Molecular docking analysis of mTOR protein kinase with chromatographically characterized compounds from Clerodendrum inerme L. leaves extract

The mTOR protein is known to be linked with cancer. Therefore, it is of interest to document the molecular docking analysis of mTOR protein kinase with chromatographically characterized compounds from Clerodendrum inerme L. leaves extract. The GC-MS analysis suggested that, totally 25 bioactive compounds were present in the extract of Clerodendrum inerme. Molecular docking analysis show that the bioactive compounds such as Triethoxysilanol, Piperazine dihydrochloridehydrate, 2,4(1H,3H)-Pyrimidinedione, 5-methyl and 4'',7-Dihydroxyflavanone showed good glide score and glide energy within the acceptable and permissible limits of ADME properties for further consideration in drug discovery.     

Molecular docking analysis of potential compounds from an Indian medicinal soup "kabasura kudineer" extract with IL-6

The use of "kabasura kudineer" (liquid soup made from Indian medicinal plants) for combating COVID-19 has been common in the states of Tamilnadu and Puducherry, India during the pandemic. Therefore, it is of interest to document the molecular docking analysis of IL-6 inhibitors with potential antiviral compounds from "kabasura kudineer" extract. We show the optimal binding features of gallic acid and luteolin with the Interleukin-6 protein for further consideration.     

辣木种子主要成分分离制备及功能应用研究进展

辣木是亚洲和非洲广泛种植的一种药食同源植物。辣木生长快、种子产量高,每公顷辣木可产种子24 t。辣木种子含油19%～47%,蛋白质10%～52%,硫代葡萄糖苷及其水解产物异硫氰酸酯6.2%～8.6%。辣木油具有抗氧化、抗菌和抗炎作用,其不饱和脂肪酸含量高达71.7%～83.1%,是优质的食用油来源。辣木蛋白具有抗菌作用,是良好的食用和饲料用蛋白源。辣木种子所含硫代葡萄糖苷及其水解产物异硫氰酸酯有抗炎、抗肿瘤和降血糖等作用。辣木种子具有较高的开发利用价值。本文综述辣木种子上述四种主要成分分离制备和功能应用的研究进展,为辣木种子综合开发利用提供参考。     

Determination and quantification of sinigrin glucosinolates in Alternaria solani susceptible tomato (Solanum lycopersicum) leaves treated with moringa (Moringa oleifera) leaf extract

Abstract

The study investigates the presence and quantity of antimicrobial sinigrin glucosinolates in tomato leaves after spraying them with moringa (Moringa oleifera) leaf extract (MLAE). Moringa concentrates (0.5, 0.75, 1.00 and 1.5?kg?L^?1 (w v^?1)) were prepared. Distilled water was the control. Sampled tomato leaves were air-dried, freeze-dried and extracted firstly using pure methanol in a hot water bath and then pellet re-extracted using 5?mL of hot aqueous methanol (70% v v^?1). An ion exchange column, and sulphatase was used to achieve glucosiodesulphonation. High performance liquid chromatography (HPLC) was employed in the identification and quantitative analysis of the sinigrin glucosinolates. Tomato (Solanum lycopersicum) leaves treated with MLAE revealed highly significant (p?<?.001) content of sinigrin glucosinolates. The sinigrin standard and the desulphated sinigrin glucosinolates had a 7?s retention time difference; 5?kg?L^?1 (w v^?1) resulted in a superior amount of sinigrin in tomato leaves as compared to all the other MLAE concentrations. The study reveals that spraying MLAE on putatively diseased tomato leaves donates specific quantifiable glucosinolates like sinigrin, which may be involved in defense against tomato diseases and, hence, recommends use of 5?kg?L^?1 (w v^?1) for the highest sinigrin defense tag.     

Unique antioxidant effects of herbal leaf tea and stem tea from Moringa oleifera L. especially on superoxide anion radical generation systems

ABSTRACT

This study aimed to investigate the unique antioxidative effects of Japanese moringa products, herbal leaf tea and stem tea, using established free radical assays, focusing on superoxide anion (O₂^?) radical generation systems. Hot-water extracts from moringa teas resulted in different but lower scavenging activities than Trolox in four synthetic free radical models. Interestingly, these extracts further showed higher O₂^? radical scavenging effects than Trolox in the phenazine methosulfate-NADH-nitroblue tetrazolium and xanthine oxidase assay systems. Incubating human neutrophils in the presence of these tea extracts rather than Trolox effectively suppressed cellular O₂^? radical generation. Among the eight known phenolic constituents of moringa leaves, caffeic acid and chlorogenic acid may be responsible for the O₂^–specific radical scavenging capacity stronger than that of Trolox. These results suggest that moringa herbal teas are a good source of natural antioxidants for preventing O₂^? radical-mediated disorders.

Abbreviations: O₂^?: superoxide anion; ROS: reactive oxygen species; H₂O₂: hydrogen peroxide; XOD: xanthine oxidase; DPPH: 1,1-diphenyl-2-picrylhydrazyl; ABTS⁺: 2,2′-azinobis(2-ethylbenzothiazoline-6-sulfonic acid) cation; CPZ⁺: chlorpromazine cation; PMS: phenazine methosulfate; NBT: nitroblue tetrazolium; PMA: phorbol 12-myristate 13-acetate     

Molecular docking based screening of predicted potential inhibitors for VP40 from Ebola virus

Ebola virus is a member of Filoviridae and cause severe human disease with 90 percent mortality. The life cycle of Ebola contains an assembly stage which is mediated by VP40 proteins. VP40 subunits oligomerize and form ring-structures which are either octamers or hexamers. Prevention of VP40 matrix protein assembly prevents virus particle formation as well as virus budding. In the present study we simulated the biological condition for a single VP40 subunit. Then a library containing 120.000 drugs like chemicals was used as the virtual screening database. Top 10 successive hits were then analyzed regarding absorption, distribution, metabolism, and excretion properties. Moreover probable accessorial human protein targets and toxicity properties of successive hits were analyzed by in silico tools. We found 4 chemicals that could bind VP40 subunits in a manner that by making an interfering steric condense prevents matrix protein oligomerization. The pharmacokinetic and toxicity studies also validated the potential of 4 finlay successive hits to be considered as a new anti-Ebola drugs.     

Synthesis,antioxidant, antifungal,molecular docking and ADMET studies of some thiazolyl hydrazones

Some thiazolyl hydrazones were synthesized by one pot reaction of thiophene-2-carbaldehyde or 2, 4-dichlorobenzaldehyde, thiosemicarbazide and various phenacyl bromides which were preliminarily screened for in vitro antioxidant and antifungal activities. Excellent DPPH and H₂O₂ radical scavenged antioxidant activities were observed with almost all the tested compounds. Compounds 4a, 4b, 4c, 4e, 4f and 4i showed comparable DPPH scavenged antioxidant potential (90.26–96.56%) whereas H₂O₂ scavenged antioxidant activity (90.98–92.08%) was noticeable in case of 4a and 4f; showing significant antioxidant potential comparable with the standard ascorbic acid (95.3%). In vitro antifungal activity of synthesized compounds against fungal species Candida albicance, Aspergillus niger and Aspergillus flavus was found to be moderate to good as compared with the standard fluconazole and MIC values were found in the range of 3.12–25 μg/mL. Molecular docking studies revealed that the compounds 4a, 4b and 4c have a potential to become lead molecules in drug discovery process. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized antioxidants which expressed good oral drug like behaviour and non-toxic nature.     

Phytoconstituents screening and antimicrobial activity of the invasive species Nicotiana glauca collected from Al-Baha region of Saudi Arabia

Nicotiana glauca belonging to the family Solanaceae is an exotic perinnial bushy species that recently has invaded the mountainous areas of Al-Baha region at the south-west of Saudi Arabia, causing degredation to soil and vegetation composition of those mountains. Accordingly, this plant must be either removed or exploited as a source of useful products such as medicines as it has been proven to contain many effective compounds with therapeutic properties. Thus, the current study aimd to screening N. glauca preliminary phytoconsitiuents and its anticmicrobial activity. Results showed that varying amounts of alkaloids, steroid, tannins, flavonoid, were present in the extracts of N. glauca leaves, stems and flowers. Saponins were present only in the flowers extract. However, all previuos bioactive compounds were absent in the roots except alkaloids, therefore, roots posses lesser amount of the phytoconstituents compared to the other parts of the plants. Leaves extracts inhibited the growth of E. coli (16.3 ± 0.71 mm) and also inhibited the growth of S. aureus (11.0 ± 0.23 mm), while, the flower extracts also inhibited the growth of E. coli (6.7 ± 0.65 mm), and also inhibited the growth of S. aureus (15.8 ± 0.52 mm). This result coincide with the previous results of the screening of N, glauca phytochemicals where the highest amounts found in leaves and flowers extracts. The inhibition zone of the antibiotic gentamycin (reference control) were 32 mm in S. aureus and 38 mm in E. coli. The inhibition zone of gentamycin (reference control) were 32 mm in S. aureus and 38 mm in E. coli. The minimum inhibitory concentration (MIC) of ethyl acetate was ranged (1.5–2 mg/ml). The lower MIC is an indication of high effectiveness of extract. Therefore, such bioactive property would support the idea that removing N. glauca from the mountainous areas of Al-Baha, Saudi Arabia, is not the only solution, but the plant can be exploited as a beneficial source of medicinal and economic purposes such as; antibacterial, antifungal and insecticidal, however, further comprehensive exploration is recommended to confirm such propreties.     

Deciphering the CNS anti-depressant,antioxidant and cytotoxic profiling of methanol and aqueous extracts of Trametes versicolor and molecular interactions of its phenolic compounds

The present study sought to evaluate the central nervous system (CNS) depressant, antioxidant, and cytotoxicity activity of methanol and aqueous extract of Trametes versicolor (METV and AETV). The CNS activity was assessed by the open field, hole-cross, forced swimming, thiopental sodium-induced sleeping time, hole-board, and rotarod tests in Swiss albino mice. For both extracts, a substantial decrease in locomotion was observed in open field and hole-cross tests. In addition, the molecular docking study has been implemented through Maestro V11.1. The higher dose of METV (400 mg/kg) and the lower dose of AETV (200 mg/kg) exhibited a significant decrease in immobility time in forced swimming test and increased prolongation of sleep in thiopental sodium-induced sleeping time test, respectively. In contrast, a moderate finding was observed for the hole-board and rotarod tests. Additionally, a significant DPPH scavenging assay and a high toxicity effect in brine shrimp lethality assay were observed. Besides, five phenolic compounds, namely baicalin, quercetin, catechin, p-hydroxybenzoic acid, and quinic acid, were used for the molecular docking study, whereas catechin demonstrated the highest binding affinity towards the targets. The findings conclude that the T. versicolor could be an alternative source for CNS anti-depressant and antioxidant activity.     

GC-MS-employed phytochemical characterization,synergistic antioxidant,and cytotoxic potential of Triphala methanol extract at non-equivalent ratios of its constituents

Triphala is a famous triherbal drug, comprising three herb fruits, including Terminalia chebula (Haritaki), Terminalia bellirica (Bibhitaki), and Phyllanthus emblica (Amalaki). It is enriched with vitamin C, polyphenols, flavonoids, sterols, saponins, etc., and is well-documented for its potent antioxidant, anticancer, chemoprotective, antimicrobial, and anti-inflammatory effects. This research was conducted to evaluate the synergistic antioxidative and cytotoxic potential of mixtures of the individual constituents of Triphala at their nonequivalent ratios along with the chemical characterization of individual constituents of Triphala to identify and quantify individual compounds. The antioxidative potential was measured using total antioxidant capacity (TAC), DPPH free radical scavenging assay, and total phenolic content (TPC) tests. The cytotoxic potential was assessed on brain cancer cells (N4X4) using MTT assay, and phytochemical characterization was performed by GS-MS analysis. Nonequivalent ratios of Triphala constituents exhibited significantly higher synergistic antioxidant and cytotoxic potential than the equivalent ratios of them. Moreover, the nonequivalent ratio where the quantity of Amalaki was doubled than the other two constituents showed the highest synergistic antioxidant and cytotoxic effect. GC-MS analysis of individual constituents of Triphala identified and quantified the presence of a wide array of compounds, and fatty acid, fatty acid ester, triterpene, and aminoglycoside remained the predominant class of compounds. Thus, it can be inferred that the observed bioactivities can be attributed to the phytocompounds characterized and extracts at the nonequivalent ratio of Triphala constituents where Amalaki is doubled can be more effective in treating oxidative degenerative diseases and glioblastoma.     

Repurposing of phytomedicine-derived bioactive compounds with promising anti-SARS-CoV-2 potential: Molecular docking,MD simulation and drug-likeness/ADMET studies

In view of the potential of traditional plant-based remedies (or phytomedicines) in the management of COVID-19, the present investigation was aimed at finding novel anti-SARS-CoV-2 molecules by in silico screening of bioactive phytochemicals (database) using computational methods and drug repurposing approach. A total of 160 compounds belonging to various phytochemical classes (flavonoids, limonoids, saponins, triterpenoids, steroids etc.) were selected (as initial hits) and screened against three specific therapeutic targets (Mpro/3CLpro, PLpro and RdRp) of SARS-CoV-2 by docking, molecular dynamics simulation and drug-likeness/ADMET studies. From our studies, six phytochemicals were identified as notable ant-SARS-CoV-2 agents (best hit molecules) with promising inhibitory effects effective against protease (Mpro and PLpro) and polymerase (RdRp) enzymes. These compounds are namely, ginsenoside Rg2, saikosaponin A, somniferine, betulinic acid, soyasapogenol C and azadirachtin A. On the basis of binding modes and dynamics studies of protein–ligand intercations, ginsenoside Rg2, saikosaponin A, somniferine were found to be the most potent (in silico) inhibitors potentially active against Mpro, PLpro and RdRp, respectively. The present investigation can be directed towards further experimental studies in order to confirm the anti-SARS-CoV-2 efficacy along with toxicities of identified phytomolecules.     

Eco-friendly synthesis of silver nanoparticles from the whole plant of Cleome viscosa and evaluation of their characterization,antibacterial, antioxidant and antidiabetic properties

The current research is to develop an easy and eco-friendly method for the synthesis of three different concentrations of silver nanoparticles (1mMCvAgNPs, 2mMCvAgNPs and 3mMCvAgNPs) using aqueous whole plant extract of Cleome viscosa and to evaluate their antibacterial, antioxidant and antidiabetic properties. CvAgNPs were characterized by Using UV–vis spectrophotometer, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), scanning electron microscope (SEM) and transmission electron microscope (TEM). The formation of CvAgNPs was confirmed by the observation of band between 250 nm to 600 nm UV–vis spectrum. The crystalline structure of CvAgNPs with a face-centered cubic (FCC) was confirmed by XRD. The responsible phytochemicals for the reduction and capping material of CvAgNPs were observed with FT-IR. The SEM analysis confirmed the size and shapes of CvAgNPs. The CvAgNPs have shown the rich content of total phenolic and total flavonoid components. The CvAgNPs have shown significant antibacterial activity on multi drug resistance Gram-negative and Gram-positive bacteria and also have shown significant strong antioxidant activities (DPPH, ABTS, H₂O₂ scavenging, Phosphomolybdenum assay and reducing power). The inhibitory action of CvAgNPs on α-glucosidase and α-amylase was stronger than the inhibitory action of acarbose. To best of our knowledge, this is the first attempt on the synthesis of AgNPs using C. viscosa whole plant aqueous extract. The synthesized CvAgNPs exhibited good antimicrobial, antioxidant and antidiabetic properties. Hence, to validate our results, the in vivo studies at the molecular level are needed to develop Cleome viscosa as an antibacterial, antioxidant and anti-diabetic agent.     

Phytochemical profiling,antioxidant and antiproliferation potential of Euphorbia milii var.: Experimental analysis and in-silico validation

This study was aimed to investigate the anticancer potential of Euphorbia milii (E. milii) using an exquisite combination of phytopharmacological and advanced computational techniques. The chloroform fraction (Em-C) of E. milii methanol extract showed the highest antioxidant activity (IC₅₀: 6.41 ± 0.99 µg/ml) among all studied fractions. Likewise, Em-C also showed significant cytotoxicity (IC₅₀: 11.2 ± 0.8 µg/ml) when compared with that of standard compound 5-fluorouracil (5-FU) (IC₅₀: 4.22 ± 0.6 µg/ml) against hepatocarcinoma cell line (HepG2). However, in a human cervical cancer cell line (HeLa), Em-C demonstrated a non-significant difference in cytotoxicity (22.1 ± 0.8 µg/ml) when compared with that of 5-FU (IC₅₀: 6.87 ± 0.5 µg/ml). Furthermore, Western blot and qRT-PCR analysis revealed that the suppression of HepG2 cells was the consequence of a tremendous decrease in CDK2 and E2F1 protein expression. The GC–MS analysis of Em-C revealed the unique presence of cyclobarbital (CBT) and benzodioxole derivative (BAN) as major constituents. Furthermore, molecular docking of compounds BAN, CBT, and MBT into the binding site of different molecular targets i.e. cyclin dependent kinase 2 (CDK2), thymidylate synthase (TS), caspase 3, BCL2 and topoisomerase II was carried out. Compounds BAN and CBT have demonstrated remarkable binding affinity towards CDK2 and thymidylate synthase, respectively. Molecular dynamic simulation studies have further confirmed the finding of docking analysis, suggesting that CDK2 and TS can act as an attractive molecular target for BAN and CBT, respectively. It can be concluded that these E. milii phytoconstituents (BAN and CBT) may likely be responsible for anti-invasive activity against HepG2 cells.     

Meglumine as a green,efficient and reusable catalyst for synthesis and molecular docking studies of bis(indolyl)methanes as antioxidant agents

An efficient and convenient Meglumine catalyzed procedure for the synthesis of bis(indolyl) methanes at ambient temperature under aqueous conditions in high yields. The catalytic reaction proceeds very smoothly. Clean reaction, ease of product isolation/purification, easily available reactants, metal free and environmentally friendly reaction conditions are the notable advantages of the present methodology. All the entitled compounds were characterized by IR, ¹H, ¹³C NMR, mass spectra and evaluated for their antioxidant (DPPH, H₂O₂ and NO scavenging methods). They exhibited potent in vitro antioxidant activity dose-dependently. The binding interactions and molecular docking studies for entitled compounds were studied against 3MNG protein. 4d exhibited marked binding affinity with excellent docking score of −7.6 K.cal/mol and emerged as a lead compound.     

Studies on the antioxidant activity and phenolic compounds of enzyme-assisted water extracts from Du-zhong (Eucommia ulmoides Oliv.) leaves

Enzyme-assisted water extracts (EWEDL) and ethanol extracts of Du-zhong leaves (EEDL) were evaluated for their antioxidant activities using the DPPH radical-scavenging assay, Fe²⁺-chelating assay, and inhibition ability of the linoleic acid peroxidation assay. In general, the antioxidant activity of Du-zhong leaf extracts increased with increasing concentration. Based on the two extracting methods with different antioxidative reactions, it was shown that the enzyme-assisted water extracting method was more effective for antioxidant extraction from Du-zhong leaves. By HPLC-MS analysis, the main phenolic compounds (geniposidic acid, epicatechin, and chlorogenic acid) identified in EWEDL and EEDL were similar. EWEDL and EEDL had total phenolic contents of 13.84?±?0.11 and 14.72?±?0.14?mg chlorogenic acid equivalents (CAE) in each gram of extract, respectively. However, there was no positive correlation between total phenolic content and antioxidant activities of EWEDL and EEDL measured by the three different assays.     

Molecular docking and structure-based virtual screening studies of potential drug target,CAAX prenyl proteases,of Leishmania donovani

Targeting CAAX prenyl proteases of Leishmania donovani can be a good approach towards developing a drug molecule against Leishmaniasis. We have modeled the structure of CAAX prenyl protease I and II of L. donovani, using homology modeling approach. The structures were further validated using Ramachandran plot and ProSA. Active site prediction has shown difference in the amino acid residues present at the active site of CAAX prenyl protease I and CAAX prenyl protease II. The electrostatic potential surface of the CAAX prenyl protease I and II has revealed that CAAX prenyl protease I has more electropositive and electronegative potentials as compared CAAX prenyl protease II suggesting significant difference in their activity. Molecular docking with known bisubstrate analog inhibitors of protein farnesyl transferase and peptidyl (acyloxy) methyl ketones reveals significant binding of these molecules with CAAX prenyl protease I, but comparatively less binding with CAAX prenyl protease II. New and potent inhibitors were also found using structure-based virtual screening. The best docked compounds obtained from virtual screening were subjected to induced fit docking to get best docked configurations. Prediction of drug-like characteristics has revealed that the best docked compounds are in line with Lipinski’s rule. Moreover, best docked protein–ligand complexes of CAAX prenyl protease I and II are found to be stable throughout 20 ns simulation. Overall, the study has identified potent drug molecules targeting CAAX prenyl protease I and II of L. donovani whose drug candidature can be verified further using biochemical and cellular studies.     

Biological evaluation,molecular docking and DNA interaction studies of coordination compounds gleaned from a pyrazolone incorporated ligand

Abstract

In this work, we have synthesized a few novel mononuclear complexes of Cu(II), Co(II), Ni(II) and Zn(II) using a pyrazolone-derived Schiff base ligand. They were characterized by spectroscopic and analytical methods. The elemental analyses, UV-Vis, magnetic moment values and molar conductance of the complexes reveal that the complexes adopt an octahedral arrangement around the central metal ions. The interaction of complexes with CT-DNA was studied by absorption spectral titration and viscosity measurements. The observed data show that the complexes bind with CT-DNA via an intercalation mode. Efficient pUC18 DNA cleavage ability of the synthesized compounds was explored by gel electrophoresis. The antimicrobial activity of these compounds against a set of bacterial and fungal strains reveals that the complexes exhibit better activity than the free ligand. Moreover, all the complexes were evaluated against two cancer (HeLa and HepG2) and one normal (NHDF) cell lines. The data were compared with cisplatin. Anti–inflammatory activity has been experimentally validated which proves that theoretical predictions concur with the experimental results. In addition, molecular docking studies have been performed to consider the nature of binding mode and binding affinity of these compounds with DNA (1BNA) and protein (3hb5). These studies reveal that the mode of binding is intercalation and the complexes have higher binding energy scores than the free ligand.     

Identification,characterization, kinetics,and molecular docking of flavonoid constituents from Archidendron clypearia (Jack.) Nielsen leaves and twigs

In our search for natural soluble epoxide hydrolase (sEH) inhibitors from plants, we found that the methanolic extract of the leaves and twigs of Archidendron clypearia (Jack.) Nielsen (Fabaceae) significantly inhibits sEH in vitro. In a phytochemical investigation of the water layer of A. clypearia, we isolated two new chalcones, clypesides A–B (1–2), 13 flavonoid derivatives (3–15) and established their structures based on an extensive 1D and 2D NMR, CD data, and MS analysis. All of the flavonoid derivatives inhibited sEH enzymatic activity in a dose-dependent manner, with IC₅₀ values ranging from 10.0 ± 0.4 to 30.1 ± 2.1 μM. A kinetic analysis of compounds 4, 8–10, 12, 13, and 15 revealed that the compounds 8–10 were non-competitive, 4, 13, and 15 were mixed-type, and 12 was competitive inhibitors. Additionally, molecular docking increased our understanding of their receptor-ligand binding. These results demonstrated that flavonoid derivatives from A. clypearia are potential sEH inhibitors.     

Design,synthesis and biological evaluation of 2-mercapto-3-phenethylquinazoline bearing anilide fragments as potential antitumor agents: Molecular docking study

A novel series of 2-(3-phenethyl-4(3H)quinazolin-2-ylthio)-N-substituted anilide and substituted phenyl 2-(3-phenethyl-4(3H) quinazolin-2-ylthio)acetate were designed, synthesized and evaluated for their in-vitro antitumor activity. Compound 15 possessed remarkable broad-spectrum antitumor activity which almost sevenfold more active than the known drug 5-FU with GI₅₀ values of 3.16 and 22.60 μM, respectively. Compound 15 exhibited remarkable growth inhibitory activity pattern against renal cancer (GI₅₀ = 1.77 μM), colon cancer (GI₅₀ = 2.02 μM), non-small cell lung cancer (GI₅₀ = 2.04 μM), breast cancer (GI₅₀ = 2.77 μM), ovarian cancer (GI₅₀ = 2.55 μM) and melanoma cancer (GI₅₀ = 3.30 μM). Docking study was performed for compound 15 into ATP binding site of EGFR-TK which showed similar binding mode to erlotinib.