Integrated computational approaches for designing potent pyrimidine-based CDK9 inhibitors: 3D-QSAR, docking, and molecular dynamics simulations.

CDK9 is an emerging target for the development of anticancer drugs. The development of CDK9 inhibitors with significant potency had consistently posed a formidable challenge. In the current research, a number of computational methodologies, such as, 3D-QSAR, molecular docking, fingerprint analysis, molecular dynamic (MD) simulations followed by MMGB/PBSA and ADMET studies were used systemically to uncover the binding mechanism of pyrimidine derivatives against CDK9. The CoMFA and CoMSIA models having high q2 (0.53, 0.54) and r2 values (0.96, 0.93) respectively indicating that model could accurately predict the bioactivities of CDK9 inhibitors. Using the R-group exploration technique implemented by the Spark™ by Cresset group, the structural requirements revealed by the contour maps of model were utilized strategically to create an in-house library of 100 new CDK9 inhibitors. Additionally, the compounds from the in-house library were mapped into 3D-QSAR model which predicted pIC50 values comparable to the experimental values. A comparison between 3D-QSAR generated contours and molecular docking conformation of ligands was performed to elucidate the essentials of CDK9 inhibitor design. MD simulations (100 ns) were performed on the selected docked complexes A21, A14 and D98 which contributed in validating the binding interactions. According to the findings of binding free energy analysis (MMGB/PBSA), It was observed that residues CYS106 and GLU107 had a considerable tendency to facilitate ligand-protein interactions via H-bond interactions. The aforementioned findings have the potential to enhance researchers comprehension of the mechanism underlying CDK9 inhibition and may be utilized in the development of innovative and efficacious CDK9 inhibitors.

Comparative phytochemical composition, oleuropein quantification, antioxidant and cytotoxic properties of Olea europaea L. leaves.

In the present research, oleuropein (OLE) contents from two Saudi Arabian wild olive trees (Olea europaea L.) leaves (O1 and O2), were collected from two nearby geographical sites differing in altitudes, and were determined via UHPLC-MS analysis. Moreover, total bioactive contents, antioxidant, and cytotoxicity (against MCF-7 and MDA-MB-231 cells) potential were also evaluated. The sample (O2) was found to contain significantly (p < 0.05) higher OLE content (4.13 ± 1.0 mg/g DW) compared with the sample (O1) having OLE content (3.63 ± 1.1 mg/g DW). A similar trend was observed regarding total bioactive contents and antioxidant potential. However, both samples exhibited low cytotoxicity against tested cell lines. Furthermore, with hierarchical cluster analysis that compared the results of our samples (O1 and O2) to other samples reported in the literature, it was found that the variance in OLE content and biological activities from Al Baha region leaves had a resemblance to other reported superior cultivars.

Bioassay-Guided Isolation and in Silico Study of Antibacterial Compounds From Petroleum Ether Extract of Peperomia blanda (Jacq.) Kunth.

Bioassay-guided isolation protocol was performed on petroleum ether extract of Peperomia blanda (Jacq.) Kunth using column chromatographic techniques. Five compounds were isolated and their structures were elucidated via one-dimensional (1D) and two-dimensional (2D) NMR, gas chromatography mass sectroscopy (GCMS), liquid chromatography mass spectroscopy (LCMS), and ultraviolet (UV) and infrared (IR) analyses. Dindygulerione E (a new compound), and two compounds isolated from P. blanda for the first time-namely, dindygulerione A and flavokawain A-are reported herein. Antimicrobial activity was screened against selected pathogenic microbes, and minimum inhibitory concentrations (MIC) were recorded within the range of 62-250 µg/mL. Assessment of the pharmacotherapeutic potential has also been done for the isolated compounds, using the Prediction of Activity spectra for Substances (PASS) software, and different activities of compounds were predicted. Molecular docking, molecular dynamics simulation and molecular mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) calculations have proposed the binding affinity of these compounds toward methylthioadenosine phosphorylase enzyme, which may explain their inhibitory actions.

Ethnopharmacological Survey of Medicinal Plants in Albaha Region, Saudi Arabia.

BACKGROUND: Local natural medicinal resource knowledge is important to define and elaborate usage of herbs, in systematic and organized manner. Until recently, there has been little scientifically written document regarding the traditional uses of medicinal plants in Al Bahah region. OBJECTIVE: This pilot study aims to collect the ethnobotanical information from native populations regarding the benefits of medicinal plants of Al Bahah region, and determine if the traditional usage is scientifically established (proved) from literature. MATERIALS AND METHODS: The survey collected data for 39 plant species recorded by informants for their medicinal benefits. The recorded species were distributed among 28 plant families. Leguminosae and Euphorbiaceae were represented each by 3 species, followed by Asteraceae (2 species), Lamiaceae (2 species), Apocynaceae (2 species), and Solanaceae (2 species). All the medicinal plants were reported in their local names. Analysis of ethnopharmacological data was done to obtain percentage of plant families, species, parts of plants used, mode of administration, and preparation types. RESULTS: Total 43 informants were interviewed, maximum number of species were used to cure skin diseases including burns (3), wounds (7), warts (1), Leishmania (7), topical hemostatic (2), followed by gastrointestinal system, rheumatism, respiratory tract problems, diabetes mellitus, anti-snake venom, malaria, and eye inflammation. CONCLUSIONS: The study covered Al Bahah city and its outskirts. Ten new ethnobotanical uses were recorded such as antirheumatic and anti-vitiligo uses for Clematis hirsute, leishmaniasis use of Commiphora gileadensis, antigout of Juniperus procera, removing warts for Ficus palmata. SUMMARY: 39 plant species from 28 plant families are used for treating more than 20 types of diseases.Maximum number of species (23 species) was used for treating skin diseases (42.6%) including leishmaniasis, wound healing, dermatitis, psoriasis, vitiligo and warts.Ten ethnobotanical uses of 8 studied plants have not been previously reported.The most used medicinal plants, according to their Use Index (UI) were Juniperus procera, Rumex nervosus, and Ziziphus spina-christi. Abbreviations Used: UI : Use Index, GI: Gastrointestinal tract, RD: Rheumatic disease, CVS: Cardiovascular diseases, UTI: Urinary tract infection, DM: Diabetes mellitus, RT: Respiratory infection, KSA: Kingdom of Saudi Arabia.

Hierarchical cluster analysis and chemical characterisation of Myrtus communis L. essential oil from Yemen region and its antimicrobial, antioxidant and anti-colorectal adenocarcinoma properties.

The hydrodistilled essential oil obtained from the dried leaves of Myrtus communis, collected in Yemen, was analysed by GC-MS. Forty-one compounds were identified, representing 96.3% of the total oil. The major constituents of essential oil were oxygenated monoterpenoids (87.1%), linalool (29.1%), 1,8-cineole (18.4%), α-terpineol (10.8%), geraniol (7.3%) and linalyl acetate (7.4%). The essential oil was assessed for its antimicrobial activity using a disc diffusion assay and resulted in moderate to potent antibacterial and antifungal activities targeting mainly Bacillus subtilis, Staphylococcus aureus and Candida albicans. The oil moderately reduced the diphenylpicrylhydrazyl radical (IC50 = 4.2 µL/mL or 4.1 mg/mL). In vitro cytotoxicity evaluation against HT29 (human colonic adenocarcinoma cells) showed that the essential oil exhibited a moderate antitumor effect with IC50 of 110 ± 4 µg/mL. Hierarchical cluster analysis of M. communis has been carried out based on the chemical compositions of 99 samples reported in the literature, including Yemeni sample.

Variations in Essential Oil Compositions of Lavandula pubescens (Lamiaceae) Aerial Parts Growing Wild in Yemen.

Lavandula pubescens Decne. is one of five Lavandula species growing wild in Yemen. The plant is used in Yemeni traditional medicine, and the essential oil tends to be rich in carvacrol. In this work, L. pubescens was collected from eight different locations in Yemen, the essential oils obtained by hydrodistillation, and the oils analyzed by gas chromatography/mass spectrometry (GC/MS). Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used to differentiate between the L. pubescens samples. The essential oils were rich in carvacrol (60.9 - 77.5%), with lesser concentrations of carvacrol methyl ether (4.0 - 11.4%), caryophyllene oxide (2.1 - 6.9%), and terpinolene (0.6 - 9.2%). The essential oil compositions in this study showed very high similarity, but it was possible to discern two separate groups based on minor components, in particular the concentrations of terpinolene, carvacrol methyl ether, m-cymen-8-ol, and caryophyllene oxide.

Nematicidal and antimicrobial activities of methanol extracts of 17 plants, of importance in ethnopharmacology, obtained from the Arabian Peninsula.

AIM/BACKGROUND: The development of resistance to synthetic drugs by target organisms is a major challenge facing medicine, yet locked within plants are phytochemicals used in herbal medicine (especially in the Arabian Peninsula) that may find application in this regard. In pursuit of unlocking these "hidden treasures," the methanol extracts of leaves, aerial parts, fruits, and resins of 17 plants used in the Arabian Peninsula were screened for antimicrobial activities. MATERIALS AND METHODS: The nematicidal, antibacterial, and antifungal activities were determined using appropriate assays. Steinernema feltiae, Staphylococcus carnosus, Escherichia coli, and Saccharomyces cerevisiae were used as test organisms. Concentrations of the extracts ranging from 0.5 to 20 mg/ml were tested and appropriate statistical tests performed on the data generated. RESULTS: The results show that extracts from Solanum incanum, Chenopodium murale, Commiphora myrrha, Anthemis nobilis, and Achillea biebersteinii were the most active and had very high activities against two or more of the test organisms at low concentrations. Extracts of the leaves of S. incanum and resins of Ferula asafoetida were the most active nematicides, with significant activity at 0.5 mg/ml. Extracts of C. myrrha and C. murale had the most active antibacterial activity with inhibition zones of 12-15 mm and minimum inhibitory concentrations (MICs) of 2.5 mg/ml for both bacteria. Extracts of the leaves of A. biebersteinii were the most active fungicide, giving an MIC of 1.5 mg/ml. CONCLUSION: The results validate the use of these plants in ethnopharmacology, and open new vistas of opportunities for the development of cheap but effective agents that may be useful against infectious diseases.

Turning Waste into Value: Nanosized Natural Plant Materials of Solanum incanum L. and Pterocarpus erinaceus Poir with Promising Antimicrobial Activities.

Numerous plants are known to exhibit considerable biological activities in the fields of medicine and agriculture, yet access to their active ingredients is often complicated, cumbersome and expensive. As a consequence, many plants harbouring potential drugs or green phyto-protectants go largely unnoticed, especially in poorer countries which, at the same time, are in desperate need of antimicrobial agents. As in the case of plants such as the Jericho tomato, Solanum incanum, and the common African tree Pterocarpus erinaceus, nanosizing of original plant materials may provide an interesting alternative to extensive extraction and isolation procedures. Indeed, it is straightforward to obtain considerable amounts of such common, often weed-like plants, and to mill the dried material to more or less uniform particles of microscopic and nanoscopic size. These particles exhibit activity against Steinernema feltiae or Escherichia coli, which is comparable to the ones seen for processed extracts of the same, respective plants. As S. feltiae is used as a model nematode indicative of possible phyto-protective uses in the agricultural arena, these findings also showcase the potential of nanosizing of crude "waste" plant materials for specific practical applications, especially-but not exclusively-in developing countries lacking a more sophisticated industrial infrastructure.

The Chemical Diversity of Lantana camara: Analyses of Essential Oil Samples from Cuba, Nepal, and Yemen.

The aerial parts of Lantana camara L. were collected from three different geographical locations: Artemisa (Cuba), Biratnagar (Nepal), and Sana'a (Yemen). The essential oils were obtained by hydrodistillation and analyzed by gas chromatography/mass spectrometry. A cluster analysis of 39 L. camara essential oil compositions revealed eight major chemotypes: ß-caryophyllene, germacrene D, ar-curcumene/zingiberene, γ-curcumen-15-al/epi-ß-bisabolol, (E)-nerolidol, davanone, eugenol/alloaromadendrene, and carvone. The sample from Cuba falls into the group dominated by (E)-nerolidol, the sample from Nepal is a davanone chemotype, and the sample from Yemen belongs to the ß-caryophyllene chemotype. The chemical composition of L. camara oil plays a role in the biological activity; the ß-caryophyllene and (E)-nerolidol chemotypes showed antimicrobial and cytotoxic activities.

Anticholinesterase activity of endemic plant extracts from Soqotra.

A total of 30 chloroform and methanol extracts from the following endemic Soqotran plants Acridocarpus socotranus Olive, Boswellia socotranao Balf.fil, Boswellia elongata Balf. fil., Caralluma socotrana N. Br, Cephalocroton socotranus Balf.f, Croton socotranus Balf. fil.., Dendrosicycos socotrana Balf.f., Dorstenia gigas Schweinf. ex Balf. fil., Eureiandra balfourii Cogn. & Balf. fil., Kalanchoe farinaceae Balf.f, Limonium sokotranum (Vierh) Radcl. Sm), Oldenlandia pulvinata, Pulicaria diversifolia (Balf. and Pulicaria stephanocarpa Balf. were screened for their acetylcholinesterase inhibitory activity by using in vitro Ellman method at 50 and 200 µg/ml concentrations. Chloroform extracts of Croton socotranus, Boswellia socotrana, Dorstenia gigas, and Pulicaria stephanocarpa as well as methanol extracts of Eureiandra balfourii exhibited inhibitory activities higher than 50 % at concentration of 200 µg. At a concentrations of 50 µg, the chloroform extract of Croton socotranus exhibited an inhibition of 40.6 %.