Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking

Rosemary and neem: an insight into their combined anti-dandruff and anti-hair loss efficacy

Dandruff, a common scalp disorder characterized by flaking dead skin, is often treated with conventional topical products. However, limitations exist due to potential side effects and high costs. Therefore, searching for natural, cost-effective solutions for dandruff and hair loss is crucial. Rosemary herb and neem tree, both cultivated in Egypt, possess well-documented anti-inflammatory properties derived from their rich phenolic phytoconstituents. This study formulated a standardized combined extract of rosemary and neem (RN-E 2:1) into hair gel and leave-in tonic formats. This extract demonstrated superior efficacy against Malassezia furfur (a causative agent of dandruff) and Trichophyton rubrum (associated with scalp disorders) compared to the conventional antifungal agent, ketoconazole. The combined extract (RN-E 2:1) also exhibited potent anti-inflammatory activity. Additionally, the suppression of iNOS expression is considered concentration-dependent. Quality control verified formulation stability, and ex-vivo studies confirmed effective ingredient penetration into the epidermis, the primary site of fungal presence. Remarkably, both formulations outperformed the standard treatment, minoxidil in hair growth trials. These findings highlight the potential of natural extracts for scalp and hair health.

Plasma Concentrations of Rosmarinic Acid in Patients on Antiretroviral Therapy: In Silico Exploration Based on Clinical Data

Rosmarinic acid (RA) is a phenolic compound with antiviral properties, often encountered in dietary supplements and herbal drugs. Data on the pharmacokinetics of RA are lacking in cases of the chronic use of supplements containing this compound, and only limited data on the metabolism and distribution of RA are available. The aim of the study was to investigate the plasma levels of RA after 12 weeks of use and determine potential interactions of RA and selected antiretroviral drugs. Patients infected with human immunodeficiency virus took a supplement containing RA for 12 weeks, after which the RA concentrations in the plasma samples were analyzed. A detailed in silico analysis was conducted in order to elucidate the potential interactions between RA and the drugs efavirenz, darunavir and raltegravir. It was found that RA can be detected in patients' plasma samples, mainly in the form of sulphoglucuronide. The potential interactions are suggested on the level of liver metabolizing enzymes and efflux P-glycoprotein, with RA competing with antiretroviral drugs as a substrate in metabolism and distribution systems. The present study suggests that the simultaneous use of RA and antiretroviral therapy (containing efavirenz, darunavir or raltegravir) may affect the plasma levels of RA after prolonged supplementation.

Validating Interactions of Pathogenic Proteins of Staphylococcus aureus and E. coli with Phytochemicals of Ziziphus jujube and Acacia nilotica

This study focused on the assessment of the antimicrobial resistance of Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) isolated from bovine mastitis milk samples and the revealing anti-mastitis potential of phytocompounds of Ziziphus jujube and Acacia nilotica through molecular docking analysis. The mastitis milk samples were collected from various dairy farms for the isolation of the bacteria (S. aureus and E. coli) and their response to antibiotics. Ethanolic extracts of both plants were prepared. Their antibacterial activity was evaluated, and they were processed for phytochemical analysis after which, molecular docking analysis with pathogenic proteins of the bacteria was carried out. Parametric and non-parametric statistical analyses were performed to reach the conclusions of this study. The findings of the study revealed a higher drug resistance (≥40%) of E. coli against ampicillin, amikacin, and vancomycin, while S. aureus exhibited the highest resistance to ampicillin, erythromycin, and ciprofloxacin. The ethanolic extracts of the Ziziphus jujube and Acacia nilotica plants produced a ZOI between 18 and 23 mm against multidrug-resistant S. aureus and E. coli. Gas chromatography-mass spectrophotometry (GC-MS) was used to explore 15 phytocompounds from Ziziphus jujube and 18 phytocompounds from Acacia nilotica. The molecular docking analysis of 2cyclopenten-1-one,3,4,4 trimethyl and Bis (2ethylhexyl) phthalate of Ziziphus jujube showed a binding affinity of -4.8 kcal/mol and -5.3 kcal/mol and -5.9 kcal/mol and -7.1 kcal/mol against the DNA Gyrase and toxic shock syndrome toxin-1 proteins of S. aureus and E. coli, respectively. The suberic acid monomethyl ester of Acacia nilotica showed a binding affinity of -5.9 kcal/mol and -5 kcal/mol against the outer membrane protein A and Topoisomerase IV protein of E. coli and -5.1 kcal/mol and -5.8 kcal/mol against the toxic shock syndrome toxin-1 and Enterotoxin B proteins of S. aureus. Similarly, 2,2,4-trimethyl-1,3-pentanediol di-iso-butyrate showed a binding affinity of -6.5 kcal/mol and -5.3 kcal/mol against the outer membrane protein A and Topoisomerase IV of E. coli and -5.2 kcal/mol and -5.9 kcal/mol against the toxic shock syndrome toxin-1 and Enterotoxin B proteins of S. aureus, respectively. The study concluded that there was an increasing trend for the antimicrobial resistance of S. aureus and E. coli, while the Ziziphus jujube and Acacia nilotica plant extracts expressed significant affinity to tackle this resistance; hence, this calls for the development of novel evidence-based therapeutics.

More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review

The investigation of intermolecular interactions has become increasingly important in many studies, mainly by combining different analytical approaches to reveal the molecular mechanisms behind specific experimental phenomena. From spectroscopic analysis to sophisticated molecular simulation techniques like molecular docking, molecular dynamics (MD) simulation, and quantum chemical calculations (QCC), the mechanisms of intermolecular interactions are gradually being characterized more clearly and accurately, leading to revolutionary advances. This article aims to review the progression in the main techniques involving intermolecular interactions in food research and the corresponding experimental results. Finally, we discuss the significant impact that cutting-edge molecular simulation technologies may have on the future of conducting deeper exploration. Applications of molecular simulation technology may revolutionize the food research, making it possible to design new future foods with precise nutrition and desired properties.

Production of secondary metabolites using tissue culture-based biotechnological applications

Plants are the sources of many bioactive secondary metabolites which are present in plant organs including leaves, stems, roots, and flowers. Although they provide advantages to the plants in many cases, they are not necessary for metabolisms related to growth, development, and reproduction. They are specific to plant species and are precursor substances, which can be modified for generations of various compounds in different plant species. Secondary metabolites are used in many industries, including dye, food processing and cosmetic industries, and in agricultural control as well as being used as pharmaceutical raw materials by humans. For this reason, the demand is high; therefore, they are needed to be obtained in large volumes and the large productions can be achieved using biotechnological methods in addition to production, being done with classical methods. For this, plant biotechnology can be put in action through using different methods. The most important of these methods include tissue culture and gene transfer. The genetically modified plants are agriculturally more productive and are commercially more effective and are valuable tools for industrial and medical purposes as well as being the sources of many secondary metabolites of therapeutic importance. With plant tissue culture applications, which are also the first step in obtaining transgenic plants with having desirable characteristics, it is possible to produce specific secondary metabolites in large-scale through using whole plants or using specific tissues of these plants in laboratory conditions. Currently, many studies are going on this subject, and some of them receiving attention are found to be taken place in plant biotechnology and having promising applications. In this work, particularly benefits of secondary metabolites, and their productions through tissue culture-based biotechnological applications are discussed using literature with presence of current studies.

Assessment of the Antioxidant and Antimicrobial Potential of Ptychotis verticillata Duby Essential Oil from Eastern Morocco: An In Vitro and In Silico Analysis

Ptychotis verticillata Duby, referred to as Nûnkha in the local language, is a medicinal plant that is native to Morocco. This particular plant is a member of the Apiaceae family and has a longstanding history in traditional medicine and has been utilized for therapeutic purposes by practitioners for generations. The goal of this research is to uncover the phytochemical makeup of the essential oil extracted from P. verticillata, which is indigenous to the Touissite region in Eastern Morocco. The extraction of the essential oil of P. verticillata (PVEO) was accomplished through the use of hydro-distillation via a Clevenger apparatus. The chemical profile of the essential oil was then determined through analysis utilizing gas chromatography–mass spectrometry (GC/MS). The study findings indicated that the essential oil of P. verticillata is composed primarily of Carvacrol (37.05%), D-Limonene (22.97%), γ-Terpinene (15.97%), m-Cymene (12.14%) and Thymol (8.49%). The in vitro antioxidant potential of PVEO was evaluated using two methods: the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical trapping assay and the ferric reducing antioxidant power (FRAP) method. The data demonstrated considerable radical scavenging and relative antioxidative power. Escherichia coli, Staphylococcus aureus, Listeria innocua, and Pseudomonas aeruginosa were the most susceptible bacterial strains tested, while Geotrichum candidum, Candida albicans, and Rhodotorula glutinis were the most resilient fungi strains. PVEO had broad-spectrum antifungal and antibacterial properties. To elucidate the antioxidative and antibacterial characteristics of the identified molecules, we applied the methodology of molecular docking, a computational approach that forecasts the binding of a small molecule to a protein. Additionally, we utilized the Prediction of Activity Spectra for Substances (PASS) algorithm; Absorption, Distribution, Metabolism, and Excretion (ADME); and Pro-Tox II (to predict the toxicity in silico) tests to demonstrate PVEO’s identified compounds’ drug-likeness, pharmacokinetic properties, the anticipated safety features after ingestion, and the potential pharmacological activity. Finally, our findings scientifically confirm the ethnomedicinal usage and usefulness of this plant, which may be a promising source for future pharmaceutical development.

Mechanistic Insights of Polyphenolic Compounds from Rosemary Bound to Their Protein Targets Obtained by Molecular Dynamics Simulations and Free-Energy Calculations

Rosemary represents an important medicinal plant that has been attributed with various health-promoting properties, especially antioxidative, anti-inflammatory, and anticarcinogenic activities. Carnosic acid, carnosol, and rosmanol, as well as the phenolic acid ester rosmarinic acid, are the main compounds responsible for these actions. In our earlier research, we carried out an inverse molecular docking at the proteome scale to determine possible protein targets of the mentioned compounds. Here, we subjected the previously identified ligand-protein complexes with HIV-1 protease, K-RAS, and factor X to molecular dynamics simulations coupled with free-energy calculations. We observed that carnosic acid and rosmanol act as viable binders of the HIV-1 protease. In addition, carnosol represents a potential binder of the oncogene protein K-RAS. On the other hand, rosmarinic acid was characterized as a weak binder of factor X. We also emphasized the importance of water-mediated hydrogen-bond networks in stabilizing the binding conformation of the studied polyphenols, as well as in mechanistically explaining their promiscuous nature.

Identification of Potential Insect Growth Inhibitor against Aedes aegypti: A Bioinformatics Approach

Aedes aegypti is the main vector that transmits viral diseases such as dengue, hemorrhagic dengue, urban yellow fever, zika, and chikungunya. Worldwide, many cases of dengue have been reported in recent years, showing significant growth. The best way to manage diseases transmitted by Aedes aegypti is to control the vector with insecticides, which have already been shown to be toxic to humans; moreover, insects have developed resistance. Thus, the development of new insecticides is considered an emergency. One way to achieve this goal is to apply computational methods based on ligands and target information. In this study, sixteen compounds with acceptable insecticidal activities, with 100% larvicidal activity at low concentrations (2.0 to 0.001 mg·L−1), were selected from the literature. These compounds were used to build up and validate pharmacophore models. Pharmacophore model 6 (AUC = 0.78; BEDROC = 0.6) was used to filter 4793 compounds from the subset of lead-like compounds from the ZINC database; 4142 compounds (dG < 0 kcal/mol) were then aligned to the active site of the juvenile hormone receptor Aedes aegypti (PDB: 5V13), 2240 compounds (LE < −0.40 kcal/mol) were prioritized for molecular docking from the construction of a chitin deacetylase model of Aedes aegypti by the homology modeling of the Bombyx mori species (PDB: 5ZNT), which aligned 1959 compounds (dG < 0 kcal/mol), and 20 compounds (LE < −0.4 kcal/mol) were predicted for pharmacokinetic and toxicological prediction in silico (Preadmet, SwissADMET, and eMolTox programs). Finally, the theoretical routes of compounds M01, M02, M03, M04, and M05 were proposed. Compounds M01−M05 were selected, showing significant differences in pharmacokinetic and toxicological parameters in relation to positive controls and interaction with catalytic residues among key protein sites reported in the literature. For this reason, the molecules investigated here are dual inhibitors of the enzymes chitin synthase and juvenile hormonal protein from insects and humans, characterizing them as potential insecticides against the Aedes aegypti mosquito.

Carnosic Acid Encapsulated in Albumin Nanoparticles Induces Apoptosis in Breast and Colorectal Cancer Cells

Carnosic acid (CA) is a natural phenolic compound with several biomedical actions. This work was performed to study the use of CA-loaded polymeric nanoparticles to improve the antitumor activity of breast cancer cells (MCF-7) and colon cancer cells (Caco-2). CA was encapsulated in bovine serum albumin (BSA), chitosan (CH), and cellulose (CL) nanoparticles. The CA-loaded BSA nanoparticles (CA-BSA-NPs) revealed the most promising formula as it showed good loading capacity and the best release rate profile as the drug reached 80% after 10 h. The physicochemical characterization of the CA-BSA-NPs and empty carrier (BSA-NPs) was performed by the particle size distribution analysis, transmission electron microscopy (TEM), and zeta potential. The antitumor activity of the CA-BSA-NPs was evaluated by measuring cell viability, apoptosis rate, and gene expression of GCLC, COX-2, and BCL-2 in MCF-7 and Caco-2. The cytotoxicity assay (MTT) showed elevated antitumor activity of CA-BSA-NPs against MCF-7 and Caco-2 compared to free CA and BSA-NPs. Moreover, apoptosis test data showed an arrest of the Caco-2 cells at G2/M (10.84%) and the MCF-7 cells at G2/M (4.73%) in the CA-BSA-NPs treatment. RT-PCR-based gene expression analysis showed an upregulation of the GCLC gene and downregulation of the BCL-2 and COX-2 genes in cells treated with CA-BSA-NPs compared to untreated cells. In conclusion, CA-BSA-NPs has been introduced as a promising formula for treating breast and colorectal cancer.

Gossypol from Gossypium spp. Inhibits Helicobacter pylori Clinical Strains and Urease Enzyme Activity: Bioactivity and Safety Assessments

This study investigates the inhibitory activities of gossypol, a natural polyphenolic compound from Gossypium spp., against Helicobacter pylori (HP) clinical strains and a urease enzyme that plays a key role in the pathogenesis of HP. Gossypol was detected to exhibit a bacteriostatic action against all the HP strains tested with minimum inhibitory concentration (MIC) values ranging from 3.51 to 4.14 µg/mL. The activity of HP urease (HPU) was efficiently impeded by gossypol with a 50% inhibitory concentration (IC50) value of 3.3 µM using an Electrospray Ionization–Mass Spectrometry (ESI-MS)-based method. The in vitro cytotoxicity assay showed no significant cytotoxic properties of gossypol against human gastric epithelial cells. Additionally, molecular docking studies were performed to assess the binding mode and the molecular interactions of gossypol with HPU with a binding affinity value of −8.1 kcal/mol compared with an HPU–acetohydroxamic acid (a standard urease inhibitor) docking complex (–6.1 kcal/mol). The overall results reveal that gossypol might help fight against HP infection by two mechanisms of action: inhibition of the growth of HP and inhibition of urease.

Structure Identification and Functional Mechanism of Natural Active Components: A Special Issue

The natural active components derived from plants have attracted widespread attention due to their abundant species and source advantages [...]

Inverse Molecular Docking Elucidating the Anticarcinogenic Potential of the Hop Natural Product Xanthohumol and Its Metabolites

Natural products from plants exert a promising potential to act as antioxidants, antimicrobials, anti-inflammatory, and anticarcinogenic agents. Xanthohumol, a natural compound from hops, is indeed known for its anticarcinogenic properties. Xanthohumol is converted into three metabolites: isoxanthohumol (non-enzymatically) as well as 8- and 6-prenylnaringenin (enzymatically). An inverse molecular docking approach was applied to xanthohumol and its three metabolites to discern their potential protein targets. The aim of our study was to disclose the potential protein targets of xanthohumol and its metabolites in order to expound on the potential anticarcinogenic mechanisms of xanthohumol based on the found target proteins. The investigated compounds were docked into the predicted binding sites of all human protein structures from the Protein Data Bank, and the best docking poses were examined. Top scoring human protein targets with successfully docked compounds were identified, and their experimental connection with the anticarcinogenic function or cancer was investigated. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using retrospective metrics. More than half of the human protein targets of xanthohumol with the highest docking scores have already been connected with the anticarcinogenic function, and four of them (including two important representatives of the matrix metalloproteinase family, MMP-2 and MMP-9) also have a known experimental correlation with xanthohumol. Another important protein target is acyl-protein thioesterase 2, to which xanthohumol, isoxanthohumol, and 6-prenylnaringenin were successfully docked with the lowest docking scores. Moreover, the results for the metabolites show that their most promising protein targets are connected with the anticarcinogenic function as well. We firmly believe that our study can help to elucidate the anticarcinogenic mechanisms of xanthohumol and its metabolites as after consumption, all four compounds can be simultaneously present in the organism.

Antibacterial and Antioxidant Activity of Dysphania ambrosioides (L.) Mosyakin and Clemants Essential Oils: Experimental and Computational Approaches

Dysphania ambrosioides (L.) Mosyakin and Clemants, also known as Mexican tea, and locally known as Mkhinza, is a polymorphic annual and perennial herb, and it is widely used in folk medicine to treat a broad range of illnesses in Morocco. The aim of this study was to determine the phytochemical content and the antioxidant and the antibacterial properties of essential oils isolated from D. ambrosioides aerial components, growing in Eastern Morocco (Figuig). Hydrodistillation was used to separate D. ambrosioides essential oils, and the abundance of each phytocompound was determined by using Gas Chromatography coupled with Mass Spectrometry (GC–MS). In vitro 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and inhibition of β-carotene/linoleic acid bleaching assays were used to determine D. ambrosioides essential oils’ antioxidant activity. The findings revealed relative antioxidative power and modest radical scavenging. The antibacterial activity of the essential oils was broad-spectrum, with Escherichia coli, Staphylococcus aureus, and Enterococcus faecalis as the most susceptible strains tested. To elucidate the physicochemical nature, drug-likeness, and the antioxidant and antibacterial action of the identified phytocomponents, computational techniques, such as ADMET analysis, and molecular docking were used.

Antioxidant and Antiproliferation Activities of Lemon Verbena (Aloysia citrodora): An In Vitro and In Vivo Study

Aloysia citrodora (Verbenaceae) is traditionally used to treat various diseases, including bronchitis, insomnia, anxiety, digestive, and heart problems. In this study, this plant’s antioxidant and anti-proliferation effects were evaluated. In addition to volatiles extraction, different solvent extracts were prepared. The GC-MS, LC-MS analysis and the Foline-Ciocalteu (F-C) method were used to investigate the phytochemical components of the plant. MTT assay was used to measure the antiproliferative ability for each extract. Antioxidant activity was determined using the 2,2-diphenylpicrylhydrazyl (DPPH) assay. In in vivo anti-proliferation experiments, Balb/C mice were inoculated with tumor cells and IP-injected with ethyl acetate extract of A. citrodora. After treatment, a significant reduction in tumor size (57.97%) and undetected tumors (44.44%) were obtained in treated mice, demonstrating the antiproliferative efficacy of the ethyl acetate extract. Besides, ethanol extract revealed the most potent radical scavenging effect. The findings of this study displayed that A. citrodora has promising cytotoxic and antioxidant activities. Still, further testing is required to investigate the extract’s chemical composition to understand its mechanisms of action.