Insight into binding mechanisms of EGFR allosteric inhibitors using molecular dynamics simulations and free energy calculations

Next-generation EGFR tyrosine kinase inhibitors to overcome C797S mutation in non-small cell lung cancer (2019-2024)

Lung cancer is a leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC) accounts for the major portion (80-85%) of all lung cancer cases. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are commonly used as the targeted therapy for EGFR-mutated NSCLC. The FDA has approved first-, second- and third-generation EGFR-TKIs as therapeutics options. Osimertinib, the third-generation irreversible EGFR-TKI, has been approved for the treatment of NSCLC patients with the EGFRT790M mutation. However, due to the EGFRC797S mutation in the kinase domain of EGFR, resistance to osimertinib is observed and that limits the long-term effectiveness of the drug. The C797S mutation is one of the major causes of drug resistance against the third-generation EGFR TKIs. The C797S mutations including EGFR double mutations (19Del/C797S or L858R/C797S) and or EGFR triple mutations (19Del/T790M/C797S or L858R/T790M/C797S) cause major resistance to the third-generation EGFR-TKIs. Therefore, the discovery and development of fourth-generation EGFR-TKIs to target triple mutant EGFR with C797S mutation is a challenging topic in medicinal chemistry research. In this review, we discuss the discovery of novel fourth-generation EGFR TKIs, medicinal chemistry approaches and the strategies to overcome the C797S mutations. In vitro activities of EGFR-TKIs (2019-2024) against mutant EGFR TK, anti-proliferative activities, structural modifications, binding modes of the inhibitors and in vivo efficacies in animal models are discussed here.

Identification of New EGFR Inhibitors by Structure-Based Virtual Screening and Biological Evaluation

Epidermal growth factor receptor (EGFR) inhibitors have been used in clinical for the treatment of non-small-cell lung cancer for years. However, the emergence of drug resistance continues to be a major problem. To identify potential inhibitors, molecular docking-based virtual screening was conducted on ChemDiv and Enamine commercial databases using the Glide program. After multi-step VS and visual inspection, a total of 23 compounds with novel and varied structures were selected, and the predicted ADMET properties were within the satisfactory range. Further molecular dynamics simulations revealed that the reprehensive compound ZINC49691377 formed a stable complex with the allosteric pocket of EGFR and exhibited conserved hydrogen bond interactions with Lys 745 and Asp855 of EGFR over the course of simulation. All compounds were further tested in experiments. Among them, the most promising hit ZINC49691377 demonstrated excellent anti-proliferation activity against H1975 and PC-9 cells, while showing no significant anti-proliferation activity against A549 cells. Meanwhile, apoptosis analysis indicated that the compound ZINC49691377 can effectively induce apoptosis of H1975 and PC-9 cells in a dose-dependent manner, while having no significant effect on the apoptosis of A549 cells. The results indicate that ZINC49691377 exhibits good selectivity. Based on virtual screening and bioassays, ZINC4961377 can be considered as an excellent starting point for the development of new EGFR inhibitors.

Pharmacokinetics, dynamics, toxicology and molecular docking of bioactive alkaloid vasicine from Adhatoda vasica: a promising toxin binder against aflatoxin B1 and ochratoxin A

Vasicine from Adhatoda vasica was investigated in the management of aflatoxicosis and ochratoxicosis by in silico molecular docking approach. The computational analysis was carried out using Discovery Studio Autodock 4.5 tool. Absorption, distribution, metabolism, and excretion (ADME), pharmacodynamics and toxicity studies were also carried out using Swiss ADME and PASS online server, respectively. The standard drug compound used was silymarin and the structure were retrieved from the protein data bank for both the test compound vasicine and the standard drug. Vasicine interacted with aflatoxin B1 at 10 different poses and the maximum dock score was found to be 83.04 and the binding energy was -37.54 kcal/mol. Silymarin interacted with aflatoxin B1 at 10 different poses and the maximum dock score was found to be 143.578 and the binding energy was -67.32 kcal/mol. Vasicine interacted with ochratoxin A at 10 different poses and the maximum dock score was found to be 73.75 and the binding energy was -56.20 kcal/mol. Silymarin interacted with ochratoxin A at 10 different poses and the maximum dock score was found to be 89.23 and the binding energy was -98.86 kcal/mol. The compounds possess good gastro intestinal absorption with antioxidant property and exhibits minimum adverse effects. The obtained results support the toxin mitigating potential of the test compound with minimum adverse effects and hence vasicine can be regarded as a potential toxin binder of aflatoxin B1 and ochratoxin A, wherein it can be implemented for alleviating aflatoxicosis and ochratoxicosis.

Systematic analysis and molecular profiling of EGFR allosteric inhibitor cross-reactivity across the proto-oncogenic ErbB family kinases by integrating dynamics simulation, energetics calculation and biochemical assay

Human ErbB family of proteins contains four receptor tyrosine kinases (EGFR, Her2, Her3 and Her4) and has been established as a group of attractive druggable targets against diverse cancers. Over the past decades, a variety of ATP-competitive inhibitors have been discovered to target the orthosteric site of EGFR, which, however, would eventually develop acquired drug resistance due to the missense mutations T790M/C797S occurring in orthosteric site. In recent years, a number of forth-generation inhibitors have been successfully designed to overcome the T790M/C797S-induced drug resistance by targeting EGFR allosteric site instead of orthosteric site. Considering that the four proto-oncogenic ErbB kinases share a high conservation in sequence, structure and function, we herein attempted to investigate the binding potency and cross-reactivity of cognate EGFR allosteric inhibitors over noncognate Her2, Her3 and Her4 kinases--they are closely related to gynecological tumors such as ovarian cancer but no allosteric inhibitors have been reported specifically for them to date. A systematic affinity profile of 12 allosteric inhibitors and 4 orthosteric inhibitors to the 4 ErbB kinases was created by integrating dynamics simulations, energetics calculations and biochemical assays, which was then used to derive a systematic inhibitor selectivity profile for EGFR over other three kinases. It is found that allosteric and orthosteric inhibitors exhibit moderate and modest cross-reactivity across the ErbB family, respectively, but the former generally has a higher binding potency than the latter due to the additional energy cost used for inducing kinase conformational change. Moreover, most allosteric inhibitors can be sensitized by Her2 T798M gatekeeper mutation, a counterpart of EGFR T790M gatekeeper mutation that has been previously reported to cause generic drug resistance for orthosteric inhibitors.

In-silico study of seaweed secondary metabolites as AXL kinase inhibitors

AXL kinase is an attractive cancer target for drug design and it is involved in different cancers. A set of molecule databases with 1072 secondary metabolites from seaweeds were screened against the AXL kinase active site and eight molecules were shortlisted for further studies. From the docking analysis of the complexes, four molecules GA011, BE005, BC010, and BC005 are showing prominent binging. From the 100 ns of molecular dynamics simulations and ligand-bound complex MM-PBSA free energy analysis, two molecules BC010 (ΔG = −135.38 kJ/mol) and BE005 (ΔG = −141.72 kJ/mol) are showing molecule stability in the active site also showing very strong binding free energies. It suggests these molecules could be the potent molecules for AXL kinase.

Challenge and countermeasures for EGFR targeted therapy in non-small cell lung cancer

Lung cancer causes the highest mortality compared to other cancers in the world according to the latest WHO reports. Non-small cell lung cancer (NSCLC) contributes about 85% of total lung cancer cases. An extensive number of risk factors are attributed to the progression of lung cancer. Epidermal growth factor receptor (EGFR), one of the most frequently mutant driver genes, is closely involved in the development of lung cancer through regulation of the PI3K/AKT and MAPK pathways. As a representative of precision medicine, EGFR-tyrosine kinase inhibitors (TKIs) targeted therapy significantly relieves the development of activating mutant EGFR-driven NSCLC. However, treatment with TKIs facilitates the emergence of acquired resistance that continues to pose a significant hurdle with respect to EGFR targeted therapy. In this review, the development of current approved EGFR-TKIs as well as the related supporting clinical trials are summarized and discussed. Mechanisms of action and resistance were addressed respectively, which serve as important guides to understanding acquired resistance. We also explored the corresponding combination treatment options according to different resistance mechanisms. Future challenges include more comprehensive characterization of unclear resistance mechanisms in different populations and the development of more efficient and precision synthetic therapeutic strategies.

Direct proof of soft knock-on mechanism of ion permeation in a voltage gated sodium channel

Sodium channels selectively conduct Na⁺ ions across cellular membrane with extraordinary efficiency, which is essential for initiating action potentials. However, how Na⁺ ions permeate the ionic channels remains obscure and ambiguous. With more than 40 conductance events from microsecond molecular dynamics simulation, the soft knock-on ion permeation mediated by water molecules was observed and confirmed by the free energy profile and electrostatic potential calculation in this study. During the soft knock-on process, the change of average distance between four oxygen atoms in Glu177-Glu177 plays a very important role for the permeation of Na⁺ ion. Exploration of the ionic conductance mechanism could provide a guideline for designing ion channel targeted drug.

Next-Generation Kinase Inhibitors Targeting Specific Biomarkers in Non-Small Cell Lung Cancer (NSCLC): A Recent Overview

Lung cancer causes many deaths globally. Mutations in regulatory genes, irregularities in specific signal transduction events, or alterations of signalling pathways are observed in cases of non-small cell lung cancer (NSCLC). Over the past two decades, a few kinases have been identified, validated, and studied as biomarkers for NSCLC. Among them, EGFR, ALK, ROS1, MET, RET, NTRK, and BRAF are regarded as targetable biomarkers to cure and/or control the disease. In recent years, the US Food and Drug Administration (FDA) approved more than 15 kinase inhibitors targeting these NSCLC biomarkers. The kinase inhibitors significantly improved the progression-free survival (PFS) of NSCLC patients. Challenges still remain for metastatic diseases and advanced NSCLC cases. New discoveries of potent kinase inhibitors and rapid development of modern medical technologies will help to control NSCLC cases. This article provides an overview of the discoveries of various types of kinase inhibitors against NSCLC, along with medicinal chemistry aspects and related developments in next-generation kinase inhibitors that have been reported in recent years.

Molecular mechanism study of EGFR allosteric inhibitors using molecular dynamics simulations and free energy calculations

ABTRACTThe epidermal growth factor receptor (EGFR) kinase inhibitors Gefitinib, Erlotinib, Afatinib and Osimertinib have been approved for the treatments of non-small cell lung cancer patients harboring sensitive EGFR mutations, but resistance arises rapidly. To date all approved EGFR inhibitors are ATP-competitive inhibitors, highlighting the need for therapeutic agents with alternative mechanisms of action. Allosteric kinase inhibitors offer a promising new therapeutic strategy to ATP-competitive inhibitors. The mutant-selective allosteric EGFR inhibitors EAI045 exhibited higher potency for EGFR^L858R&T790M compared to WT, which was also effective in EGFR-mutant models including those harboring the C797S mutation. However, it was not effective as a single-agent inhibitor, and require the co-administration of the anti-EGFR antibody Cetuximab. Further efforts produced a more potent analog JBJ-04-125-02, which can inhibit cell proliferation as a single-agent inhibitor. In the present study, molecular dynamics simulations and free energy calculations were performed and revealed the detailed inhibitory mechanism of JBJ-04-125-02 as more potent EGFR inhibitor. Moreover, the energy difference between HOMO and LUMO calculated by DFT implied the higher interaction of JBJ-04-125-02 than EAI045 in the active site of the EGFR. The identified key features obtained from the molecular modeling enabled us to design novel EGFR allosteric inhibitors.Communicated by Ramaswamy H. Sarma.

Enhanced metastable state models of TAM kinase binding to cabozantinib explains the dynamic nature of receptor tyrosine kinases

Receptor tyrosine kinases (RTKs) are essential proteins in the regulation of cell signaling. Tyro3, Axl and Mer are members of TAM RTKs and are overexpressed in several cancer forms. Kinase inhibitors such as cabozantinib, foretinib are reported to inhibit TAM kinases at nanomolar concentrations. The atomistic details of structure and mechanism of functional regulation is required to understand their normal physiological process and when bound to an inhibitor. The docking of cabozantinib into the active state conformations of TAM kinases (crystal structure and computational models) revealed the best binding pose and the complex formation that is mediated through non-bonding interactions involving the hinge region residues. The alterations in the conformations and the regions of flexibility in apo and complexed TAM kinases as a course of time are studied using 250 ns molecular dynamics (MD) simulations. The post-MD trajectory analysis using Python libraries like ProDy, MDTraj and PyEMMA revealed encrypted protein dynamic motions in active kinetic metastable states. Comparison between Principal component analysis and Anisotropic mode analysis deciphered structural residue interactions and salt bridge contacts between apo and inhibitor bound TAM kinases. Various structural changes occurred in αC-helix and activation loop involving hydrogen bonding between residues from Lys-(β3 sheet), Glu-(αC-helix) and Asp-(DFG-motif) resulting in higher RMSD. Mechanical stiffness plots revealed that similar regions in apo and cabozantinib bound Axl fluctuated during MD simulations whereas different regions in Tyro3 and Mer kinases. The residue interaction network plots revealed important salt bridges that lead to constrained domain motions in the TAM kinases.Communicated by Ramaswamy H. Sarma.

How Different Substitution Positions of F, Cl Atoms in Benzene Ring of 5-Methylpyrimidine Pyridine Derivatives Affect the Inhibition Ability of EGFRL858R/T790M/C797S Inhibitors: A Molecular Dynamics Simulation Study

Lung cancer is the most frequent cause of cancer-related deaths worldwide, and mutations in the kinase domain of the epidermal growth factor receptor (EGFR) are a common cause of non-small-cell lung cancers, which is a major subtype of lung cancers. Recently, a series of 5-methylpyrimidine-pyridinone derivatives have been designed and synthesized as novel selective inhibitors of EGFR and EGFR mutants. However, the binding-based inhibition mechanism has not yet been determined. In this study, we carried out molecular dynamic simulations and free-energy calculations for EGFR derivatives to fill this gap. Based on the investigation, the three factors that influence the inhibitory effect of inhibitors are as follows: (1) The substitution site of the Cl atom is the main factor influencing the activity through steric effect; (2) The secondary factors are repulsion between the F atom (present in the inhibitor) and Glu762, and the blocking effect of Lys745 on the phenyl ring of the inhibitor. (3) The two factors function synergistically to influence the inhibitory capacity of the inhibitor. The theoretical results of this study can provide further insights that will aid the design of oncogenic EGFR inhibitors with high selectivity.