Investigating molecular dynamics-guided lead optimization of EGFR inhibitors

Design, synthesis, X-ray crystal structures, anticancer, DNA binding, and molecular modelling studies of pyrazole-pyrazoline hybrid derivatives

We have designed and synthesized three pyrazole analogs (4, 5a, 5b), pyrazole-based chalcones (6a-6d) and (8a-8h), and N-formyl/acetyl 1,3,5-trisubstituted pyrazoline analogs (7a-7d), (9a-9d). FT-IR, 1H, 13C NMR, and mass spectrometry techniques were used to describe the structures of all the synthesized analogs. The single crystal X-ray method was used to identify the molecular structure of derivatives 4 and 5a. All synthesized analogs were screened by MTT assay on two cancer cell lines, the human lung cancer cell line (A549) and cervical cancer cell line (HeLa). Among all compounds, analog 9d demonstrates significant anticancer activity against HeLa (IC50 = 23.6 μM) and A549 (IC50 = 37.59 μM). The non-interactive interaction of active compound (9d) with Calf thymus DNA (Ct-DNA) has been investigated through various methods, such as UV-vis absorption, emission, cyclic voltammetry and circular dichroism. The DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical has been used to measure the antioxidant capacity of the pyrazoline derivative (9d). The outcomes showed that active analog has significant antioxidant activity. In addition, MD simulation of the EGFR tyrosine kinase protein-ligand complex was performed at a time scale of 100 ns. The MMGBSA data of ligand-protein complex are showed stable interactions up to 100 ns.

Overcoming Paradoxical Kinase Priming by a Novel MNK1 Inhibitor

Targeting the kinases MNK1 and MNK2 has emerged as a valuable strategy in oncology. However, most of the advanced inhibitors are acting in an adenosine triphosphate (ATP)-competitive mode, precluding the evaluation of different binding modes in preclinical settings. Using rational design, we identified and validated the 4,6-diaryl-pyrazolo[3,4-b]pyridin-3-amine scaffold as the core for MNK inhibitors. Signaling pathway analysis confirmed a direct effect of the hit compound EB1 on MNKs, and in line with the reported function of these kinases, EB1 only affects the growth of tumor but not normal cells. Molecular modeling revealed the binding of EB1 to the inactive conformation of MNK1 and the interaction with the specific DFD motif. This novel mode of action appears to be superior to the ATP-competitive inhibitors, which render the protein in a pseudo-active state. Overcoming this paradoxical activation of MNKs by EB1 represents therefore a promising starting point for the development of a novel generation of MNK inhibitors.

Ligand binding effects on the activation of the EGFR extracellular domain

The epidermal growth factor receptor (EGFR) is one of the most common target proteins in anti-cancer therapy. The binding of the EGF ligand to the EGFR extracellular domain (EGFR-ECD) promotes its inactive-to-active conformational transition (activation) but the relevant detailed mechanism remains elusive still. Here, the structural characterization and energetics of the EGFR-ECD conformational transition with and without the binding of the EGF are quantitatively explored using an innovative enhanced sampling MD simulation method. Intriguingly, the EGF offers hydrophobic interactions (e.g., EGF residues of Tyr44 and Leu47) and electrostatic interactions (e.g., the EGF residues of Glu5, Asp11, Asp17, and Arg41) to play a dominant role in dragging domain III to close the ligand binding domain gap. Subsequently, the correlation between domains III and II is enhanced through salt-bridges among Glu376, Arg403, and Arg405 from domain III and Glu293, Glu295, and Arg300 from domain II. Finally, the structural bending of domain II is regulated to facilitate the disengagement of domain II from domain IV. In this regard, the functional conformational transition of EGFR-ECD is a consequence of the cooperative motion of protein domains driven by the EGF ligand binding. The present study shows a detailed scenario of the EGF induced activation of EGFR-ECD and provides valuable information for drug discovery targeting the EGFR.