Identification of potential Akt activators: a ligand and structure-based computational approach

Comparative anti-oxidant and anti-inflammatory study of diverse honey types of Kashmir valley through In Vitro, analytical chemistry and computational approach

Diverse factors including geographical and floral origin have marked impact on honey parameters. These factors in the long run influence the different activities exerted by honey. Herein, we performed the novel comparative study of five different honey types of Kashmir valley differing in floral origin apart from latitude, longitude and altitude. Following the rigorous comparison of their antioxidant and anti-inflammatory activity through In vitro study, the most promising honey was screened for various molecules using high-resolution liquid chromatography mass spectrometry (HR-LCMS) approach. Moreover, the identified molecules were docked against the inflammation implicated molecular targets namely histone deacetylase (HDAC)-3 and cyclooxygenase-2 (COX-2). Eventually, the binding free energy assessment was performed using conventional and thermal molecular mechanics with generalized Born surface area (MM-GBSA). The maximum binding affinity demonstrating molecule was evaluated for stability and compatibility with COX-2 by making the use of extended molecular dynamics simulation method. This study proved Robinia pseudoacacia honey has the maximum potential for alleviating the free radicals and inflammation. Further, the luteolin and genistein confirmed through HR-LCMS evinced the highest propensity of binding towards COX-2 and HDAC3 respectively.

Target Validation Studies of PS48, a PDK-1 Allosteric Agonist, for the Treatment of Alzheimer's Disease Phenotype in APP/PS1 Transgenic Mice

The Alzheimer's disease (AD)-affected brain is known to be deficient in the utilization of glucose, its main energy substrate, and systemic diabetes is a significant risk factor for AD. In the course of biochemical and molecular investigations into this puzzling relationship, it has been shown that resistance to insulin action is a prominent feature of early stages of AD in the brain, thereby contributing to an energy failure state and a decline in synaptic function. In one AD-like cellular model, we found that β-amyloid (Aβ) accumulation inhibited insulin signaling and cell viability through an alteration of the PI3K/PDK-1/Akt signal pathway, an effect overcome by mTORC2 stimulation. A PDK-1 allosteric agonist, PS48, as well as newly synthesized analogs, were also found to reverse the metabolic defects caused by intracellular Aβ42 accumulation. In vivo, we previously showed that oral dosing of PS48 significantly improves learning and memory in APP/PS1 transgenic mice. Herein, we present evidence using unbiased immunohistological quantification and Western blot analyses demonstrating that ingested PS48 crosses into brain tissue where it targeted Akt and GSK3-β activities. Beneficial effects on neuronal number and Tau phosphorylation were found. Not unexpectedly, Aβ levels remained unchanged. These results support a path toward a future therapeutic trial of this untested strategy and agent in humans.

HDAC3_VS_assistant: cheminformatics-driven discovery of histone deacetylase 3 inhibitors

Histone deacetylase 3 (HDAC3) inhibitors keep significant therapeutic promise for treating oncological, neurodegenerative, and inflammatory diseases. In this work, we developed robust QSAR regression models for HDAC3 inhibitory activity and acute toxicity (LD50, intravenous administration in mice). A total of 1751 compounds were curated for HDAC3 activity, and 15,068 for toxicity. The models employed molecular descriptors such as Morgan fingerprints, MACCS-166 keys, and Klekota-Roth, PubChem fingerprints integrated with machine learning algorithms including random forest, gradient boosting regressor, and support vector machine. The HDAC3 QSAR models achieved Q2test values of up to 0.76 and RMSE values as low as 0.58, while toxicity models attained Q2test values of 0.63 and RMSE values down to 0.41, with applicability domain (AD) coverage exceeding 68%. Internal validation by fivefold cross-validation (Q2cv = 0.70 for HDAC3 and 0.60 for toxicity) and y-randomization confirmed model reliability. Shapley additive explanation (SHAP) was also used to explain the influence of modeling features on model prediction results. The most predictive QSAR models are integrated into the developed HDAC3_VS_assistant application, which is freely available at https://hdac3-vs-assistant-v2.streamlit.app/ . Virtual screening conducted using the HDAC3_VS_assistant web application allowed us to reveal a number of potential inhibitors, and the nature of their bonds with the active HDAC3 site was additionally investigated by molecular docking.

Identification of phytomolecules as isoform and mutation specific PI3K-α inhibitor for protection against breast cancer using e-pharmacophore modeling and molecular dynamics simulations

PI3K-α mutation plays a critical role in cancer development, notably in breast cancer, particularly within HR + /HER2- subtypes. These mutations drive tumor growth and survival by activating the PI3K/AKT/mTOR pathway, which is essential for cell proliferation and survival. Our research aimed to identify natural compounds that can inhibit mutant and specific isoforms of PI3K-α to prevent tumor progression. e-Pharmacophore model was generated using Receptor-Ligand complex using the Inavolisib drug (PDB:8EXV) and phase screening was performed using the Molport database of natural compounds. Through molecular docking studies we identified seven promising compounds for further molecular dynamics simulations. Among these, three compounds-STOCK1N-85097, STOCK1N-85998, and STOCK1N-86060-showed significant stability and interaction with PI3K-α. These compounds demonstrated favorable results in several parameters, including RMSD, RMSF, Rg, SASA, PCA, FEL, and total energy evaluations. Therefore, these compounds are projected to function as PI3K-α inhibitors and because of its natural origin it can possess fewer side effects than the conventional medicine, which should be validated by proper in vivo and in vitro models.

Effect of bioactive compounds of Mucuna pruriens on proteins of Wnt/β catenin pathway in pulmonary hypertension by in silico approach

Modulation of the Wnt/β-catenin signaling pathway may aid in discovering new medications for the effective management of pulmonary artery hypertension (PAH). Given the therapeutic potential of Mucuna pruriens in several diseases, the present study aimed to analyze interactions of different bioactive compounds of Mucuna pruriens plant seeds with Wnt/β-catenin pathway targeting its various components like Wnt 3a, Frizzled 1, LRP 5/6, β-catenin, Disheveled, cyclin D1 by in silico analysis. The proposed work is based on computational analysis including ADME/T properties, by a Swiss ADME server. To understand the molecular interaction pattern Schrodinger, suit a stand-alone software was used to predict the interaction of bioactive molecules of Mucuna Pruriens with target proteins that are involved in Wnt/ β catenin pathway. Further, the simulation pattern of the top docked complex was subjected to MD simulation in Desmond for 100 ns. Bioactive molecules from Mucuna Pruriens have drug-like properties and minimal toxicity. Further, the docking study revealed that among the nine compounds, three compounds (Gallic acid, L-dopa, and β-sitosterol) showed good interaction with target proteins. As gallic acid showed good interaction with all target proteins, the docked complex was subjected to MD simulation which was stable throughout the simulation time in terms of RMSD and RMSF. These findings suggest that the bioactive molecules of Mucuna pruriens compounds have potential therapeutic value in the treatment of pulmonary vascular disease. Further, in vivo and in vitro studies are necessary to determine its efficacy and validate its pharmacological activity conclusively.

3D-QSAR, Scaffold Hopping, Virtual Screening, and Molecular Dynamics Simulations of Pyridin-2-one as mIDH1 Inhibitors

Isocitrate dehydrogenase 1 (IDH1) is a necessary enzyme for cellular respiration in the tricarboxylic acid cycle. Mutant isocitrate dehydrogenase 1 (mIDH1) has been detected overexpressed in a variety of cancers. mIDH1 inhibitor ivosidenib (AG-120) was only approved by the Food and Drug Administration (FDA) for marketing, nevertheless, a range of resistance has been frequently reported. In this study, several mIDH1 inhibitors with the common backbone pyridin-2-one were explored using the three-dimensional structure-activity relationship (3D-QSAR), scaffold hopping, absorption, distribution, metabolism, excretion (ADME) prediction, and molecular dynamics (MD) simulations. Comparative molecular field analysis (CoMFA, R2 = 0.980, Q2 = 0.765) and comparative molecular similarity index analysis (CoMSIA, R2 = 0.997, Q2 = 0.770) were used to build 3D-QSAR models, which yielded notably decent predictive ability. A series of novel structures was designed through scaffold hopping. The predicted pIC50 values of C3, C6, and C9 were higher in the model of 3D-QSAR. Additionally, MD simulations culminated in the identification of potent mIDH1 inhibitors, exhibiting strong binding interactions, while the analyzed parameters were free energy landscape (FEL), radius of gyration (Rg), solvent accessible surface area (SASA), and polar surface area (PSA). Binding free energy demonstrated that C2 exhibited the highest binding free energy with IDH1, which was -93.25 ± 5.20 kcal/mol. This research offers theoretical guidance for the rational design of novel mIDH1 inhibitors.

Effects of an Akt-activating peptide obtained from walnut protein degradation on the prevention of memory impairment in mice

Akt acts as a central protein influencing multiple pathologies in neurodegenerative diseases including AD and PD, and using Akt activators is a promising management strategy. The current study characterized the effects of an Akt-activating peptide (Glu-Pro-Glu-Val-Leu-Pro, EPEVLR) obtained from walnut protein degradation on D-gal-induced memory impairment in mice. EPEVLR was obtained by hydrolysis of walnut proteins, identification of peptide sequences, and screening for molecular docking sequentially. The MWM test in mice indicated that the oral administration of EPEVLR (80, 200 and 400 mg per kg per day) significantly (p < 0.05) reversed D-gal-induced memory impairment. WB tests of the mouse hippocampus confirmed that EPEVLR could activate Akt by promoting its phosphorylation. In addition, further characterization (including TEM, ELISA, and immunohistochemistry) related to Akt phosphorylation showed lower Aβ and p-tau levels, as well as more autophagosomes than those in the model group. Moreover, the EPEVLR treatment significantly increased Lactobacillus abundance and reduced Helicobacter abundance in the gut microbiome and caused up-regulation of SCFAs and down-regulation of LPS of serum metabolites. Therefore, EPEVLR ingestion reversed cognitive impairment symptoms, possibly related to the activation of Akt and regulation of the intestinal flora pathway. Consumption of an EPEVLR-containing diet is beneficial for treating cognitive dysfunction.

The Essential Oil from Conyza bonariensis (L.) Cronquist (Asteraceae) Exerts an In Vitro Antimelanoma Effect by Inducing Apoptosis and Modulating the MAPKs, NF-κB, and PKB/AKT Signaling Pathways

The characterization and cytotoxicity of the essential oil from Conyza bonariensis (L.) aerial parts (CBEO) were previously conducted. The major compound was (Z)-2-lachnophyllum ester (EZ), and CBEO exhibited significant ROS-dependent cytotoxicity in the melanoma cell line SK-MEL-28. Herein, we employed the Molegro Virtual Docker v.6.0.1 software to investigate the interactions between the EZ and Mitogen-Activated Protein Kinases (MAPKs), the Nuclear Factor kappa B (NF-κB), and the Protein Kinase B (PKB/AKT). Additionally, in vitro assays were performed in SK-MEL-28 cells to assess the effect of CBEO on the cell cycle, apoptosis, and these signaling pathways by flow cytometry and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay using MAPKs inhibitors. CBEO induced a significant increase in the sub-G1 peak, as well as biochemical and morphological changes characteristic of apoptosis. The in-silico results indicated that EZ interacts with Extracellular Signal-Regulated Kinase 1 (ERK1), c-Jun N-terminal Kinase 1 (JNK1), p38α MAPK, NF-κB, and PKB/AKT. Moreover, CBEO modulated the ERK1/2, JNK, p38 MAPK, NF-κB, and PKB/AKT activities in SK-MEL-28 cells. Furthermore, CBEO's cytotoxicity against SK-MEL-28 cells was significantly altered in the presence of MAPKs inhibitors. These findings support the in vitro antimelanoma effect of CBEO through apoptosis induction, and the modulation of ERK, JNK, p38 MAPK, NF-κB, and PKB/AKT activities.