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.

Biomarker Quantification, Spectroscopic, and Molecular Docking Studies of the Active Compounds Isolated from the Edible Plant Sisymbrium irio L

Phytochemical investigation of the ethanolic extract of the aerial parts of Sisymbrium irio L. led to the isolation of four unsaturated fatty acids (1–4), including a new one (4), and four indole alkaloids (5–8). The structures of the isolated compounds were characterized with the help of spectroscopic techniques such as 1D, 2D NMR, and mass spectroscopy, and by correlation with the known compounds. In terms of their notable structural diversity, a molecular docking approach with the AutoDock 4.2 program was used to analyze the interactions of the identified fatty acids with PPAR-γ and the indole alkaloids with 5-HT1A and 5-HT2A, subtypes of serotonin receptors, respectively. Compared to the antidiabetic drug rivoglitazone, compound 3 acted as a potential PPAR-γ agonist with a binding energy of −7.4 kcal mol−1. Moreover, compound 8 displayed the strongest affinity, with binding energies of −6.9 kcal/mol to 5HT1A and −8.1 kcal/mol to 5HT2A, using serotonin and the antipsychotic drug risperidone as positive controls, respectively. The results of docked conformations represent an interesting target for developing novel antidiabetic and antipsychotic drugs and warrant further evaluation of these ligands in vitro and in vivo. On the other hand, an HPTLC method was developed to quantify α-linolenic acid in the hexane fraction of the ethanol extract of S. irio. The regression equation/correlation coefficient (r2) for linolenic acid was Y = 6.49X + 2310.8/0.9971 in the linearity range of 100–1200 ng/band. The content of α-linolenic acid in S. irio aerial parts was found to be 28.67 μg/mg of dried extract.

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.

Cytotoxic activity of guaiane-type sesquiterpene lactone (deoxycynaropicrin) isolated from the leaves of Centaurothamnus maximus

Guaianolide is a type of naturally occurring sesquiterpene lactone compounds that have attracted attention due to their diverse biological properties. In this work, a guaiane-type sesquiterpene lactone identified as deoxycynaropicrin (compound 1) was isolated and reported for the first time from the leaves of Centaurothamnus maximus with two known flavonoid derivatives namely luteolin 6-O-methyl ether (compound 2) and quercetin 3-methyl ether 5-O-glucopyranoside (compound 3). The cytotoxic activity of all the three compounds was evaluated against the THP-1 human leukemia cell lines. Moreover, flow cytometry was employed to explore the cell cycle arrest and apoptosis induction for the active compound. We found that compound 1 (deoxycynaropicrin) exerted the highest cytotoxicity while compounds 2 and 3 showed no activity. Cell cycle analysis showed that compound 1 arrested the cells’ population at the G2/M phase. Furthermore, THP-1 cells treated with compound 1 exhibited a marked increase in the apoptotic cells compared to the control. Overall, this study showed that deoxycynaropicrin induces cytotoxicity against human leukemia cell lines and provided an important insight into its potential therapeutic effects against leukemia cells.

A Major Diplotaxis harra-Derived Bioflavonoid Glycoside as a Protective Agent against Chemically Induced Neurotoxicity and Parkinson's Models; In Silico Target Prediction; and Biphasic HPTLC-Based Quantification

Oxidative stress and chronic inflammation have a role in developing neurodegenerative diseases such as Parkinson’s disease (PD) and inflammatory movement disorders such as rheumatoid arthritis that affect millions of populations. In searching for antioxidant and anti-inflammatory molecules from natural sources that can counteract neurodegenerative diseases and arthritis, the flavonoid-rich extract of Diplotaxis harra (DHE) was selected based on its in vitro antioxidant and anti-inflammatory activities. DHE could inhibit the inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) expressions in the lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages from 100% to the level of 28.51 ± 18.67 and 30.19 ± 5.00% at 20 μg/mL, respectively. A TLC bioautography of DHE fractions using 1,1-diphenyl-2-picryl-hydrazyl radical (DPPH) led to the isolation of a major antioxidant compound which was identified by X-ray diffraction analysis as isorhamnetin-3-O-β-D-glucoside (IR3G). IR3G also exhibited a potent anti-inflammatory activity, particularly by suppressing the upregulation of iNOS expression, similar to that of dexamethasone (DEX) at 10 μM to the level of 35.96 ± 7.80 and 29.34 ± 6.34%, respectively. Moreover, IR3G displayed a strong neuroprotectivity (>60% at 1.0−4−1.0−3 μM) against 6-hydroxydopamine (6-OHDA)-challenged SHSY5Y neuroblastoma, an in vitro model of dopaminergic neurons for Parkinson’s disease (PD) research. Accordingly, the in vivo anti-Parkinson potentiality was evaluated, where it was found that IR3G successfully reversed the 6-OHDA-induced locomotor deficit in a zebrafish model. A study of molecular docking and molecular dynamic (MD) simulation of IR3G and its aglycone isorhamnetin (IR) against human acetylcholine esterase (AChE), monoamine oxidase B (MAO-B), and Polo-like kinase-2 (PLK2) was performed and further outlined a putative mechanism in modulating neurodegenerative diseases such as PD. The free radical scavenging, anti-inflammatory through anti-iNOS and anti-COX-2 expression, and neuroprotective activities assessed in this study would present partial evidence for the potentiality of D. harra-derived IR3G as a promising natural therapeutic agent against neurodegenerative diseases and inflammatory arthritis. Finally, a biphasic HPTLC method was developed to estimate the biomarker IR3G in D. harra quantitatively.

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.

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.

Flavonoid fromViburnum cotinifolium

From the leaves of Viburnum cotinifolium, a new biflavonoid named as I-5, II-5, I-7, II-7, I-4’, II-4′-hexahydroxy [6-O-8] biflavone along with seven known flavonoids have been isolated. Their structures were elucidated from their chemical and physical data (IR, UV,1H NMR,13C NMR and mass spectra).

Flavonoids from Acacia Tortilis

A novel isoflavone, 5,7-dihydroxy-4′- p-methyl benzyl isoflavone 1a, and three known flavonoids apigenin, luteolin and quercetin have been isolated from the leaves of Acacia tortilis. Their structures were elucidated by chemical and physical data (IR, UV, 1H-NMR, 13C-NMR and MS spectra).

Comparative anticancer and antimicrobial activity of aerial parts of Acacia salicina, Acacia laeta, Acacia hamulosa and Acacia tortilis grown in Saudi Arabia

The standardized ethanol extract (EE) of aerial parts of four Acacia species [A. salicina (ASEE), A. laeta (ALEE), A. hamulosa (AHEE), and A. tortilis (ATEE)] were examined in order to compare their cytotoxic and antimicrobial activities. All the extracts were standardized by UPLC- PDA method using rutin as standard compound. The extracts ALEE, AHEE and ATEE were found to contain rutin along with several other phytoconstituents while rutin was absent in ASEE. All the extracts showed varying level of antimicrobial activity with zone of inhibition ranged from 11 to 21 mm against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Candida albicans. The ALEE and ATEE showed relatively high antimicrobial potency (MIC = 0.2 to 1.6 mg mL⁻¹) in comparison to other extracts. All the extracts were found to reduce the biofilm of P. aeruginosa PAO1 strain significantly in comparison to the untreated control. The cytotoxic property of ASEE, ALEE, AHEE, ATEE were evaluated against HepG2 (Liver), HEK-293 (Kidney), MCF-7 (Breast) and MDA-MB 231 (Breast) cancer cells. Of these, ALEE, AHEE and ATEE exhibited moderate cytotoxic property against human liver carcinoma cells (HepG2; IC50 = 46.2, 39.2 and 42.3 μg mL⁻¹, respectively) and breast cancer cell lines (MCF-7; IC50 = 57.2, 55.3 and 65.7 μg mL⁻¹, respectively). The ATEE and ALEE showed moderate cytotoxicity against HEK-293 (kidney) cells with IC50 = 49.1 and 53.5 μg mL⁻¹, respectively. Since, Acacia species (A. laeta and A. hamulosa) contains numerous polyphenols which might prove to be highly cytotoxic and antimicrobial agents, we suggest that these species can be further subjected to the isolation of more cytotoxic and antimicrobial compounds.

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.

Acetylcholinesterase and Cytotoxic Activity of Chemical Constituents of Clutia lanceolata Leaves and its Molecular Docking Study

Phytochemical investigations of the ethanolic extract of leaves of Clutia lanceolata (Family: Euphorbiaceae) resulted in the isolation of four compounds viz. 3,4-dihydroxy-2-methylbenzoic acid (1), 2,2'-dihydroxy-1,1'-binaphthyl (2), 1,3,8-trihydroxy-6-methylanthracene-9,10-dione (3) and 5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one (4). Although all the isolated compounds were known but this was the first report from this plant source. Their structures were established on the basis of chemical and physical evidences viz. elemental analysis, FT-IR, ¹H-NMR, ¹³C-NMR and mass spectral analysis. Structure of compound 2 and 4 was further authenticated by single-crystal X-ray analysis and density functional theory calculations. The isolated compounds (1-4) were screened for AChE enzyme inhibition assay in which compound 3 and 4 were found to be more potent AChE inhibitor. Molecular docking study of potent AChE inhibitor was performed to find the probable binding mode of the compounds into the active site of receptor. Moreover, the isolated compounds were also screened for in vivo cytotoxicity by brine shrimp lethality assay.

Comparative study of antioxidant activity and validated RP-HPTLC analysis of rutin in the leaves of different Acacia species grown in Saudi Arabia

The present study assessed the comparative antioxidant potential of the ethanol extract (EE) of leaves of four Acacia species (Acacia salicina, AS; Acacia laeta, AL; Acacia hamulosa AH; and Acacia tortilis, AT) grown in Saudi Arabia, including RP-HPTLC quantification of antioxidant biomarker rutin. In vitro DPPH radical scavenging and β-carotene-linoleic acid bleaching assays showed the promising antioxidant activities of Acacia extracts: ASEE (IC₅₀: 60.39 and 324.65 μg/ml) >ALEE (IC₅₀: 217.06 and 423.36 μg/ml) >ATEE (IC₅₀: 250.13 and 747.50 μg/ml) >AHEE (IC₅₀: 255.83 and 417.28 μg/ml). This was comparable to rutin tested at 500 μg/ml. Further, a RP- HPTLC densitometric method was developed (acetonitrile:water; 6:4; v/v) using glass-backed RP-18 silica gel F₂₅₄ plate, and scanned at UV max 254 nm. The method was validated as per the ICH guidelines. Analysis of the validated RP-HPTLC displayed an intense peak (R_f = 0.65 ± 0.004) of rutin that was estimated (μg/mg dry weight) to be highest in ASEE (10.42), followed by ALEE (2.67), AHEE (1.36) and ATEE (0.31). Taken together, presence of rutin strongly supported the high antioxidant property of the tested Acacia species, especially Acacia salicina. The developed RP-HPTLC method therefore, affirms its application in the quality control of commercialized herbal drugs or formulation containing rutin.

New acyclic secondary metabolites from the biologically active fraction of Albizia lebbeck flowers

The total extract of Albizia lebbeck flowers was examined in vivo for its possible hepatoprotective activity in comparison with the standard drug silymarin at two doses. The higher dose expressed promising activity especially in reducing the levels of AST, ALT and bilirubin. Fractionation via liquid–liquid partition and reexamination of the fractions revealed that the n-butanol fraction was the best in improving liver biochemical parameters followed by the n-hexane fraction. However, serum lipid parameters were best improved with CHCl₃ fraction. The promising biological activity results initiated an intensive chromatographic purification of A. lebbeck flowers fractions. Two compounds were identified from natural source for the first time, the acyclic farnesyl sesquiterpene glycoside1-O-[6-O-α-l-arabinopyranosyl-β-d-glucopyranoside]-(2E,6E-)-farnesol (6) and the squalene derivative 2,3-dihydroxy-2,3-dihydrosqualene (9), in addition to eight compounds reported here for the first time from the genus Albizia; two benzyl glycosides, benzyl 1-O-β-d-glucopyranoside (1) and benzyl 6-O-α-l-arabinopyranosyl β-d-glucopyranoside (2); three acyclic monoterpene glycosides, linalyl β-d-glucopyranoside (3) and linalyl 6-O-α-l-arabinopyranosyl-β-d-glucopyranoside (4); (2E)-3,7-dimethylocta-2,6-dienoate-6-O-α-l arabinopyranosyl-β-d-glucopyranoside (5), two oligoglycosides, n-hexyl-α-l arabinopyranosyl-(1 → 6)-β-d-glucopyranoside (creoside) (7) and n-octyl α-l-arabinopyranosyl-(1 → 6)-β-d-glucopyranoside (rhodiooctanoside) (8); and ethyl fructofuranoside (10). The structures of the isolated compounds were elucidated based on extensive examination of their spectroscopic 1D and 2D-NMR, MS, UV, and IR data. It is worth mentioning that, some of the isolated linalol glycoside derivatives were reported as aroma precursors.

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.

A novel 6-hydroxy-8,11,11-trimethyl-bicyclo[7.2.0]undec-4-ene-4-carboxylic acid: a potent antioxidant agent from Iphiona scabra

A novel 6-hydroxy-8,11,11-trimethyl-bicyclo[7.2.0]undec-4-ene-4-carboxylic acid 1 has been isolated from leaves of Iphiona scabra DC. Its structure has been established on the basis of chemical and physical evidence (IR, ¹H NMR, ¹³C NMR, and MS) and further confirmed by single-crystal X-ray diffraction study. The in vitro antioxidant activities of isolated compound 1 and extracts were evaluated by 1,1-diphenyl-2-picrylhydrazyl method.

A new benzofuranic acid from the leaves of Rhus alata

From leaves of Rhus alata, one new benzofuranic acid named [(2E)-3-(4-hydroxy-5,7-dimethyl- benzo[3,4-b] furan-6-yloxy)-prop-2-enoic acid has been isolated together with eight known compounds: dimethyl ester of terephthalic acid, beta-amyrin, friedelin, lupeol, beta-sitosterol, oleanolic acid, taraxerone and ethyl gallate. Structural elucidations were done on the basis of chemical and physical data (IR, UV, 1H-NMR, 13C-NMR and MS spectra).

A new chromone from Ficus lyrata

A new chromone, named 5,6-dihydroxy-2-methylchromone (FL-2), along with seven known flavonoids, 5-hydroxy-7,3,3',4'-tetramethoxyflavone (FL-3), 5,4'-dihydroxy-6,7,8-trimethoxyflavone (FL-4), 5,4'-dihydroxy-7,8-dimethoxyflavone (FL-5), 4-methoxychalcone (FL-6), 7,4'-dimethoxyapigenin (FL-7), 5,7,4'-trihydroxy-2',3',6'-trimethoxyisoflavone (FL-8 a rare flavonoid), acacetin-7-O-glucoside (FL-9) and acacetin-7-O-neohesperidoside (FL-10), and beta-sitosterol-D-glucoside (FL-1) have been isolated from the leaves of Ficus lyrata. Their structures have been established on the basis of chemical and spectral evidence (IR, UV, 1H NMR, 13C NMR and mass spectra).