Molecular docking assisted biological functions and phytochemical screening of Amaranthus lividus L. extract

In this study, phytochemical analysis and multi-biological functions of A. lividus leaf extract were investigated. Total phenolic, total flavonoid, saponin and condensed tannin contents were determined in phytochemical analyzes and also GC–MS and HPLC analyzes were performed. The biological functions of the extract were determined by testing its free radical scavenging, anti-bacterial, anti-fungal, anti-mutagenic and anti-proliferative activities. Each biological function was evaluated concerning the phytochemical content and compared with the literature examples. The mechanisms of anti-bacterial and antiproliferative activity of the extract were also interpreted by molecular docking studies.

Extraction efficiency, phenolic and flavonoid content

A. lividus leaves were extracted in different solvents and the extraction efficiency was determined by investigating extracted substance, the phenolic and flavonoid content in each solvent. The total phenolic and flavonoid contents obtained by extraction in different solvents and the amount of extracted substance are given in Fig. 1. The highest extractable yield was obtained with water extraction, followed by methanol and ethanol, respectively. After extraction with water, methanol and ethanol, 1.9 g, 1.4 g and 1.3 g solids were obtained, respectively. The role of phenolic and flavonoid compounds in the antioxidant properties of herbal extracts is quite high. Although the amount of extract obtained with water is high, methanol and ethanol solvents were found to be more effective in the extraction of phenolic and flavonoid substances. A medium level of phenolic content was determined in A. lividus leaf extract and the highest phenolic content was found as 3.9 mgGAE/100 mg in the extraction with methanol. In terms of phenolic content, the performances of the solvents showed an order of methanol > ethanol > water. Flavonoid compounds obtained from A. lividus leaf extract were found as 1.49, 2.01 and 1.56 mgQE/100 mg for water, methanol and ethanol solvents, respectively. In terms of flavonoid content, the efficiency of the solvents were ranked as methanol > ethanol > water, but the performances of ethanol and water solvents were similar.

Many studies have shown that methanol and ethanol are effective solvents, especially for the extraction of phenolic compounds²⁶. The polarity of the solvent used in the extraction of phenolic and flavonoid compounds and the solubility of each compound are very important factors. Differences in the polarity of the solvents used in the extraction may also cause variation in the solubility of bioactive compounds. The high efficiency of polar solvents in the extraction of plant tissues has been demonstrated by many studies. Plant tissues contain polar compounds with high solubility in polar solvents such as water, methanol and ethanol. In this study, the higher yield of phenolics and flavonoids obtained in the methanolic extract may be associated with the higher solubility of these compounds in methanol. Similarly, Truong et al.²⁷ reported that the methanolic extract of Severinia buxifolia, which they extracted with different solvents, exhibited higher phytochemical content, anti-oxidant and anti-inflammatory activity compared to all other extracts tested. Another important result obtained from our study is that the phenolic content detected in the leaf extract of A. lividus is higher than the flavonoids. It has been reported in the literature that various phytochemical compounds were determined in A. lividus extracts. Ozsoy et al.⁵ extracted the leaf and flower tissues of A. lividus and reported that the highest phenolic content was obtained by ethyl acetate extraction and they found a phenolic content of 22.8 mg GAE/g. Nehal et al.¹⁰ identified flavonoid content at the range of 4.81–5.04 RE/mg under different extraction conditions in A. lividus leaves.

Condensed tannin and total saponin content

Condensed tannin and saponin contents of the A. lividus leaf extract obtained in different solvents are given in Fig. 1. While the highest saponin and tannin contents were obtained in the extracts obtained with methanol, similar levels of each content were obtained in the ethanol and water extracts. It was determined that methanol, ethanol and water extracts contained 15.7 mg QAE/g, 10.6 mg QAE/g and 8.5 mg QAE/g saponin, respectively. The condensed tannin content was determined as 5.6 mg GAE/g in the methanol extract at a lower level compared to the saponin. Saponins are a phytochemical found structurally in many species of both wild and arable plants. It is also known that saponins protect plants against microorganisms, fungus and insect attacks. Saponins have hypoglycemic activity, cholesterol-lowering effect, anti-inflammatory and anti-oxidant activity²⁸. The wide varieties of biological activities of saponins enable them to exhibit protective properties against many diseases and toxicities. The intense saponin content detected in the extract indicates that consumption of A. lividus in the daily diet will reduce risks such as hyperglycemia, inflammation and hypercholesterolemia.

A. lividus leaves, which contain less condensed tannin compared to saponins, gain various biological properties due to the biological activities of tannin molecules. Condensed tannins, also known as proanthocyanidins, are composed of numerous flavonoid units linked by carbon–carbon bonds. In addition to their high anti-oxidant properties, condensed tannins have anti-inflammatory, anti-asthmatic, anti-cancer, anti-viral, anti-carcinogenic, anti-allergic, anti-microbial, anti-hypertension and preventive properties against cardiovascular risks. Wound healing, reducing insulin resistance, protection against drug toxicity, and cholesterol-lowering effects of condensed tannins are also reported in the literature²⁹. Saponin and condensed tannins, which have intense biological activity, ensure that the leaves of A. lividus exhibit significant effects.

GC–MS and HPLC analysis

The GC–MS spectrum of A. lividus extract is given in Fig. 2 and the presence of various bioactive compounds was determined. The compounds detected in extract were ranked as phytol > β-sitosterol > octademethylcyclononasiloxane > heptadecane > tetradecane > cyclodecane according to their presence rates. Among the active ingredients, phytol has a high rate as the major component. Phytol has anti-cancer, anti-oxidant, anti-inflammatory, anti-tumor, anti-microbial, diuretic properties and is frequently used in vaccine formulations³⁰. Phytol has strong anti-oxidant activity due to the allylic structure of the alcohol group. The antioxidant activity of phytol occurs by the reaction of hydrogen atoms with free radicals, resulting in the conversion of free radicals to less reactive species³¹. Phytol, which has a lipophilic character, also exhibits anti-bacterial properties by passing through bacterial cell membranes and damaging macromolecules such as proteins, lipids and DNA within the cell³². β-sitosterol, one of the other major compounds detected in GC–MS, plays an important role in the regulation of fatty acid chains in the cell membrane. The anti-microbial and anti-tumor properties of β-sitosterol are also reported³³. Hydrocarbons with high molecular weight such as heptadecane, tetradecane and cyclodecane detected in the extract content exhibit anti-microbial activity by showing an inhibitory effect on microorganisms³⁴. Biological activities of all bioactive components detected by GC–MS analysis ensure that A. lividus leaves also exhibit multi-biological activity. In the literature, the phytochemical contents of Amaranthus species collected from different ecological environments were investigated by GC–MS analysis. Nehal et al.¹⁰ reported that A. lividus leaf and stem extract contains high levels of β-sitosterol and phytols as a result of GC–MS analysis, and minor compounds such as ergost-5-en-3-ol, (3, β), hexadecanoic acid and tetradecane. Paranthaman et al.³⁵ determined that the extracts of Amaranth caudatus contain high levels of phytol, while at lower rates they contain many minor compounds such as pseudoephedrinei, 1,2,4-butanetriol, N-ethyl-N′-nitroguanidine.

HPLC spectrum of A.lividus extract is given in Fig. 2 and the presence of various phenolic compounds in the extract was determined. Gallic acid, vanillin, caffeic acid, rutin, kaemferol, ferulic acid and quercetin were used as standards, and the presence of gallic acid, caffeic acid, quercetin, vanillin and kaemferol compounds were determined in the A. lividus extract among the tested standards. The rates of gallic acid and caffeic acid in the extract are higher than the other active ingredients, and therefore these two compounds were identified as the major compounds in the extract, while quercetin, vanillin and kaemferol were defined as minor compounds. Gallic acid (3,4,5-trihydroxybenzoic acid), a low molecular weight triphenolic compound, is a powerful anti-oxidant, anti-inflammatory, anti-tumor, anti-diabetic and anti-obesity agent^36,37. Caffeic acid, one of the major compounds in the extract, has many pharmacological properties such as anti-inflammatory, anti-cancer and anti-viral. It is also an antioxidant that can reduce oxidative stress caused by free radicals³⁸. Vanillin and kaemferol detected as minor compounds in the extract have a wide variety of pharmacological effects, including anti-oxidant, anti-microbial, anti-cancer, neuroprotective and anti-diabetic activities^39,40. Quercetin, a flavonoid glycoside detected in the extract by HPLC analysis, is a compound with anti-cancer, anti-tumor, anti-ulcer, anti-allergy, anti-viral, anti-inflammatory, anti-diabetic, anti-hypertensive and immunomodulatory activities⁴¹. The cumulative effects of active metabolites such as gallic acid, caffeic acid, quercetin, vanillin and kaemferol provide a high biological and pharmacological effect to A. lividus leaf extract. Similarly, Paranthaman et al.³⁵ found that Amaranthus caudatus extract contains intense amounts of gallic acid and rutin, and lower amounts of caffeic acid, ferulic acid and quercetin by HPLC analysis.

Radical scavenging activity

The radical scavenging activity of A. lividus leaf extract, which has rich phytochemical content, was tested against DPPH and superoxide radicals, and the results are given in Fig. 3. The radical scavenging activities of A. lividus extract and standard BHT increased with the increase in dose and the highest scavenging activity of A. lividus extract was obtained at a dose of 4 mg/mL. DPPH removal activity of 4 mg/mL BHT and A.lividus extract was determined as 90.1% and 75.6%, respectively. Superoxide removal activity was determined as 80.9% for BHT and 85.2% for A. lividus extract. A. lividus extract showed a higher activity in removing superoxide, which is a dangerous free radical in organisms, compared to BHT, a synthetic antioxidant. Superoxide formed during the reduction of oxygen in cells has radical properties and is an important reactive oxygen product. The superoxide radical reacts with organic substrates in the cell, leading to the formation of more intermediates that cause oxidative damage⁴². The superoxide radical formed in the cell under normal conditions can be neutralized by the endogenous anti-oxidants. However, the formation of superoxide at a higher level that can disrupt oxidant/antioxidant balance causes oxidative damage in the cell, and therefore exogenous anti-oxidant supplementation gains importance. The determination of superoxide removal activities of plants with high anti-oxidant content also comes to the fore. DPPH is a free radical and anti-oxidants react with DPPH by providing an electron or hydrogen atom and form the reduced product DPPH-H. Spectrophotometric measurement of this reduction reaction is used to determine the anti-oxidant activity of medicinal plants, fruits or other biological substrates⁴³.

The high superoxide and DPPH scavenging activity of A. lividus extract show its high anti-oxidant activity. This activity is related to the phytochemical content of A. lividus extract. The saponins in A. lividus contribute to the radical scavenging activity with their proton supply capacity, free radical inhibition and primary anti-oxidant functions⁴⁴. Tannins, like saponins, contribute to the radical scavenging activity by providing hydrogen atoms or electrons⁴⁵. Phytol, the major compound, also contributes to the radical scavenging activity. Phytol exhibits good anti-oxidant activity due to the allylic structure of the alcohol group. The anti-oxidant activity of phytol is realized by the mechanism of reaction with free radicals and conversion to less reactive species³¹. Phenolic compounds detected in the extract by HPLC analysis also have an intense contribution to the radical scavenging activity. Gallic acid, the major compound in the extract, is a versatile radical scavenger that provides rapid neutralization of a wide variety of reactive oxygen species via electron transfer⁴⁶. Bioactive compounds detected in all phytochemical analyzes carried out within the scope of this study provide the formation of radical scavenging activity of A. lividus leaf extract, and major compounds such as gallic acid, caffeic acid and phytol contribute to this effect being stronger. Natural antioxidant production in organisms decreases due to increasing age and exposure to intense oxidative stress. It is an important alternative to herbal antioxidants to close this gap. Herbal antioxidants play a role in preventing abnormal cell proliferation and protecting cells damaged by oxidation. With its intense antioxidant content and high radical scavenging activity, A. lividus protects macromolecules against oxidation and ensures the continuation of cell viability. In the literature, the radical scavenging activity of A. lividus samples grown under different ecological conditions was tested against various radical species and different results were obtained. Nehal et al.¹⁰ reported that A. lividus leaf extract, distributed in India, exhibited a DPPH removal activity of approximately 80% at a dose of 5 mg/mL. Ozsoy et al.⁵ determined that A. lividus samples grown in Bartın (Turkey) exhibited 89.9% DPPH removal activity at 40 mg/mL concentration and 92.8% hydroxyl radical removal activity at 20 mg/mL concentration.

Anti-bacterial and anti-fungal activity

The anti-bacterial and anti-fungal activities of A. lividus extract are given in Table 1. Different inhibition zones were formed against all tested bacterial species. The highest inhibition zone was 14.3 ± 0.7 mm against B. subtilis, and the lowest zone was 7.7 ± 0.5 mm against P. aeruginosa. The fact that A. lividus extract forms an inhibition zone against all tested gram-negative and gram-positive bacteria indicates that it has a broad spectrum. However, A. lividus extract generally showed higher anti-bacterial activity against gram positives when compared to gram-negatives. This selectivity against bacteria is due to the structural difference between gram-positive and gram-negative bacteria. In gram-negative bacteria, the inner and outer membrane surrounding the cell is the main cause of resistance to anti-microbial compounds. The outer membrane of gram-negative bacteria provides resistance to bactericidal effects by preventing many compounds from entering the cell. Since this selective outer membrane is absent in gram-positive bacteria, anti-microbial compounds show higher efficacy⁴⁷. A. lividus extract formed a similar inhibition zone against C. krusei and C. albicans. When the anti-fungal and anti-bacterial activities of A. lividus extract were compared, it was observed that a higher inhibition zone was formed against bacteria. This indicates that the extract is more effective against bacteria compared to fungi. This result is closely related to the cell wall of fungi, especially rich in chitin and ergosterol. It is known that Candida species increase the development of resistance by increasing chitin levels in the cell wall in the presence of anti-microbial agents⁴⁸. The anti-bacterial and anti-fungal activity of A. lividus extract is closely related to the active ingredients it contains. Phytol, which is determined as a major compound and has a lipophilic character, can easily pass through the cell membrane in bacteria, causing disruption of membrane integrity, loss of basic cellular components and oxidative damage by damaging macromolecules such as proteins, lipids and DNA³². Gallic acid detected in the extract inhibits efflux pumps, folate synthesis and arginase activity in bacteria⁴⁹. The interaction of gallic acid and phytol with bacterial components was also demonstrated by molecular docking study and potential bindings were also revealed in this study. Vanillin, one of the minor compounds, disrupts the membrane integrity in bacteria, causes intracellular K ions to leak out of the cell and changes the intracellular pH homeostasis⁵⁰. The active compounds detected by GC–MS and HPLC have cidal effects on bacteria and fungi by different mechanisms, which enables A. lividus to exhibit anti-bacterial and anti-fungal activity.

In the literature, the anti-microbial activity of Amaranthus species was tested and different degrees of inhibition zones were reported. Nehal et al.¹⁰ investigated the anti-bacterial activity of A. lividus leaf and stem extract and reported that the highest effect was obtained against B. subtilis with an inhibition zone of 12.7 mm. They determined that an inhibition zone was not formed against S. aureus and P. aeruginosa. Mayio et al.⁵¹ observed that A. hybridus, A. spinosus and A. caudatus species had different degrees of anti-bacterial activity and were ineffective against Candida albicans. They stated that the anti-bacterial activity of the Amaranthus species was related to active pharmacological compounds such as flavonoids, steroids and terpenoids.

Molecular docking for anti-bacterial activity

In order to understand the mechanism of antimicrobial activity of the extract, molecular docking of active ingredients in extract with bacterial proteins was performed. The major components, which are intensely found in an extract, have an important role in the formation of biological activity compared to the minor components. For this reason, gallic acid and phytol, which are the major compounds detected in A. lividus extract by HPLC and GC–MS analyses, respectively, were used in molecular docking studies. Molecular docking of both components was done with aquaporin and arginase. Cell membrane integrity in bacteria is an important factor for the viability of the cell. In particular, cell membrane permeability has an important place in the regulation of intracellular and extracellular osmotic pressure. Aqauporins are important pumps in the cell membrane and are target molecules of many bacteriocidal agents. Therefore, molecular docking with aquaporin and major components of extract was investigated. Another protein (enzyme) arginase was investigated within the scope of molecular docking. Arginase is an enzyme involved in the metabolism of arginine, which is an important pathway in bacterial pathogenesis. Inhibitions in this pathway in bacterial infections are an important beacon of hope for treatment. For this reason, the interaction of the major components in the extract with arginase was also investigated. The results of molecular docking based on binding energy revealed that phytol and gallic acid have capable to interact with aquaporin-z and arginase. The phytol made hydrogen bonding and hydrophobic interaction to amino acid residues of aquaporin-z with a binding energy of − 5.21 kcal/mol and inhibition constant of 150.52 uM (Fig. 4a, Table 2). The amino acid residues of aquaporin-z have interacted with gallic acid made hydrogen bond and hydrophobic interactions which involved binding energy of − 3.62 kcal/mol and inhibition constant of 2.21 mM (Fig. 4b, Table 2). With binding energy of − 3.75 kcal/mol and inhibition constant of 1.78 mM, the phytol formed hydrogen bonds and hydrophobic interactions with amino acid residues of arginase (Fig. 5a, Table 2). Gallic acid formed hydrogen bonds and hydrophobic interactions with arginase amino acid residues with a binding energy of − 4.13 kcal/mol and an inhibition constant of 943.01 uM (Fig. 5b, Table 2). Phytol and gallic acid interact with many proteins and provide protection against various microbial infections. In literature, it is reported that phytol makes molecular docking by forming hydrogen bonds with glycine amino acids in the receptor to which Mycobacterium tuberculosis binds, and causes receptor inhibition⁵². Arsianti et al.⁵³ reported that gallic acid derivatives interact strongly with malarial dihydrofolate reductase in molecular docking study and reported that gallic acid derivatives were protective against malaria caused by Plasmodium parasite.

Anti-proliferative activity

The anti-proliferative activity of A. lividus extract was determined by the Allium test based on MI percentages and the results are given in Table 3. The anti-proliferative effect of A. lividus extract was evaluated by comparing the negative and positive control groups. While 291 out of 5.000 cells in the negative control group were in the dividing stage, the number of dividing cells decreased by 2.9 times to 99 in the glyphosate treated group. The proliferation-reducing effect of glyphosate is associated with abnormality in cell cycle checkpoints, particularly at the G₂/M transition point^54,55. A. lividus extract showed a proliferation-reducing effect in dividing A. cepa meristem cells. It has been determined that A. lividus extract has a reducing effect on the number of dividing cells and exhibits an anti-proliferative effect of 25.7% compared to the control group. These results indicate that A. lividus has an anti-proliferative effect, but does not cause a toxic effect as far as glyphosate.

The anti-proliferative effect of A. lividus extract can be explained by the active ingredients it contains. Tannins and flavonoids can delay or reduce cell division and inhibit cell division in A. cepa⁵⁶. Many plant sterols, such as β-sitosterol, also have a retarding effect on cell division. Lopez-Garcia et al.⁵⁷ reported that high sterols such as β-sitosterol, campesterol and stigmasterol obtained from plants have anti-proliferative effects. β-sitosterol, which was detected in the GC–MS analysis of A. lividus extract, contributes to the anti-proliferative effect. Gallic acid, the major compound detected in A. lividus extract, has been found to exhibit dose-dependent increasing anti-proliferative activity as well as anti-oxidant activity⁵⁸. The fact that many agents obtained from natural sources and used in cancer treatment act by inhibiting the proliferation of cancer cells, reveals the importance of researching plants with anti-proliferative activity such as A. lividus. In addition, the anti-proliferative capacity of A. lividus extract, which does not show mutagenic activity and exhibits anti-mutagenic activity, also reveals its anti-aging activity.

Molecular docking for anti-proliferative activity

In order to evaluate the anti-proliferative effect mechanism of the extract, molecular docking of the major active compounds of the extract and telomerase enzyme was performed. Telomerase is the enzyme that prevents the shortening of telomeres at the ends of chromosomes, and telomeres in plants are protected by telomerase, as in mammals. There is intense telomerase activity especially in highly dividing meristem cells such as flowers and flower buds, seedlings, young and middle-aged leaves and root tips⁵⁹. The decrease in telomerase activity causes regression in cell proliferation. For this reason, the interaction of gallic acid and phytol, which are the major components of A.lividus extract, with telomerase was investigated. The phytol made hydrogen bonding and hydrophobic interaction to amino acid residues of telomerase with binding energy − 6.25 kcal/mol and inhibition constant 26.01 uM (Fig. 6a, Table 4). The amino acid residues of telomerase have interacted with gallic acid made hydrogen bond and hydrophobic interactions which involved binding energy − 5.02 kcal/mol and inhibition constant 207.95 uM (Fig. 6b, Table 4). Regulation of telomere length and telomerase inhibition is defined as an important strategy in cancer diagnosis and treatment. In the literature, molecular docking of catechin with telomerase, which is frequently found in plants, was investigated and it has been reported that catechin bound to N-terminal amino acids has a potential anti-cancer effect. The interaction of gallic acid and phytol with telomerase demonstrated by molecular docking shows that A. lividus containing these components has a high anti-proliferative activity and naturally anti-cancer effect⁶⁰.

Anti-mutagenic activity

The anti-mutagenic activity of A. lividus extract was determined using the Allium test and the results are given in Table 5. As seen in the table, no statistically significant differences were observed between Groups I and III (p > 0.05). This result indicates that A. lividus extract does not cause any mutagenic effect, formation of CAs or MN. Serious mutagenic effects were detected in the positive control group. High frequency of MN formation, fragments, sticky chromosomes, bridges, vagrant chromosomes and unequal distribution of chromatin were detected in the NaN₃ treated group (Fig. 7). NaN₃ exhibits a mutagenic effect by causing chromosomal breaks and deficiencies in the DNA repair mechanism⁶¹. Chromosomal abnormalities such as fragments, bridges, vagrant chromosomes and unequal distribution of chromatin indicate aneugenic and clastogenic effects^62,63. Abnormalities detected in the positive control group in this study confirmed the mutagenic effect of NaN₃. In Group IV, in which NaN₃+ extract was applied, there was a decrease in the frequency of these abnormalities. MN frequency decreased by 1.1 times in Group IV compared to the positive control group. This result revealed that the plant extract has a strong protective property and the frequency of NaN₃-induced MN decreased.

Similarly, the frequency of CAs decreased in the extract applied group and A. lividus extract exhibited an anti-mutagenic effect in the range of 33.13–68.59% against NaN₃-induced chromosomal damages. The highest anti-mutagenic effect was determined as 68.59% against unequal distribution of chromatin. A. lividus extract, which provides 33.13%, 48.09%, 51.24% and 44.18% reductions in the fragment, sticky chromosome, bridge and vagrant chromosome frequencies, respectively, exhibited anti-mutagenic effects at different rates (Fig. 7). The reducing effect of A. lividus extract against CAs and MN formations is related to the active ingredients it contains. Phytol, one of the major compounds detected in the content, is an important factor in the emergence of the anti-mutagenic effect. Phytol exhibits anti-mutagenic activity by activating enzymatic detoxification systems, capturing radicals produced by mutagens, preventing DNA damage and scavenging radicals⁶⁴. Gallic acid, another major compound detected in the extract, acts as a nucleophile that clears electrophilic mutagens. It also prevents the transfer of mutagens to the cytosol by binding to their carriers in the cell membrane⁶⁵. It is reported in the literature that gallic acid, which reduces NaN₃ mutagenicity by 82%, is one of the most effective anti-mutagenic phenols⁶⁶. Although there is no study in the literature evaluating the anti-mutagenic effect of A. lividus extract, the anti-mutagenic activities of different Amaranthus species have been investigated by various tests. Kumari et al.⁶⁷ found that 100 μg/mL A. viridis extract significantly reduced H₂O₂-induced DNA damage. Jadhav and Biradar⁶⁸ reported that the mutagenic effect induced by ethyl methane sulfonate was inhibited by 96% with Amaranthus hybridus extract and 95% by Amaranthus spinosus extract.