Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation of EGFR for the Clinical Treatment of Glioblastoma

Abstract

Glioblastoma (GBM) is a WHO Grade IV tumor with poor visibility, a high risk of comorbidity, and limited treatment options. Resurfacing from second-rate glioma was originally classi ed as either mandatory or optional. Recent interest in personalized medicine has motivated research toward biomarker strati cation-based individualized illness therapy. GBM biomarkers have been investigated for their potential utility in prognostic strati cation, driving the development of targeted therapy, and customizing therapeutic treatment. Due to the availability of a speci c EGFRvIII mutational variation with a clear function in glioma-genesis, recent research suggests that EGFR has the potential to be a prognostic factor in GBM, while others have shown no clinical link between EGFR and survival. The pre-existing pharmaceutical lapatinib (PubChem ID: 208908) with a higher a nity score is used for Structure-based Virtual Screening. As a result, the current study revealed a newly screened chemical (PubChem CID: 59671768) with a higher a nity than the previously known molecule. When the two compounds are compared, the former has the lowest re-rank score. The time-resolved features of a virtually screened chemical and an established compound were investigated using Molecular Dynamics Simulation. Both compounds are equivalent, according to the ADMET study. This report implies that the virtual screened chemical could be a promising Glioblastoma therapy.

HSYA prevents IL‐1β‐induced human chondrocyte damage in osteoarthritis by inhibiting NF‐κB activation

“…Using OPLS‐AA, up to 32 conformations of HSYA were generated (Kari et al., 2023). The lowest energy‐minimized conformation of the three proteins and ligands was employed for molecular docking calculations (Bhrdwaj et al., 2023). As the NF‐κB lacked active site information, active site prediction was conducted using a sitemap tool.…”

Pentafuhalol-B, a Phlorotannin from Brown Algae, Strongly Inhibits the PLK-1 Overexpression in Cancer Cells as Revealed by Computational Analysis

“…In the current study, the PSA for polar atoms of PtB that interacted with amino acids in the active site was estimated from 508.501 to 597.879 Å 2 in a 200 ns simulation (Table 3). Initially, the polar atoms of PtB deviated up to 560.750 Å 2 for 2 but the polar surface area was decremented, and PtB bound with amino acids of protein via intermolecular interactions in the enzymatic site at the end of the simulation [47].…”

Ethyl gallate concurrent administration protects against acetaminophen‐induced acute liver injury in mice: An in vivo and in silico approach

“…Similarly, the ligand molecule EG is refined to attain its original state in neutral pH conditions, and with OPLS-AA, up to 32 conformations are generated (Kari et al, 2023). The lowest energyminimized conformation of three proteins and ligands is subject to molecular docking calculations (Bhrdwaj et al, 2023). Among the three proteins, the NF-κB and IL-1β lack the active site information and, thus, the active site prediction is performed with a sitemap tool, and the predicted amino acids are manually picked for the Glide grid generation program, and for the TNF-α protein, the co-crystal ligand structure is manually picked, and the grids are generated (Anjugam et al, 2022;Sakkiah et al, 2021).…”