Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID-19 virus main protease and spike protein

The lack of any effective cure for the infectious COVID-19 disease has created a sense of urgency and motivated the search for effective antiviral drugs. Abyssomicins are actinomyces-derived spirotetronates polyketides antibiotics known for their promising antibacterial, antitumor, and antiviral activities. In this study, computational approaches were used to investigate the binding mechanism and the inhibitory ability of 38 abyssomicins against the main protease (Mpro) and the spike protein receptor-binding domain (RBD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The results identified abyssomicins C, J, W, atrop-O-benzyl abyssomicin C, and atrop-O-benzyl desmethyl abyssomicin C as the most potential inhibitors of Mpro and RBD with binding energy ranges between -8.1 and -9.9 kcal mol-1; and between -6.9 and -8.2 kcal mol-1, respectively. Further analyses of physicochemical properties and drug-likeness suggested that all selected active abyssomicins, with the exception of abyssomicin J, obeyed Lipinski's rule of five. The stability of protein-ligand complexes was confirmed by performing molecular dynamics simulation for 100 ns and evaluating parameters such as such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), total number of contacts, and secondary structure. Prime/MM-GBSA (Molecular Mechanics-General Born Surface Area) and principal component analysis (PCA) analyses also confirmed the stable nature of protein-ligand complexes. Overall, the results showed that the studied abyssomicins have significant interactions with the selected protein targets; therefore, they were deemed viable candidates for further in vitro and in vivo evaluation.Communicated by Ramaswamy H. Sarma.

Chemical constituents from Centaurothamnus maximus and their antimicrobial activity

A new sesquiterpene lactone, 3β,10α-dihydroxy-10β-(hydroxymethyl)-8α-(4-hydroxymethacrylate)-1αH,5αH,6βH,7αH-guai-4(15), 11(13)-dien-6,12-olide (1), along with twenty-one known compounds, were identified from the aerial parts of Centaurothamnus maximus. The structures of the isolated compounds were elucidated on the basis of spectroscopic evidences and correlated with known compounds. Compounds (2, 3, 5‒13 and 15‒22) were identified from C. maximus for the first time. Antibacterial and antifungal activities of the isolated compounds were tested using the agar disc diffusion method. Compounds that demonstrated promising antimicrobial activity were evaluated for their minimum inhibitory concentration (MIC). The results showed that compounds 3 and 7 were the most effective antibacterial compounds against B. subtilis ATCC 6633, S. aureus ATCC 25923 and S. pyogenes ATCC 27736, with MIC estimates between 8 and 32 mg/mL. In addition, compound 2 exhibited the strongest antifungal activity against C. albicans ATCC 14243 and C. krusei ATCC 14243 with MIC 8 mg/mL.

Insecticidal Activity and Free Radical Scavenging Properties of Isolated Phytoconstituents from the Saudi Plant Nuxia oppositifolia (Hochst.)

Chromatographic purification of the alcoholic extract from the aerial parts of the Saudi plant Nuxia oppositifolia (Hochst.), Benth., resulted in five isolated phenolic compounds. Two flavones, hispidulin (1) and jaceosidin (2), and the phenylethanoid glycosides, verbascoside (3), isoverbascoside (4), and conandroside (5), were identified and their chemical structures were determined by spectroscopic analyses. The insecticidal activity of compounds 1 and 2, in addition to 11 compounds isolated in a previous research (6-16), was evaluated against the Yellow Fever mosquito, Aedes aegypti. Four compounds displayed adulticidal activity with LD₅₀ values of 2-2.3 μg/mosquito. Free radical scavenging properties of the plant extracts and compounds (1-5) were evaluated by measuring the 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonate radical cation (ABTS^•+) scavenging activity. All compounds exhibited notable activity, compared with the positive control, l-Ascorbic acid. This study suggests that N. oppositifolia could be a promising source of secondary metabolites, some with lethal adulticidal effect against Ae. aegypti.

Sterols and Triterpenes from Dobera glabra Growing in Saudi Arabia and Their Cytotoxic Activity

A new lupane caffeoyl ester, lup-20(29)-ene 3β-caffeate-30-al (7), and a new oleanane-type triterpene, 3β-hydroxyolean-13(18)-en-12-one (17), were isolated from the aerial parts of Dobera glabra (Forssk), along with ten known triterpenes, including seven lupane-type lupeol (1), 30-nor-lup-3β-ol-20-one (2), ∆1-lupenone (3), lup-20(29)-en-3β,30-diol (4), lupeol caffeate (5), 30-hydroxy lup-20(29)-ene 3β-caffeate (6), and betunaldehyde (8); three oleanane-type compounds were also identified, comprising δ-amyrone (15), δ-amyrin (16), and 11-oxo-β-amyrin (18); together with six sterols, comprising β-sitosterol (9), stigmasterol (10), 7α-hydroxy-β-sitosterol (11), 7α-hydroxy-stigmasterol (12), 7-keto-β-sitosterol (13), and 7-keto-stigmasterol (14). Their structures were elucidated using a variety of spectroscopic techniques, including 1D (1H, 13C, and DEPT-135 13C) and 2D (1H-1H COSY, 1H-13C HSQC, and 1H-13C HMBC) nuclear magnetic resonance (NMR) and accurate mass spectroscopy. Subsequently, the different plant extracts and some of the isolated compounds (1-9, 11 and 13) were investigated for their possible cytotoxic activity in comparison to cisplatin against a wide array of aggressive cancer cell lines, such as colorectal cancer (HCT-116), hepatocellular carcinoma (HepG-2), and prostate cancer (PC-3) cell lines. Compound 11 displayed broad cytotoxicity against all of the tested cell lines (IC50 ≅ 8 µg/mL in all cases), and a high safety margin against normal Vero cells (IC50 = 70 µg/mL), suggesting that 11 may be a highly selective and effective anticancer agent candidate. Notably, the evidence indicated that the mode of action of compound 11 could possibly consist of the inhibition of phosphodiesterase I (80.2% enzyme inhibition observed at 2 µM compound concentration).

Vacillantins A and B, New Anthrone C-glycosides, and a New Dihydroisocoumarin Glucoside from Aloe vacillans and Its Antioxidant Activities

A new dihydroisocoumarin glucoside, vacillanoside (3), and two new anthrone C-glycosides microdantin derivatives; vacillantin A (10) and B (11), together with nine known compounds belonging to the anthraquinone, anthrone and isocoumarin groups were isolated from the leaves of Aloe vacillans. The structures were determined based on spectroscopic evidence including 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and high resolution mass spectrometry (HRESIMS) data, along with comparisons to reported data. The leaves were used to extract compounds with different solvents. The extracts were tested for antioxidant activity with a variety of in vitro tests including 2,2-diphenyl-1-picrylhydrazyl (DPPH^•), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonate (ABTS^•+), ferric reducing antioxidant power assay (FRAP), superoxide, and nitric oxide radical scavenging assays. The dichloromethane fraction was most active, displaying significant free radical scavenging activity. The n-butanol fraction also showed notable activity in all assays. Therefore, these findings support the potential use of A. vacillans leaves as an antioxidant medication due to the presence of polyphenolic compounds.

Evaluation of cytotoxicity, cell cycle arrest and apoptosis induced by Anethum graveolens L. essential oil in human hepatocellular carcinoma cell line

Anethum graveolens L. (A. graveolens) commonly known as dill, is an essential oil bearing plant extensively being used in traditional system of medicine. However, the reports on the components and biological responses of A. graveolens essential oil (AG-EO) from Saudi Arabia are scarce. The present study was designed to explore the presence of basic constituents and apoptosis induced by AG-EO in HepG2 cells. The constituents in AG-EO was analyzed by Gas chromatography-Mass spectroscopy (GC-MS). Cytotoxicity of AG-EO was measured by MTT assay and cell cycle arrest and apoptosis assays were conducted by using flow cytometer. Based on GC-MS analysis, the main constituents present in AG-EO were carvone (53.130%), dillapole (25.420%), dihydrocarvone 2 (11.350%) and dihydrocarvone 1 (6.260%). A few other minor components were also identified viz. cis-dihydrocarveol (0.690%), limonene (0.580%), isodihydrocarveol (0.370%), myristicin (0.210%) and cis-arsone (0.190%). The cytotoxicity results showed that AG-EO decrease the cell viability and inhibit the cell growth of HepG2 cells in a concentration-dependent manner. The inhibitory activity of AG-EO was found with IC50 = 59.6 ± 5.64. The cell cycle arrest results showed that HepG2 cells exposed to AG-EO exhibited an increase in G2/M and pre-G1 cell population after 24 h exposure. Furthermore, the flow cytometry data revealed the primarily activation of cell death by apoptosis manners in HepG2 cells exposed to AG-EO. Overall, results from this study highlighted the anticancer potential of AG-EO, which could be considered as a new agent for the management of hepatocellular carcinoma.

Molluscicidal activity of cardiac glycosides isolated from Adenium obesum

BACKGROUND

Terrestrial mollusks are one of most important agricultural pests worldwide. Natural phytochemicals have an extended history as a source of pesticides. This study was planned to isolate molluscicidal active compounds from the stems of Adenium obesum.

RESULTS

The benzene-soluble fraction of the hydroethanolic extract displayed the most potent molluscicidal activity against Monacha obstructa among different solvent fractions with a median lethal dose (LD₅₀ ) of 4.91 µg g^-1 body weight (bw). The bioactivity-guided chemical exploration of the benzene-soluble fraction led to the isolation of two known cardiac glycosides, cerberin and neriifolin which showed significant molluscicidal activity with LD₅₀ values of 5.39 and 4.3 µg g^-1 bw, respectively.

CONCLUSION

Isolation of the cardiac glycoside neriifolin from A. obesum and the molluscicidal activity of cerberin and neriifolin against terrestrial snails are reported for the first time. © 2019 Society of Chemical Industry.

Comparative evaluation of cytotoxic, antimicrobial and antioxidant activities of the crude extracts of three Plectranthus species grown in Saudi Arabia

Natural products from medicinal plants represent major resource of novel therapeutic substances for combating serious diseases including cancers and microbial infections. The genus Plectranthus (Family: Labiatae) represents a large and widespread group of species with a diversity of traditional uses in treatment of various ailments. Therefore, this research study aimed to evaluate the cytotoxic, antimicrobial and antioxidant activities of three Plectranthus species growing in Saudi Arabia namely P. cylindraceus Hocst. ex Benth., P. asirensis JRI Wood and P. barbatus Andrews. Moreover, this work focused on the isolation of the active constituents responsible for the activities from the most active Plectranthus species.

The extracts were tested for their cytotoxic activity against three cancer cell lines (Hela, HepG2 and HT-29), using MTT-test, antimicrobial activity against Gram positive, Gram negative bacterial and fungal strains using broth micro-dilution assay for minimum inhibitory and bactericidal concentrations (MIC and MBC) and antioxidant activity using scavenging activity of DPPH radical and β-carotene-linoleic acid methods. The ethanolic extracts of the Plectranthus species showed remarkable cytotoxic activity against all cancer cell lines with IC₅₀ values ranging between 10.1 ± 0.33 to 102.6 ± 8.66 μg/mL and a great and antimicrobial activity with MIC values between 62.5 and 250 µg/mL. In addition, the three Plectranthus species showed almost moderate antioxidant activity. The most interesting cytotoxic and antimicrobial results were observed with the extract of P. barbatus. Consequently, this extract was partitioned between water and n-hexane, chloroform and n-butanol and tested. The cytotoxic activity resided predominantly in the n-hexane and chloroform fractions. The analysis of the chloroform fraction led to the isolation of four diterpenoid compounds, two of labdane- and two of abietane-type, which were identified as coleonol B, forskolin, sugiol and 5,6-dehydrosugiol. Purification of the n-hexane fraction led to isolation of a major abietane-type diterpene, which was identified as ferruginol. Sugiol, 5,6-dehydrosugiol and ferruginol were isolated for the first time from P. barbatus in this study. The isolated diterpenoids showed variable cytotoxic effects with IC₅₀ values between 15.1 ± 2.03 and 242 ± 13.3 µg/mL, a great antimicrobial activity with MIC values between 15.6 and 129 µg/mL and a total antioxidant activity ranging from 23.1 ± 2.9 to 69.2 ± 3.8%.

The Phytochemical and Biological Investigation of Jatropha pelargoniifolia Root Native to the Kingdom of Saudi Arabia

Extensive phytochemical analysis of different root fractions of Jatropha pelargoniifolia Courb. (Euphorbiaceae) has resulted in the isolation and identification of 22 secondary metabolites. 6-hydroxy-8-methoxycoumarin-7-O-β-d-glycopyranoside (15) and 2-hydroxymethyl N-methyltryptamine (18) were isolated and identified as new compounds along with the known diterpenoid (1, 3, 4, and 7), triterpenoid (2 and 6), flavonoid (5, 11, 13, 14, and 16), coumarinolignan (8⁻10), coumarin (15), pyrimidine (12), indole (17, 18), and tyramine-derived molecules (19⁻22). The anti-inflammatory, analgesic, and antipyretic activities were evaluated for fifteen of the adequately available isolated compounds (1⁻6, 8⁻11, 13, 14, 16, 21, and 22). Seven (4, 6, 10, 5, 13, 16, and 22) of the tested compounds showed a significant analgesic effect ranging from 40% to 80% at 10 mg/kg in two in vivo models. Compound 1 could also prove its analgesic property (67.21%) when it was evaluated on a third in vivo model at the same dose. The in vitro anti-inflammatory activity was also recorded where all compounds showed the ability to scavenge nitric oxide (NO) radical in a dose-dependent manner. However, eight compounds (1, 4, 5, 6, 10, 13, 16, and 22) out of the fifteen tested compounds exhibited considerable in vivo anti-inflammatory activity which reached 64.91% for compound 10 at a dose of 10 mg/kg. Moreover, the tested compounds exhibited an antipyretic effect in a yeast-induced hyperthermia in mice. The activity was found to be highly pronounced with compounds 1, 5, 6, 10, 13, and 16 which decreased the rectal temperature to about 37 °C after 2 h of the induced hyperthermia (~39 °C) at a dose of 10 mg/kg. This study could provide scientific evidence for the traditional use of J. pelargoniifolia as an anti-inflammatory, analgesic, and antipyretic.

Prenylated flavonoids from Commiphora opobalsamum stem bark

A phytochemical study on the stem bark of Commiphora opobalsamum looking for cytotoxic compounds afforded eleven flavonoids, including six previously undescribed prenylated congeners, comophorin A-E, and comophoroside A. The structures of the isolated compounds were elucidated on the basis of spectroscopic evidences and correlated with known compounds. Isolated compounds were biologically evaluated using in vitro cytotoxicity MTT-based assay against two cancer cell lines; namely human hepato-cellular carcinoma (HepG-2) and human breast adenocarcinoma (MCF-7). Comophoroside A revealed to retain the strongest cytotoxic activity against MCF-7 and HepG-2 cell lines with IC₅₀ values of 8 and 12 μg/mL, respectively.

Noncyanogenic Cyanoglucoside Cyclooxygenase Inhibitors from Simmondsia chinensis

Two new noncyanogenic cyanoglucoside dimers, simmonosides A and B (1 and 2), were identified from the aqueous extract of jojoba (Simmondsia chinensis) leaves. Compounds 1 and 2 are the first examples of noncyanogenic cyanoglucoside dimers containing a unique four-membered ring, representing novel dimerization patterns at α,β-unsaturated carbons of a nitrile group in 1 and γ,δ-unsaturated carbons in 2. Their structures were elucidated based on spectroscopic evidence and electronic circular dichroism (ECD) calculations. Compounds 1 and 2 exhibit promising COX-2 inhibition activity, with IC50 values of 13.5 and 11.4 μM, respectively.

Lipoxygenase inhibitors from the latex of Calotropis Procera

A radical-scavenging, guided phytochemical study of the latex of Calotropis Procera afforded five lignans (1-5), including a new one (4). The structural determination was accomplished using 1D- and 2D-NMR, high-resolution electrospray ionization mass spectrometry (HRESIMS), and correlation with known compounds. Among the isolated compounds, acylated lignans (3-5) showed stronger antioxidant activity than non-acylated derivatives (1,2). Anti-inflammatory activity was evaluated by determining the inhibitory potential against 5- and 15-lipoxygenase enzymes. The highest anti-inflammatory activity was observed in compound 4, with IC50s values of 7.6 µM and 2.7 µM against 5-LOX and 15-LOX, respectively.

Socotroside, a New Pentacyclic Cucurbitane Glycoside from Dendrosicyos socotrana

Phytochemical investigation of the ethyl acetate extract of the stem of Dendrosicyos socotrana Balf. f. resulted in the isolation of a new pentacyclic cucurbitane glycoside Socotroside, in addition to the three known cucurbitacins, dihydrocucurbitacin D, dihydrocucurbitacin F and cucurbitacin G. The structures of the isolated compounds were established on the basis of their spectral data. The isolated cucurbitacin aglycones showed marked cytotoxic activity.

Sulfur-containing polybromoindoles from the Formosan red alga Laurencia brongniartii

Five new sulfur-containing polybromoindoles, 2-methylsulfinyl-3-methylthio-4,5,6-tribromoindole (1), 3-methylsulfinyl-2,4,6-tribromoindole (2), 4,6-dibromo-2,3-di(methylsulfinyl)indole (3), 3,3'-bis(2'-methylsulfinyl-2-methylthio-4,6,4',6'-tetrabromo)indole (4), and 3,3-bis(4,6-dibromo-2-methylsulfinyl)indole (5), as well as seven known sulfur-containing polybromoindoles, 3-methylthio-2,4,6-tribromoindole (6), 3-methylthio-2,4,5,6-tetrabromoindole (7), 4,6-dibromo-2,3-di(methylthio)indole (8), 2,3-di(methylthio)-4,5,6-tribromoindole (9), 4,6-dibromo-2-methylsulfinyl-3-(methylthio)indole (10), 4,6-dibromo-2-(methylthio)indole (11), and 3,3-bis(4,6-dibromo-2-methylthio)indole (12), have been isolated from the Formosan red alga Laurencia brongniartii. The structures were elucidated by extensive spectral analysis, and their cytotoxicity against selected cancer cells was measured in vitro.

Dendrocyin: an isocucurbitacin with novel cyclic side chain from Dendrosicyos socotrana

Dendrosicyos socotrana Balf.f. is a unique species (Cucurbitaceae) native to Socotra island in the horn of Africa. From the chloroform extract of the stems, A new isocucurbitacin (Dendrocyin) with unusual cyclization in the side chain; 24beta-ethoxy-20-25-epoxy-3alpha,16alpha-dihydroxy-9-methyl-19-norlanost-5(6) ene-2,11,22-trione has been isolated alongside isocucurbitacin R. Their structural configuration were established by usual spectroscopic (1H NMR, 13C NMR and DEPT) and two-dimensional NMR techniques (1H-1H Cosy, HMBC and HMQC).

Sesquiterpenes from the Formosan stolonifer Tubipora musica

Eight new sesquiterpenes, tubipolides A-G (1-7) and tubiporone (8) (novel carbon skeleton), and a known sesquiterpene, spirotubipolide, have been isolated from the Formosan stolonifer Tubipora musica. The structures of compounds 1-8 were determined by 1D and 2D NMR spectral analysis.

Sesquiterpene lactones from Smyrnium olusatrum

Fruits of Smyrnium olusatrum afforded three sesquiterpene lactones, namely, 1beta,8beta-dihydroxyeudesman-3,7(11)-dien-8alpha,12-olide, 1beta,8beta-dihydroxyeudesman-4(15),7(11)-dien-8alpha,l2-olide, and 1beta,10alpha,4alpha,5beta-diepoxy-6beta-hydroxyglechoman-8alpha,12-olide. Four related known sesquiterpenes were also isolated and characterized. The structure elucidation of the isolated compounds was based primarily on 1D and 2D NMR analyses. The in vitro cytotoxicity of the extract and isolated compounds against P-388 mouse lymphoma cells will be also discussed.

Cytotoxic dolabellane diterpenes from the Formosan soft coral Clavularia inflata

Six new cytotoxic dolabellane diterpenes, (1R,12R)-dolabella-4(16),7,10-triene-3,13-dione (1), (1R*,7R*,8S*,12R*)-dolabella-4(16),10-diene-7,8-epoxy- 3,13-dione (2), (1R*,10R*,11S*,12R*)-dolabella-4(16),7-diene-10,11-epoxy-3,13-dione (3), (1R)-dolabella-4(16),7,11(12)-triene-3,13-dione (4), (1R*,3R*)-3-hydroxydolabella-4(16),7,11(12)-triene-3,13-dione (5), and (1R*,7R*)-7-hydroperoxydolabella-4(16),8(17),11(12)-triene-3,13-dione (6), have been isolated from the Formosan soft coral Clavularia inflata. The structures of compounds 1-6 were determined by 1D and 2D spectral analysis, and their cytotoxicity against selected cancer cells was measured in vitro.

A xanthanolide diol and a dimeric xanthanolide from Xanthium species

Extracts of the aerial parts of Xanthium strumarium and fruit of X. pungens afforded a new Xanthanolide diol derivative, 11alpha,13-dihydroxyxanthatin and a new dimeric xanthanolide sesquiterpene lactone, pungiolide C, in addition to some known compounds. The structures of the new compounds were determined by spectroscopic methods particularly high resolution (1)H-, (13)C-NMR and 2D (1)H- (1)H and (1)H- (13)C COSY NMR analysis.