The Conformational Transition Pathways and Hidden Intermediates in DFG-Flip Process of c-Met Kinase Revealed by Metadynamics Simulations

Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE

Kinases compose one of the largest fractions of the human proteome, and their misfunction is implicated in many diseases, in particular, cancers. The ubiquitousness and structural similarities of kinases make specific and effective drug design difficult. In particular, conformational variability due to the evolutionarily conserved Asp-Phe-Gly (DFG) motif adopting in and out conformations and the relative stabilities thereof are key in structure-based drug design for ATP competitive drugs. These relative conformational stabilities are extremely sensitive to small changes in sequence and provide an important problem for sampling method development. Since the invention of AlphaFold2, the world of structure-based drug design has noticeably changed. In spite of it being limited to crystal-like structure prediction, several methods have also leveraged its underlying architecture to improve dynamics and enhanced sampling of conformational ensembles, including AlphaFold2-RAVE. Here, we extend AlphaFold2-RAVE and apply it to a set of kinases: the wild type DDR1 sequence and three mutants with single point mutations that are known to behave drastically differently. We show that AlphaFold2-RAVE is able to efficiently recover the changes in relative stability using transferable learned order parameters and potentials, thereby supplementing AlphaFold2 as a tool for exploration of Boltzmann-weighted protein conformations (Meller, A.; Bhakat, S.; Solieva, S.; Bowman, G. R. Accelerating Cryptic Pocket Discovery Using AlphaFold. J. Chem. Theory Comput. 2023, 19, 4355-4363).

Design, synthesis and biological evaluation of sulfonylamidines as potent c-Met inhibitors by enhancing hydrophobic interaction

The dysregulation of c-Met kinase has emerged as a significant contributing factor for the occurrence, progression, poor clinical outcomes and drug resistance of various human cancers. In our ongoing pursuit to identify promising c-Met inhibitors as potential antitumor agents, a docking study of the previously reported c-Met inhibitor 7 revealed a large unoccupied hydrophobic pocket, which could present an opportunity for further exploration of structure-activity relationships to improve the binding affinity with the allosteric hydrophobic back pocket of c-Met. Herein we performed structure-activity relationship and molecular modeling studies based on lead compound 7. The collective endeavors culminated in the discovery of compound 21j with superior efficacy to 7 and positive control foretinib by increasing the hydrophobic interaction with the hydrophobic back pocket of c-Met active site.

Design, Synthesis, and Evaluation of New Mesenchymal–Epithelial Transition Factor (c-Met) Kinase Inhibitors with Dual Chiral Centers

A series of tepotinib derivatives with two chiral centers was designed, synthesized, and evaluated as anticancer agents. The optimal compound (R, S)-12a strongly exhibited antiproliferative activity against MHCC97H cell lines with an IC50 value of 0.002 μM, compared to tepotinib (IC50 = 0.013 μM). Mechanistic studies revealed that compound (R, S)-12a significantly inhibited c-Met activation, as well as the downstream AKT signaling pathway, and suppressed wound closure. Moreover, compound (R, S)-12a induced cellular apoptosis and cell cycle arrest at the G1 phase in a dose-dependent fashion.