we analyzed and compared molecular interactions using the same set of ligands against both receptors.

Methods:

We have performed molecular docking and three-dimensional quantitative structure activity relationship (3D-QSAR) studies on a series of hydrazone and triazole derivatives.

Results:

The presence of hydrophobic substituents at the triazole ring, electronegative substituents between the pyridine and triazole ring and hydrophobic substituents near the benzene ring increases the activity of both kinases. Whereas, having non-bulky substituents near the triazole ring, bulky and hydrophobic substations at the benzene ring and electronegative and H-bond acceptor substituents at the triazole ring showed a higher inhibitory preference for GRK2 over ROCK2.

Conclusion:

The outcome of this study may be used in the future development of potent GRK2 inhibitors having ROCK2 selectivity.