Multi-Targeting Bioactive Compounds Extracted from Essential Oils as Kinase Inhibitors

Combination of Chromatographic Analysis and Chemometric Methods with Bioactivity Evaluation of the Antibacterial Properties of Helichrysum italicum Essential Oil

Helichrysum italicum (immortelle) essential oil is one of the most popular essential oils worldwide and it has many beneficial properties, including antimicrobial. However, in this plant, the chemical diversity of the essential oil is very pronounced. The aim of this work was to process the GC-MS results of four samples of H. italicum essential oil of Serbian origin by chemometric tools, and evaluate the antimicrobial activity in vitro and in silico. Overall, 47 compounds were identified, the most abundant were γ-curcumene, α-pinene, and ar-curcumene, followed by α-ylangene, neryl acetate, trans-caryophyllene, italicene, α-selinene, limonene, and italidiones. Although the four samples of H. italicum essential oil used in this study were obtained from different producers in Serbia, they belong to the type of essential oil rich in sesquiterpenes (γ-curcumene and ar-curcumene chemotype). In vitro antimicrobial potential showed that five were sensitive among ten strains of tested microorganisms: Staphylococcus aureus, Listeria monocytogenes, Bacillus cereus, Saccharomyces cerevisiae, and Candida albicans. Therefore, these microorganism models were used further for in silico molecular docking through the mechanism of ATP-ase inhibitory activity. Results showed that among all compounds from H. italicum essential oil, neryl acetate has the highest predicted binding energy. Artificial neural network modeling (ANN) showed that two major compounds γ-curcumene and α-pinene, as well as minor compounds such as trans-β-ocimene, terpinolene, terpinene-4-ol, isoitalicene, italicene, cis-α-bergamotene, trans-α-bergamotene, italidiones, trans-β-farnesene, γ-selinene, β-selinene, α-selinene, and guaiol are responsible for the antimicrobial activity of H. italicum essential oil. The results of this study indicate that H. italicum essential oil samples rich in γ-curcumene, α-pinene, and ar-curcumene cultivated in Serbia (Balkan) have antimicrobial potential both in vitro and in silico. In addition, according to ANN modeling, the proportion of neryl acetate and other compounds detected in these samples has the potential to exhibit antimicrobial activity.

In Silico and In Vitro Investigation of Phytochemicals Against Shrimp AHPND Syndrome Causing PirA/B Toxins of Vibrio parahaemolyticus

In Southeast Asia, the penaeid shrimp aquaculture production faces a new pandemic bacterial disease called acute hepatopancreatic necrosis disease (AHPND). The highly profitable pacific white shrimp, Litopenaeus vannamei, has become a challenging species due to severe lethal infections. Recent research has identified a critical pathogen, Vibrio parahaemolyticus, which caused significant loss in the shrimp industry. The disease pathway involves a virulence plasmid encoding binary protein toxins (PirA/B) that cause cell death. The protein toxins were inherited and conjugatively transferred to other Vibrio species through a post-segregational killing system. In this study, "in silico" (Glide, 2021) analysis identified four phytocompounds as myricetin (Myr), ( +)-taxifolin (TF), (-)-epigallocatechin gallate (EGCG), and strychnine (STN) which could be most effective against both the toxins concerning its docking score and affinity. The interactions of complexes and the critical amino acids involved in docking were analyzed using the Discovery Studio (version 2016). Molecular dynamic studies showed lower root mean square deviations (RMSD) and improved stabilization of ( +)-taxifolin (TF) and (-)-epigallocatechin-3-gallate (EGCG) against both the protein toxins. The antibacterial potential of all four selected compounds had tested against pathogenic strains of V. parahaemolyticus through minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The best MBC results were observed at concentrations of 1 mg/mL for EGCG and 1.25 mg/mL for TF. Moreover, the complete reduction of viable cell counts in the in vitro bactericidal activity had recorded after 24 h of incubation.

Uncovering Novel Capsaicin Inhibitory Activity towards Human Carbonic Anhydrase Isoforms IX and XII by Combining In Silico and In Vitro Studies

Hot pepper (Capsicum annuum) represents one of the most widespread functional foods of the Mediterranean diet, and is associated with a reduced risk of developing cardiovascular disease, cancer, and mental disorders. In particular, its bioactive spicy molecules, named Capsaicinoids, exhibit polypharmacological properties. Among them, Capsaicin (trans-8-methyl-N-vanillyl-6-nonenamide) is the most studied and reported in variegated scientific contributions for its beneficial effects, often linked to mechanisms of action unrelated to the activation of Transient Receptor Potential Vanilloid 1 (TRPV1). In this study, we present the application of in silico methods to Capsaicin for evaluating its inhibitory activity against the tumor-associated human (h) expressed CA IX and XII. In vitro assays confirmed Capsaicin inhibitory activity towards the most relevant tumor-related hCA isoforms. In particular, the hCAs IX and XII showed an experimental K_I value of 0.28 μM and 0.064 μM, respectively. Then, an A549 model of non-small cell lung cancer, typically characterized by an elevated expression of hCA IX and XII, was employed to test the inhibitory effects of Capsaicin in vitro under both normoxic and hypoxic conditions. Finally, the migration assay revealed that Capsaicin [10 µM] inhibits cells from moving in the A549 cells model.

Identification of SET/EED dual binders as innovative PRC2 inhibitors

Background: The inhibition of PRC2, implicated in the pathogenesis of several tumors, can be a useful therapeutic strategy for cancer treatment. In the literature, two types of PRC2 modulators are reported: competitive inhibitors of S-adenosyl methionine binding to the catalytic subunit EZH2; and allosteric ligands that prevent the interaction of the trimethylated H3K27 lysine in histone 3 to the EED subunit. The lack of dual EZH2/EED modulators drove us to search for compounds capable of recognizing both domains. Materials & methods: This goal was pursued by combining pharmacophore- and docking-based virtual screening of the Multi-Target Ligand Chemotheca database. Prediction tools for absorption, distribution, metabolism and excretion and pan-assay interference compounds were also applied. Results: Finally, five 1,2,3-triazole derivatives were identified as promising dual EZH2/EED modulators. Conclusion: Our multistage screening protocol highlighted the great potential of Chemotheca for identifying polypharmacological agents.

In Silico Food-Drug Interaction: A Case Study of Eluxadoline and Fatty Meal

Food-drug interaction is an infrequently considered aspect in clinical practice. Usually, drugs are taken together with meals and what follows may adversely affect pharmacokinetic and pharmacodynamic properties, and hence, the therapeutic effects. In this study, a computational protocol was proposed to explain the different assimilations of two µ-receptors agonists, eluxadoline and loperamide, with a peculiar pharmacokinetic profile. Compared to loperamide, eluxadoline is absorbed less after the intake of a fatty meal, and the LogP values do not explain this event. Firstly, keeping in mind the different pH in the intestinal tract, the protonation states of both compounds were calculated. Then, all structures were subjected to a conformational search by using MonteCarlo and Molecular Dynamics methods, with solvation terms mimicking the water and weak polar solvent (octanol). Both computational results showed that eluxadoline has less conformational freedom in octanol, unlike loperamide, which exhibits constant behavior in both solvents. Therefore, we hypothesize that fatty meal causes the "closure" of the eluxadoline molecule to prevent the exposure of the polar groups and their interaction with water, necessary for the drug absorption. Based on our results, this work could be a reasonable "case study", useful for future investigation of the drug pharmacokinetic profile.

Analysis of Biological Screening Compounds with Single- or Multi-Target Activity via Diagnostic Machine Learning

Predicting compounds with single- and multi-target activity and exploring origins of compound specificity and promiscuity is of high interest for chemical biology and drug discovery. We present a large-scale analysis of compound promiscuity including two major components. First, high-confidence datasets of compounds with multi- and corresponding single-target activity were extracted from biological screening data. Positive and negative assay results were taken into account and data completeness was ensured. Second, these datasets were investigated using diagnostic machine learning to systematically distinguish between compounds with multi- and single-target activity. Models built on the basis of chemical structure consistently produced meaningful predictions. These findings provided evidence for the presence of structural features differentiating promiscuous and non-promiscuous compounds. Machine learning under varying conditions using modified datasets revealed a strong influence of nearest neighbor relationship on the predictions. Many multi-target compounds were found to be more similar to other multi-target compounds than single-target compounds and vice versa, which resulted in consistently accurate predictions. The results of our study confirm the presence of structural relationships that differentiate promiscuous and non-promiscuous compounds.

Natural Products Extracted from Fungal Species as New Potential Anti-Cancer Drugs: A Structure-Based Drug Repurposing Approach Targeting HDAC7

Mushrooms can be considered a valuable source of natural bioactive compounds with potential polypharmacological effects due to their proven antimicrobial, antiviral, antitumor, and antioxidant activities. In order to identify new potential anticancer compounds, an in-house chemical database of molecules extracted from both edible and non-edible fungal species was employed in a virtual screening against the isoform 7 of the Histone deacetylase (HDAC). This target is known to be implicated in different cancer processes, and in particular in both breast and ovarian tumors. In this work, we proposed the ibotenic acid as lead compound for the development of novel HDAC7 inhibitors, due to its antiproliferative activity in human breast cancer cells (MCF-7). These promising results represent the starting point for the discovery and the optimization of new HDAC7 inhibitors and highlight the interesting opportunity to apply the "drug repositioning" paradigm also to natural compounds deriving from mushrooms.

In Silico Identification and Biological Evaluation of Antioxidant Food Components Endowed with IX and XII hCA Inhibition

The tumor-associated isoenzymes hCA IX and hCA XII catalyze the hydration of carbon dioxide to bicarbonate and protons. These isoforms are highly overexpressed in many types of cancer, where they contribute to the acidification of the tumor environment, promoting tumor cell invasion and metastasis. In this work, in order to identify novel dual hCA IX and XII inhibitors, virtual screening techniques and biological assays were combined. A structure-based virtual screening towards hCA IX and XII was performed using a database of approximately 26,000 natural compounds. The best shared hits were submitted to a thermodynamic analysis and three promising best hits were identified and evaluated in terms of their hCA IX and XII inhibitor activity. In vitro biological assays were in line with the theoretical studies and revealed that syringin, lithospermic acid, and (-)-dehydrodiconiferyl alcohol behave as good hCA IX and hCA XII dual inhibitors.

Inside Perspective of the Synthetic and Computational Toolbox of JAK Inhibitors: Recent Updates

The mechanisms of inflammation and cancer are intertwined by complex networks of signaling pathways. Dysregulations in the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway underlie several pathogenic conditions related to chronic inflammatory states, autoimmune diseases and cancer. Historically, the potential application of JAK inhibition has been thoroughly explored, thus triggering an escalation of favorable results in this field. So far, five JAK inhibitors have been approved by the Food and Drug Administration (FDA) for the treatment of different diseases. Considering the complexity of JAK-depending processes and their involvement in multiple disorders, JAK inhibitors are the perfect candidates for drug repurposing and for the assessment of multitarget strategies. Herein we reviewed the recent progress concerning JAK inhibition, including the innovations provided by the release of JAKs crystal structures and the improvement of synthetic strategies aimed to simplify of the industrial scale-up.