Geraniol and Citral as potential therapeutic agents targeting the HSP90 activity: An in silico and experimental approach

Mechanistic Regulation of Epidermal Growth Factor and Hormonal Receptors by Kinase Inhibitors and Organofluorines in Breast Cancer Therapy

Differential expression patterns of growth factor (EGFR, HER-2) and hormonal (ER, PR) receptors in breast cancer (BC) remain crucial for evaluating and tailoring therapeutic interventions. This study investigates differential expression profiles of hormonal and growth factor receptors in BC patients and across age groups, major subclasses, disease stages and tumor histology and survival rates, the efficacy of emerging clinical trial drugs (Dabrafenib and Palbociclib) and elucidating their molecular interaction mechanisms for efficient therapeutic strategies. Gene and protein expression analysis in the normal vs BC and across age groups and major subclasses reveals divergent patterns as EGFR and HER-2 levels are reduced in tumors versus normal tissue, while ER and PR levels are higher, particularly in luminal subtypes. However, there was no significant difference in survival rates among high and low/medium expression levels of EGFR and PR receptors. Conversely, patients with high HER-2 and ER expression exhibited poorer survival rates compared to low or medium expression levels. The in vitro findings indicate that Dabrafenib exhibits greater effectiveness than Palbociclib in suppressing various BC cells such as MCF-7 (Luminal), MDA-MB-231 (Triple-Negative), SKBR-3 (HER-2 + ) proliferation, promoting cell death, (IC50 of Dab < Pal) at 24 and 48 h, ROS production, and reduced ER and PR, elevated HER-2 with no change in EGFR expression. Molecular simulation studies revealed Dabrafenib's thermodynamically stable interactions (ΔG), tighter binding, and less structural deviation in the order EGFR > HER-2 > ER > PR as compared to Palbociclib (HER-2 > ER > PR = EGFR). These results indicate that Dabrafenib, compared to Palbociclib, more effectively regulates breast cancer cell proliferation through specific interactions with hormonal and growth factor receptors towards a repurposing approach.

Role of HSP90 in Type 2 Diabetes Mellitus and Its Association with Liver Diseases

Non-alcoholic fatty acid liver disease (NAFLD), non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) are the fatal liver diseases which encompass a spectrum of disease severity associated with increased risk of type 2 diabetes mellitus (T2DM), a metabolic disorder. Heat shock proteins serve as markers in early prognosis and diagnosis of early stages of liver diseases associated with metabolic disorder. This review aims to comprehensively investigate the significance of HSP90 isoforms in T2DM and liver diseases. Additionally, we explore the collective knowledge on plant-based drug compounds that regulate HSP90 isoform targets, highlighting their potential in treating T2DM-associated liver diseases. Furthermore, this review focuses on the computational systems' biology and next-generation sequencing technology approaches that are used to unravel the potential medicine for the treatment of pleiotropy of these 2 diseases and to further elucidate the mechanism.

Target Enzymes of Origanum majorana and Rosmarinus officinalis Essential Oils in Black Cutworm (Agrotis ipsilon): In Vitro and In Silico Studies

In this study, in vitro and in silico approaches were employed to assess the toxicity of marjoram (Origanum majorana) and rosemary (Rosmarinus officinalis) essential oils (EOs) to A. ipsilon larvae. The study determined the activities of ATPases in the larvae after treatment with the LC20 and LC70 of each EO. α-esterase and glutathione-S-transferase (GST) activities were also determined after treatment with LC10 and LC30 of each EO. Furthermore, molecular docking was employed to determine the binding affinity of terpinene-4-ol and α-pinene, the major constituents of O. majorana, and R. officinalis EOs, respectively, compared to the co-crystallized ligand of α-esterase, diethyl hydrogen phosphate (DPF). Toxicity assays revealed that O. majorana EO was more toxic than R. officinalis EO to the A. ipsilon larvae at 96 h post-treatment. However, the LC20 and LC70 of the latter significantly inhibited the activity of the Na+-K+ pump at almost all intervals. The same concentrations significantly inhibited the Mg2+/Ca2+-ATPase and Ca2+ pump at 96 h post-treatment. In contrast, O. majorana EO showed a variable effect on the Na+-K+ pump across different time intervals. On the other hand, LC10 and LC30 of both EOs showed varied effects on α-esterase and GST over time. Molecular docking revealed energy scores of -4.51 and -4.29 kcal/mol for terpinene-4-ol and α-pinene, respectively, compared to a score of -4.67 for PDF. Our study demonstrated the toxicity of the tested EOs to A. ipsilon, suggesting their potential efficacy as insecticides.

Essential Oils: Chemistry and Pharmacological Activities-Part II

The importance of essential oils and their components in the industrial sector is attributed to their chemical characteristics and their application in the development of products in the areas of cosmetology, food, and pharmaceuticals. However, the pharmacological properties of this class of natural products have been extensively investigated and indicate their applicability for obtaining new drugs. Therefore, this review discusses the use of these oils as starting materials to synthesize more complex molecules and products with greater commercial value and clinic potential. Furthermore, the antiulcer, cardiovascular, and antidiabetic mechanisms of action are discussed. The main mechanistic aspects of the chemopreventive properties of oils against cancer are also presented. The data highlight essential oils and their derivatives as a strategic chemical group in the search for effective therapeutic agents against various diseases.

Multi-target therapeutic modulation with natural compounds towards DNA repair MRN-checkpoint sensor genes (MRN-CSGs) and oncogenic miRNAs in breast cancer patients: a Clinico-Informatic study

Breast cancer, more prevalent in women, often arises due to abnormalities in the MRN-checkpoint sensor genes (MRN-CSG), responsible for DNA damage detection and repair. Abnormality in this complex is due to the suppression of various effectors such as siRNAs, miRNAs, and transcriptional factors responsible for breast tumor progression. This study analyzed breast tumor samples (n = 60) and identified four common miRNAs (miR-1-3p, miR-210-3p, miR-16-5p, miR-34a-5p) out of 12, exploring their interactions with MRN-CSG. The 3D structures of these miRNA-MRN-CSG complexes displayed strong thermodynamic stability. Screening 7711 natural compounds resulted in two natural compounds (F0870-0001 and F0922-0471) with the lowest ligand binding energies (ΔG = -8.4 to-11.6 kcal/mol), targeting two common miRNAs. Docking results showed that one natural compound (PubChem id-5 281 614) bound to all MRN-CSG components (ΔG = -6.2 to -7.3 kcal/mol), while F6782-0723 bound only to RAD50 and NBN. These compounds exhibited minimal dissociation constants (Kd and Ki) and thermodynamically stable minimum free energy (MMGBSA) values. Molecular dynamics simulations indicated highly stable natural compound-MRN-CSG complexes, with consistent RMSD, RMSF, and strong residual correlation. These top-selected compounds displayed robust intermolecular H-bonding, low carcinogenicity, low toxicity, and drug-like properties. Consequently, these compounds hold promise for regulating miRNA and MRN-CSG DNA repair mechanisms in breast cancer therapy. Insight Box: This study investigated breast tumor samples (n = 60) and identified four miRNAs (miR-1-3p, miR-210-3p, miR-16-5p, miR-34a-5p) that interact with MRN-checkpoint sensor genes (MRN-CSG), crucial for DNA damage repair. Screening 7711 natural compounds highlighted two compounds (F0870-0001 and F0922-0471) with the lowest binding energies (ΔG = -8.4 to -11.6 kcal/mol), targeting two common miRNAs (miR-1-3p and miR-34a-5p). Another natural compound (PubChem id-5 281 614, ΔG = -6.2 to -7.3 kcal/mol) bound all MRN-CSG components, while F6782-0723 targeted RAD50 and NBN. These compounds showed strong binding stability, favorable MMGBSA values, and minimal dissociation constants. Molecular dynamics simulations confirmed the stability and drug-like properties of these compounds, indicating their potential in breast cancer therapy by modulating miRNA and MRN-CSG DNA repair mechanisms.

Structure and dynamic simulation-based interactions of benzenoids, pyrroles and organooxygen compounds for effective targeting of GPX4 in ischemic stroke

The discovery of a novel drug for ischemic stroke is plagued by expensive and unsuccessful outcomes. FDA-approved drugs could be a viable repurposing strategy for stroke therapy. Emerging evidence suggests the regulating role of Glutathione peroxidase (GPX4) in stroke and attracts as a potential target. To overcome limited therapeutic interventions, a drug repurposing in silico investigation of FDA-approved drugs is proposed for the GPX4 receptor in distinctive species (Homo sapiens and Mus musculus). The GPX4 UniProt wild type ids, that is, P36969 (Homo sapiens), P36970 (Rattus norvegicus) and O70325 (Mus musculus) are Swiss modelled, and resultant templates are 2OBI and 6HN3 for Homo sapiens, and 5L71 for Mus musculus with a sequence identity of ∼88%. Enrichment analysis reveals high sensitivity and ranked actives with ROC and AUC values of 0.59 and 0.61, respectively. Virtual screening at extra precision resulted hit Acarbosum, is similar between 2OBI and 6HN3, demonstrating a multiple-target specificity and Iopromide, targeting 2OBI. MD simulation at 100 ns following trajectory analysis provides RMSD (∼1.2-1.8Å), RMSF (∼1.6-2.7Å), Rgyr (∼15-15.6Å) depicting stabilisation of receptor-ligand complexes. Furthermore, average B-factor value of 2OBI, 6HN3 and 5L71 is 25Å, 24Å and 60Å with a defined resolution of 1.55Å, 1.01Å and 1.80Å, respectively, depicting the thermodynamic stability of the protein structures. The dynamic cross-correlation and principal component analysis of residual fluctuations reveal more positive correlation, high atomic displacements and greater residual clustering of residues from atomic coordinates. Therefore, Acarbosum, an FDA-approved drug, could act as a potential repurposing drug with a multi-target approach translating from preclinical to clinical stages.Communicated by Ramaswamy H. Sarma.

Dual functionality of pyrimidine and flavone in targeting genomic variants of EGFR and ER receptors to influence the differential survival rates in breast cancer patients

Breast cancer ranks as one of the most prevalent forms of cancer and stands as the primary global cause of mortality among women. Overexpression of EGFR and ER receptors or their genomic alterations leads to malignant transformation, disease aggression and is linked to poor patient survival outcomes. The clinical breast cancer patient's genomic expression, survival analysis, and computational drug-targeting approaches were used to identify best-hit phytochemicals for therapeutic purposes. Breast cancer patients have genomic alterations in EGFR (4%, n = 5699) and ER (9%, n = 8461), with the highest proportion being missense mutations. No statistically significant difference was observed in the patient survival rates between the altered and unaltered ER groups, unlike EGFR, with the lowest survival rates in the altered group. Computational screening of natural compound libraries (7711) against each EGFR (3POZ) and ER (3ERT) receptor shortlists the best-hit 3 compounds with minimum docking score (ΔG = -7.9 to -10.8), MMGBSA (-40.16 to -51.91 kcal/mol), strong intermolecular H-bonding, drug-like properties with least kd, and ki. MD simulation studies display stable RMSD, RMSF, and good residual correlation of best-hit common compounds (PubChem ID: 5281672 and 5280863) targeting both EGFR and ER receptors. In vitro, studies revealed that these common drugs exhibited a high anti-proliferative effect on MCF-7 and MDA-MB-231 breast cancer cells, with effective IC50 values (15-40 μM) and lower free energy, kd, and ki (5281672 > 5280863 > 5330286) much affecting HEK-293 non-cancerous cells, indicating the safety profile. The experimental and computational correlation studies suggest that the highly expressed EGFR and ER receptors in breast cancer patients having poor survival rates can be effectively targeted with best-hit common potent drugs with a multi-target therapeutic approach. Insight Box: The findings of this study provide valuable insights into the genomic/proteomic data, breast cancer patient's survival analysis, and EGFR and ER receptor variants structural analysis. The genetic alterations analysis of EGFR and ER/ESR1 in breast cancer patients reveals the high frequency of mutation types, which affect patient's survival rate and targeted therapies. The common best-hit compounds affect the cell survival patterns with effective IC50, drug-like properties having lower equilibrium and dissociation constants demonstrating the anti-proliferative effects. This work integrates altered receptor structural analysis, molecular interaction-based simulations, and ADMET properties to illuminate the identified best hits phytochemicals potential efficacy targeting both EGFR and ER receptors, demonstrating a multi-target therapeutic approach.

Terpenoid analogues as putative therapeutic agents towards glutathione peroxidase (GPX4) in neurodegenerative disorders: a dynamic computational approach

Carvacrol, a monoterpenoid phenolic phytochemical, a potent antioxidant, and neuroprotective agent is an emerging neuroprotective agent for neurodegenerative diseases (NDDs). Considering scarce information on carvacrol analogues, we hypothesized an in silico investigation emphasizing their preferential binding towards glutathione peroxidase (GPX4) as a target across different species for evaluating through preclinical to clinical studies (2OBI and 6HN3 for Homo sapiens; 5L71 for Mus musculus). Enrichment analysis suggests that ROC (0.59) and AUC (0.61) values have higher sensitivity and significant number of ranked actives. Extra Precision (XP) of 59 compounds was conducted, followed by molecular dynamics and trajectory analysis. Top three hits were chosen for each target i.e., 101203408, 101419546, 59294 (2OBI); 101419546, 100938426, and 28092 (6HN3); and 12059, 52434, 335 (5L71) implying high docking score. 101419546 is common among 2OBI and 6HN3 targets, indicating a multi-target approach. Trajectory analysis of hits provides a permissible range of RMSD, RMSF, Rgyr (∼1.3-2 Å, ∼0.84-1.09 Å, ∼15.05-15.29 Å). Overlapped dynamically simulated 3D-structures of Apo and complexes display significant conformational changes in RMSD of the complexes (∼1.40-2.0 Å) in contrast to Apo (∼1.3-1.8 Å), suggesting structural stability and compactness of the complexes within 45-90 ns. DCCM and PCA analysis shows positive correlation and residual clustering among residues of complexes. The establishment of firm H-bonding, favorable aromaticity and ADMET profile makes them promising drugs across various GPX4 targets among the species. Studies considering the targets across different species aids in anticipating and discovering a common compound for future NDDs therapeutics from bench to bedside.Communicated by Ramaswamy H. Sarma.

Food Ingredients Derived from Lemongrass Byproduct Hydrodistillation: Essential Oil, Hydrolate, and Decoction

Essential oil (EO), hydrolate, and nondistilled aqueous phase (decoction) obtained from the hydrodistillation of lemongrass byproducts were studied in terms of their potential as food ingredients under a circular economy. The EO (0.21%, dry weight basis) was composed mainly of monoterpenoids (61%), the majority being citral (1.09 g/kg). The minimal inhibitory concentrations (MIC) of lemongrass EO against Escherichia coli, Salmonella enterica, and Staphylococcus aureus, were 617, 1550, and 250 μg/mL, respectively. This effect was dependent on the citral content. Particularly for Gram-negative bacteria, a synergism between citral and the remaining EO compounds enhanced the antimicrobial activity. The polymeric material obtained from the nondistilled aqueous phase was composed of phenolic compounds (25% gallic acid equivalents) and carbohydrates (22%), mainly glucose (66 mol%). This polymeric material showed high antioxidant activity due to bound phenolic compounds, allowing its application as a functional dietary fiber ingredient. Matcha green tea formulations were successfully mixed with lemongrass hydrolate containing 0.21% EO (dry weight basis) with 58% of monoterpenoids, being citral at 0.73 g/kg, minimizing matcha astringency with a citrus flavor and extending the product shelf life. This holistic approach to essential oils’ hydrodistillation of Cymbopogon citratus byproducts allows for valorizing of the essential oil, hydrolate, and decoction for use as food ingredients.