Exploring binding stability of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with T790M/L858R EGFR-TKD

In silico and in vitro investigation of dual targeting Prima-1MET as precision therapeutic against lungs cancer

This study emphasizes the explorations of binding of Prima-1MET with two targets, p53 a tumor suppressor protein, and tyrosine kinase of epidermal growth factor receptor. In silico investigations reveal that Prima-1MET showed robust binding with both targets. Molecular docking simulations demonstrated the binding affinity of Prima-1MET with p53 and tyrosine kinase was found to be -38.601 kJ/mol and -38.976 kJ/mol. In addition, the stability of Prima-1MET was explored by molecular dynamics simulation. Prima-1MET attains stability in the binding site of the respective protein till the simulation period is over. Moreover, the free binding energy ΔGbind was calculated by the molecular mechanics Poisson Boltzmann surface area method. The ΔGbind of Prima-1MET with tyrosine kinase was found to be -58.585 ± 0.327 kJ/mol and with p53 it was -35.910 ± 0.335 kJ/mol. Next, cytotoxicity of the Prima-1MET was evaluated using multiple cancer cell lines and the IC50 value were ranging between 4.5 and 30 μM. The cell death was identified by apoptosis assay. Further, the p53 and tyrosine kinase expression was monitored using immunofluorescence techniques, it was found Prima-1MET induces the expression of p53 protein and mimics the level of tyrosine kinase oncogenic target. Also, reactive oxygen species (ROS) and membrane potential activity of Prima-1MET was evaluated by using a lung cancer cell line. A significant decrease in intracellular ROS was observed and resulted in disruption of mitochondrial transmembrane potential. This study uncovers the underlying mechanism of Prima-1MET and could be helpful to design further leads against lung cancers.Communicated by Ramaswamy H. Sarma.

Nonsynonymous mutations in VEGF receptor binding domain alter the efficacy of bevacizumab treatment

Vascular endothelial growth factor (VEGF) mediated angiogenesis is crucial for tumor progression. Isoforms of VEGF bind to different VEGF receptors (VEGFRs) to initiate angiogenesis specific cellular signaling. Inhibitors that target both the receptors and ligands are in clinical use to impede angiogenesis. Bevacizumab, a monoclonal antibody (mAb) approved by the Food and Drug Administration (FDA), binds in the VEGF receptor binding domain (RBD) of all soluble isoforms of VEGF and inhibits the VEGF-VEGFR interaction. Bevacizumab is also used in combination with other chemotherapeutic agents for a better therapeutic outcome. Understanding the intricate polymorphic character of VEGFA gene and the influence of missense or nonsynonymous mutations in the form of nonsynonymous polymorphisms (nsSNPs) on RBD of VEGF may aid in increasing the efficacy of this drug. This study has identified 18 potential nsSNPs in VEGFA gene that affect the VEGF RBD structure and alter its binding pattern to bevacizumab. The mutated RBDs, modeled using trRosetta, in addition to the changed pattern of secondary structure, post translational modification and stability compared to the wild type, have shown contrasting binding affinity and molecular interaction pattern with bevacizumab. Molecular docking analysis by ClusPro and visualization using PyMol and PDBsum tools have detected 17 nsSNPs with decreased binding affinity to bevacizumab and therefore may impact the treatment efficacy. Whereas VEGF RBD expressed due to rs1267535717 (R229H) nsSNP of VEGFA has increased affinity to the mAb. This study suggests that genetic characterization of VEGFA before bevacizumab mediated cancer treatment is essential in predicting the appropriate efficacy of the drug, as the treatment efficiency may vary at individual level.

An exploration of the binding prediction of anatoxin-a and atropine to acetylcholinesterase enzyme using multi-level computer simulations

Acetylcholinesterase (AChE) is crucial for the breakdown of acetylcholine to acetate and choline, while the inhibition of AChE by anatoxin-a (ATX-a) results in severe health complications. This study explores the structural characteristics of ATX-a and its interactions with AChE, comparing to the reference molecule atropine for binding mechanisms. Molecular docking simulations reveal strong binding affinity of both ATX-a and atropine to AChE, interacting effectively with specific amino acids in the binding site as potential inhibitors. Quantitative assessment using the MM-PBSA method demonstrates a significantly negative binding free energy of -81.659 kJ mol-1for ATX-a, indicating robust binding, while atropine exhibits a stronger binding affinity with a free energy of -127.565 kJ mol-1. Umbrella sampling calculates the ΔGbindvalues to evaluate binding free energies, showing a favorable ΔGbindof -36.432 kJ mol-1for ATX-a and a slightly lower value of -30.12 kJ mol-1for atropine. This study reveals the dual functionality of ATX-a, acting as both a nicotinic acetylcholine receptor agonist and an AChE inhibitor. Remarkably, stable complexes form between ATX-a and atropine with AChE at its active site, exhibiting remarkable binding free energies. These findings provide valuable insights into the potential use of ATX-a and atropine as promising candidates for modulating AChE activity.

An exploration of binding of Hesperidin, Rutin, and Thymoquinone to acetylcholinesterase enzyme using multi-level computational approaches

Alzheimer's disease, an intricate neurological disorder, is impacting an ever-increasing number of individuals globally, particularly among the aging population. For several decades phytochemicals were used as Ayurveda to treat both communicable and non-communicable diseases. Acetylcholinesterase (AChE) is a widely chosen therapeutic target for the development of early prevention and effective management of neurodegenerative diseases. The primary objective of the present study was to investigate the binding potential between Rutin Thymoquinone, Hesperidin and the FDA-approved drug Donepezil with AChE. Additionally, a comparative analysis was conducted. These phytochemicals were docked with the binding site of the AChE experimental complex. The molecular dockings demonstrated that the Hesperidinh showed a better binding affinity of -22.0631 kcal/mol. The ADME/T investigations revealed that the selected phytochemicals are non-toxic and drug-like candidates. Molecular dynamics simulations were implemented to determine the conformational changes of Rutin, hesperidin, Thymoquinone, and Donepezil complexed with AChE. Hesperidin and Donepezil were more stable than Rutin, Thymoquinone complexed with AChE. Next, essential dynamics and defining the secondary structure of protein were to determine the conformational changes in AChE complexed with selected phytochemicals during simulations. Overall, the MD Simulations demonstrated that all complexes in this study achieved stability until 100 ns of the simulation period was performed thrice. The structural analysis of AChE was done using multiple search engines to explore the molecular functions, biological processes, and pathways in which AChE proteins are involved and to identify potential drug targets for various diseases. This present study concludes that Hesperidin was found to be a more potent AChE inhibitors than Rutin, and further experiments are required to determine the effectivity of Hesperidin against neurodegenerative diseases.Communicated by Ramaswamy H. Sarma.

Molecular modeling and simulations of some antiviral drugs, benzylisoquinoline alkaloid, and coumarin molecules to investigate the effects on Mpro main viral protease inhibition

Background

SARS-CoV-2 is a deadly viral disease and uncounted deaths occurs since its first appearance in the year 2019. The antiviral drugs, benzylisoquinoline alkaloids, and coumarin molecules were searched using different online engines for drug repurposing with SARS-CoV-2 and to investigate the effects on main viral protease (Mpro) upon their bindings.

Methods

A database composed of antiviral drugs, benzylisoquinoline alkaloids, and Coumarin molecules was screened through a molecular docking strategy to uncover the interactions of collected molecules with SARS-CoV-2 Mpro. Further, molecular dynamics simulations (MDS) were implemented for 100 ns to calculate the stability of the best complexed molecular scaffold with Mpro. The conformations of the simulated complexes were investigated by using principal component analysis (PCA) and Gibbs energy landscape (FEL) and DSSP together. Next, free binding energy (ΔG_bind) was calculated using the mmpbsa method.

Results

Molecular docking simulations demonstrate 17 molecules exhibited better binding affinity out of 99 molecules present in the database with the viral protease Mpro, followed ADMET properties and were documented. The Coumarin-EM04 molecular scaffold exhibited interactions with catalytical dyad HIS41, CYS145, and neighboring amino acids SER165 and GLN189 in the catalytical site. The crucial factor RMSD was calculated to determine the orientations of Coumarin-EM04. The Coumarin-EM04 complexed with Mpro was found stable in the binding site during MDS. Furthermore, the free energy binding ΔG_bind of Coumarin-EM04 was found to be −187.471 ± 2.230 kJ/mol, and for Remdesivir ΔG_bind was −171.926 ± 2.237 kJ/mol with SARS-CoV-2 Mpro^.

Conclusion

In this study, we identify potent molecules that exhibit interactions with catalytical dyad HIS41 and CYS145 amino acids and unravel Coumarin-EM04 exhibited ΔG_bind higher than Remdesivir against Mpro and thus may serve better antiviral agent against SARS-CoV-2.

Identification of potent EGFR-TKD inhibitors from NPACT database through combined computational approaches

Cancer is the world's second leading cause of death, and there are no approved herbal therapies. The epidermal growth factor receptor tyrosine kinase (EGFR-TK) receptor is a transmembrane protein with eight domains that is found in almost every cancer type and plays an important role in abnormal cell cellular function and causes malignant outcomes. The current study aimed to virtually screen phytochemicals from the NPACT database against EGFR-TKD and also to identify potential inhibitors of this transmembrane protein among plant candidates for anticancer drug development. The docking scores of the chosen phytochemicals were compared with the control (erlotinib). Kurarinone, (2S)-2-methoxykurarnione, and Sophoraflavanone-G exhibited a stronger binding affinity of -18.102 kcal/mol, -14.243 kcal/mol, and -13.759 kcal/mol than erlotinib -12.783 kcal/mol. Moreover, several online search engines were used to predict ADME and toxicity. The drug-likeness of selected phytochemicals was higher than the reference (erlotinib). A 100 ns molecular dynamic (MD) simulation was also applied to the docked conformations to examine the stability and molecular mechanics of protein-ligand interactions. Furthermore, the calculated molecular mechanics Poisson Boltzmann surface area energy of (2S)-2-methoxykurarnione was found to be -129.555 ± 0.512 kJ/mol, which approximately corresponds to the free energy of the reference molecule -130.595 ± 0.908 kJ/mol. We identify phytoconstituents present in Sophora flavescens from the NPACT database, providing key insights into tyrosine kinase inhibition and may serve as better chemotherapeutic agents. Experimental validation is required to determine the anti-EGFR potency of the potent lead molecules discussed in this study.Communicated by Ramaswamy H. Sarma.

Molecular docking analysis of mefluhybenamine with lung cancer targets

Lung cancer is the most prevalent type of cancer worldwide, with 2.21 million cases and 1.80 million fatalities in 2020. The main factor influencing lung cancer is smoking, and the most common form of lung cancer, non-small cell lung cancer (NSCLC), accounts for around 80% of instances compared to small cell carcinoma, and about 75% of patients are already in an advanced stage when they are detected. Despite significant early detection and therapy improvements, the five-year survival rate for NSCLC is not encouraging. Therefore, it is essential to look into the molecular origins of non-small cell lung cancer to develop more effective therapeutic strategies-the binding affinities and energy landscape with the proteins. Cyclin Dependent kinase 2 (CDK2) and Insulin-like Growth Factor 1 Receptor (IGF1) were more substantial and sustained in lung cancer that was chosen as the two primary target proteins in this. We screened the entire Drug Bank-prepared library of 1,55,888 compounds and found (2R,3R)-7-(Methylsulfonyl)-3-(2,4,5-trifluorophenyl) -1,2,3,4-tetrahydropyrido[1,2-a] benzimidazol-2-aminium (Mefluhybenamine) to be a significant inhibitor. Mefluhybenamine showed strong hydrogen bonding and other bonding topologies, such as van der Waals force, in its high docking scores of -6.168 Kcal/mol and -5.26 Kcal/mol, and ADMET results showed excellent bioavailability, remarkable solubility, no side effects, and toxicity. The molecular dynamicsimulation confirmed the compound's stability and interaction pattern for 100 ns in an SPC water medium with the slightest deviation and fluctuation. Data shows that Mefluhybenamine is a potential candidate. However, validation of the compound is essential.