Polygonumins A, a newly isolated compound from the stem of Polygonum minus Huds with potential medicinal activities

Polygonumins A, a new compound, was isolated from the stem of Polygonum minus. Based on NMR results, the compound’s structure is identical to that of vanicoside A, comprising four phenylpropanoid ester units and a sucrose unit. The structure differences were located at C-3″″′. The cytotoxic activity of polygonumins A was evaluated on several cancer cell lines by a cell viability assay using tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The compound showed the highest antiproliferative (p < 0.05) activities against K562 (Human Leukaemia Cell Line), MCF7 (Human breast adenocarcinoma cell line), and HCT116 (Colorectal cancer cells) cells. Cytotoxic studies against V79–4 cells were carried out and showed that polygonumins A was toxic at 50 µg/ml, suggesting that this compound may be used as an anticancer drug without affecting normal cells. Polygonumins A also showed promising activity as an HIV-1 protease inhibitor with 56% relative inhibition. Molecular docking results indicated that the compound possesses high binding affinity towards the HIV protease over the low binding free energy range of -10.5 to -11.3 kcal/mol. P. minus is used in Malaysian traditional medicine for the treatment of tumour cells. This is the first report on the use of P. minus as an HIV-1 protease inhibitor.

In addition to its use as a spice in the food industry, P. minus has been reported for its use as a herbal medicine. Kesum leaf decoctions are traditionally used in indigestion relief, as ingredients in shampoo to remove dandruff 6 , and as postnatal tonics 7 . P. minus has been reported to exhibit anti-microbial activity 8 , anti-inflammatory activity 9 and cytotoxic activity against HeLa (human cervical carcinoma) cells 10 and gastric cytoprotective activity 11 . P. minus has also been reported to be a source of natural antioxidants for its high total phenolic content and reducing capacity [12][13][14] . The pharmacological properties of P. minus are based on its chemical constituents. Therefore, numerous studies on the profiling of metabolites have been performed on P. minus in the search for its active compounds [15][16][17] .
Encouraged by the aforementioned findings, we aimed to isolate novel bioactive compounds from kesum in our continued investigations on kesum as a medicinal plant. In the present study, we isolated a new polyoxygenated aromatic compound (polygonumins A) from the stem of kesum. Polygonumins A demonstrated cytotoxic activities against several cancer cell lines, which indicated that it has potential value in the treatment of cancers such as leukaemia. These data provide baseline information for possible use in controlling cancer diseases, particularly leukaemia. In addition, the present study was undertaken to evaluate the antioxidant and anticholinesterase activities of P. minus. We also examined the potential of polygonumins A to serve as an HIV-1 protease inhibitor. Finally, a molecular docking study was performed to support our findings, which could lead to a new drug discovery in the near future.

Results and Discussion
Polygonumins A structure. Spectroscopy data indicated that polygonumins A has a molecular formula of According to HRESIMS data, polygonumins A has a molecular weight of m/z 1010.2697 and a molecular formula of C 52 H 50 O 21 . FTIR spectra indicated that the compound has various functional groups i.e., hydroxyl absorbance at 3334.8 cm −1 , aliphatic carbon absorbance at 2953.3 cm −1 , carbonyl absorbance at 1704 cm −1 and aromatic absorbance at 1629.4, 1605.3, and 1513.7 cm −1 . The results are supported by NMR data ( 1 H and 13 C NMR), which showed that the structure of polygonumins A comprises four phenylpropanoid units and a sucrose unit, which could be well distinguished from the structure of vanicoside A. NMR data for vanicoside A and polygonumins A are compared in Table 1 and Fig. 1.

Biological activities.
It has been recommended that in selecting plant medicines for cancer treatment, ethnopharmacological uses in cancer-relevant diseases such as inflammation, infection, and immune and skin disorders should be taken into account 19 . In the present investigation, polygonumins A, a novel compound isolated from the stem of P. minus, was first evaluated for its antiproliferative activities against HCT116, C33A, H1299, MCF7, A549, and K-562 cancer cell lines using the MTT assay and then for its activities in radical scavenging and acetylcholinesterase inhibition. The activity towards HIV-1 protease inhibitor was also evaluated, as the newly isolated compound has a structure similar to that of vanicoside A.
The IC 50 values inhibiting cell proliferation were determined, and the results are summarized in Table 2. The results showed that polygonumins A exhibited cytotoxicity against all tested cell lines except for the A549 cell line. Considering the cutoff point of 4 µg/ml for potential anticancer compounds 20 , values below this set point were obtained for this compound in HCT116 (IC 50  against K562 (human leukaemia cell line), with an IC 50 of 2.25 µg/ml, lower than that of doxorubicin (2.97 µg/ml), highlighting the anti-leukaemia potential of polygonumins A. It has been well observed that leukaemia is more sensitive to chemotherapy than other malignancies are 21,22 .
In addition to its sensitivity towards the leukaemia cell line, polygonumins A exhibited cytotoxic activities against human breast cancer and colorectal cancer cells. This finding could well explain why polygonumins A has been widely used to treat digestive disorders. It is believed that the sugar moiety, a sucrose unit, in its structure plays an important role in determining its pharmacological and biological activities. Structure and activity relationship (SAR) analysis of several related compounds containing sugar moieties, such as CCL-34 and its natural analogues, revealed that the sugar moiety was essential to their anticancer activity 23 . In particular, the sugar moiety was recognized to be critical to the topoisomerase inhibition activity of anthracyclines as antitumour drugs. It has also been suggested that the sugar structure in daunorubicin plays a critical role in determining its anticancer activity 24 . To date, there is no report on the cytotoxicity activity of vanicoside A, except in an MCF cell line. However, vanicoside A has been classified as a member of the family of protein kinase C inhibitors 18 , which exhibit antitumour effects.
The equivalence between the therapeutic effect on cancer cell lines and the toxicological effect on target human organs is an important criterion of the applicability of an anticancer compound. Therefore, we conducted toxicological studies on the V79-4 cell line (lung fibroblast cell line derived from Chinese hamsters) to determine the safe concentration range of polygonumins A. This test has been widely used to evaluate general cytotoxicity and target organ toxicity 25 . In some cases, this test may also provide information about lethal dose in vivo 26 . The results indicated a loss of viability of V79-4 fibroblasts at concentrations above 50 µg/ml following approximately 24 hours of exposure. Thus, the compound is approximately 10 times as toxic towards cancer cells and normal cells at these concentrations, as it is at its therapeutic concentration.
Interestingly, vanicoside A also showed significant β-glucosidase inhibitory activity, indicating promising therapeutic potential in the treatment of metastatic cancer and human immunodeficiency virus infection (HIV) 27 . As polygonumins A possesses a structure similar to that of vanicoside A, we performed an HIV-1  protease inhibition test against the newly isolated compound. Based on our results (Table 3), polygonumins A showed potential activity as an HIV-1 protease inhibitor. A relative inhibition level of 56% towards HIV-1 protease was detected compared with pepstatin A as a positive control. This is the first report indicating that P. minus exhibits activity towards HIV-1 protease. Several Polygonum spp have been reported to possess anti-HIV properties, with compounds such as flavonoid glycoside, quercetin and phenolics playing an essential role in anti-HIV activity [28][29][30] . Based on the results of this study, we believe that the phenyl propanoid glycoside moiety in the structure of polygonumins A is associated with the activation of anti-HIV protease activity. Moreover, previous study have shown that the phenylpropanoid glycoside group acts as an inhibitor of HIV-1 integrase activity, thus supporting our findings 31 Several techniques have been used to determine antioxidant capacity. One of the methods we used is based on scavenging activity, in which we measured the ability of polygonumins A to donate electrons to a free radical to scavenge potential damage. The antioxidant activity determined by the DPPH free radical-scavenging method   ( Table 2) was not consistent with our expectations. The measured IC 50 value of 812 µg/ml indicated that polygonumins A is far less potent than gallic acid and ascorbic acid. It has been reported that ethanolic, methanolic, and aqueous extracts of P. minus exhibit antioxidant activity as remarkable as that of gallic acid and ascorbic acid 13,32 . This activity is due to the phenylpropane group of P. minus. The four units of the phenylpropanoid group in the structure have been show to produce lower scavenging activity 33 . However, the high antioxidant activity of P. minus extracts has been attributed to high contents of polyphenolic compounds 16 . Therefore, we measured the total phenolic content of polygonumins A by the Folin-Ciocalteu method. Phenols consist of hydroxyl groups that are able to destroy free radicals to form stable phenoxyl radicals 34 . Although the results of the DPPH assay showed a weak scavenging ability, the total phenolic content of this compound is relatively high at 124.0625 ± 0.88 mg GAE/g when compared with that of crude extract. In our previous studies, we found that the total phenolic content in crude P. minus ethanolic extract produced the highest scavenging activity, ranging from 100 to 140 mg GAE/g 16 . Perhaps the antioxidant activity of this compound is not due to DPPH scavenging activity alone. Because antioxidant activity can be realized by multiple mechanisms or a single mechanism, we analysed the reducing power capacity of polygonumins A. This assay determines a substance's ability to reduce Fe 3+ to Fe 2+ . The presence of antioxidants in the extracts result in the reduction of the ferric cyanide complex (Fe 3+ ) to the ferrous cyanide form (Fe 2+ ). We found that polygonumins A may act as an electron donor (a hydrogen electron donor), supporting its antioxidant activity, as the compound showed a comparatively high reducing capacity, with an EC 50 of 89.3 µg/ml, near the value of its reference compound gallic acid ( Table 2). The reducing power of this compound increased rapidly with its concentration. Based on this antioxidant activity, the compound's high total phenolic content was correlated with its reducing power. Hence, It can be inferred that polygonumins A could act as a strong antioxidant agent. It is well documented that the use of antioxidants may minimize neuronal degeneration and slow the progress of Alzheimer's disease 35 . Anticholinesterase activity in compounds has also been reported to be related to radical-scavenging activity 36 . Moreover, based on our previous findings on crude extracts of polygonumins A, the compound showed promising anticholinesterase activity 16 . Therefore, we evaluated the anticholinesterase activity of polygonumins A relative to that of tacrine. However, the compound showed only weak anticholinesterase activity at concentrations of up to 2 mg/ml. (Table 2), and the compound did not show potential to serve as an anticholinesterase drug. The IC 50 for this compound could not be determined due to its low activity; but we managed to determine the IC 20 value for this compound (1980 µg/ml).

Molecular docking of polygonumins A, vanicoside A and pepstatin in HIV-1 protease (pdb ID: 3OXC).
Polygonumins A appeared to possess high binding affinity towards HIV protease (pdb ID: 3OXC), as indicated by low binding free energy range of −10.5 to −11.3 kcal/mol (Table 4) recorded in 3 independent runs. The low binding free energies are comparable to those of vanicoside A (−10.5 to −11.7 kcal/mol) docked to the same protein, as illustrated in Fig. 3. Moreover, pepstatin (positive control) exhibited low binding free energies of −8.9 to −9.5 kcal/mol in 3 independent runs. Pepstatin has been used as positive control drug that exhibits anti-HIV properties through enzymatic assay 37,38 , and thus, pepstatin was included as a reference in a comparative analysis of molecular docking to determine the compound's activity as an anti-HIV protease based on its potential binding affinity. The structures possessing the lowest binding free energy were visualized, and hydrogen bond analysis was conducted using the surface/binding analysis tool in UCSF Chimera version 1.11. The residues involved in hydrogen bond interactions are summarized in Table 5. Moreover, superimposition of the structures showed that polygonumins A, vanicoside A and pepstatin were docked in a similar binding domain (Fig. 4). Recent studies have reported the anti-HIV activity of several bioactive compounds derived from plant extracts 37,38 and mushroom 39 . The current study examined the anti-HIV activity of polygonumins A, and the compound's potential activity was further evaluated to identify the potential interactions of the compound with mutant HIV-1 proteases through molecular docking simulation. Mutant HIV-1 proteases available in the protein databank were downloaded and submitted to docking analysis using VinaAutodock. Polygonumins A was found to engage in potential interactions with mutant HIV-1 proteases with the following PDB IDs: 3PWM, 4HDB, 4HDF, 4HEG, and 4YHQ; the affinities recorded were lower than −10 kcal/mol. The potential interaction was found to be particularly significant for the mutant 4YHQ, for which the affinity was as low as −13.8 kcal/mol. These results are comparable to those obtained for the positive control drug pepstatin, which showed a significant binding affinity towards the mutant HIV-1 proteases. The results are summarized in Table 6. The docked positions of pepstatin and polygonumins A are depicted in Fig. 5. This analysis indicated that polygonumins A possesses the potential to inhibit a range of HIV-1 protease mutants that are currently known to resist available antiretroviral drugs. The potential anti-HIV activities against different protease mutants were predicted based on a complementary fit of polygonumins A with the target HIV protease mutants relative to the positive control drug pepstatin. This approach is well established for identifying potent HIV protease inhibitors 40 , which can be used for drug development in the future.

Experimental procedures
Plant material. The stem of P. minus was originally collected from Ulu Yam, Malaysia, and a voucher specimen was deposited in the UKMB Herbarium, Universiti Kebangsaan Malaysia. Specimens were identified by a taxonomist and further confirmed by ITS sequencing 41 . Samples were washed and stored at −80 °C prior to use.

Isolation of polygonumins A.
A total of 5 kg of P. minus stem bark powder (230-250 mesh) was extracted using methanol 3 times for 24 hours each time at room temperature. The extracts were concentrated by a vacuum rotary evaporator at low pressure to yield a dark-green gum (260 g). A total of 150 g of methanol extract was fractionated by vacuum liquid chromatography (VLC) using a column (Φ 10 cm) with silica gel 60PF 254 (0.063-0.200 mm) as an adsorbent and a chloroform:methanol mixture with increasing polarity (100% chloroform, Table 6. Affinities of polygonumins A and pepstatin docked in HIV-1 protease mutants. Residues of HIV-1 protease mutants involved in hydrogen bond interactions with polygonumins A and pepstatin. 90-10%, 80-20%, and MeOH 100%) to yield 5 fractions i.e., F 1 (2.1 g), F 2 (4.4 g), F 3 (8.4 g), F 4 (10.3 g), and F 5 (88.3 g), respectively. Based on the spot size produced by thin layer chromatography (TLC), F 4 was refractionated by the VLC method using a column (Φ 5 cm) with silica gel 60PF 254 (0.063-0.200 mm) as an adsorbent and a chloroform:methanol mixture (100% chloroform, 90-10%, 80-20%, and MeOH 100%) as an eluent to produce 4 fractions: F 41 (0.8 g), F 42 (1.3 g), F 43 (1.8 g) and F 44 (3.3 g), respectively. The selected fractions, F 43 and F 42 (1.8 g), were combined and further purified by radial chromatography (RC) with silica gel 60PF 254 containing gypsum as an adsorbent with a chloroform:methanol mixture as an eluent with increasing polarity (95:5% 100% MeOH) to yield Fraction 4232 (0.4 g). Radial chromatography was then performed iteratively using the same eluent mixture in Tris-HCl buffer, pH 8.0) using the formula (E − S)/E × 100, where E is the activity of enzyme with DMSO and S is the activity of enzyme with the test sample. The experiments were carried out in triplicate. Tacrine was used as a reference compound.
Antioxidant activity. Free radical-scavenging assay. Radical-scavenging activities were determined by the DPPH (2,2-diphenyl-1-picrylhydrazyl) assay. Various concentrations of the experimental samples were obtained, and the volume was adjusted to 200 μl with ethanol. Approximately 100 μl of 0.5 mM DPPH in methanol was added to the samples or standard (ascorbic acid and gallic acid) in a 96-well plate. After incubation for 30 min in the dark, changes in absorbance at 600 nm were measured on a 96-well plate reader. IC 50 was calculated as the sample concentration required for a 50% decrease in the absorbance of a control solution of DPPH .
Reducing power assay. Ferric reducing antioxidant power was determined by the direct reduction of Fe 3+ (CN − ) 6 to Fe 2+ (CN − ) 6 and by measuring the absorbance resulting from the formation of the Perls' Prussian Blue complex following the addition of excess ferric ions (Fe 3+ ). The reducing power method was performed as reported by Oyaizu 43 with slight modifications. Different concentrations of samples (50 µg/ml to 500 µg/ml) were mixed with 2 ml of 0.2 M, pH 6.6 sodium phosphate buffer and 1.25 ml of potassium ferricyanide. The mixture was incubated at 50 °C for 20 minutes. After 20 minutes of incubation, 1.25 ml of trichlorocetic acid (10%) was added. Finally, 0.5 ml of FeCl 3 (0.1%) was added to the mixture and incubated for 10 minutes. The intensity of the blue-green colour was measured at 700 nm. Increases in the absorbance of the reaction mixture indicated an increase in the reduction capability. The EC 50 value (µg/mL) associated with the reducing power-the extract concentration at which the absorbance was 0.5 was calculated from a graph of absorbance at 700 nm against the extract concentration. Gallic acid was used as a positive control.
Total phenolic content. The total phenolic content was determined using the Folin-Ciocalteu method 44 . The reaction mixture was prepared by mixing 0.2 ml of sample (1 mg/mL) and 1.5 ml of 10% Folin-Ciocalteu reagent dissolved in water. The mixture was allowed to equilibrate for 5 minutes and then mixed with 1.5 ml 7.5% Na 2 CO 3 solution. After incubation for 60 minutes at room temperature in the dark, the absorbance of the mixture was read at 725 nm against a blank using a spectrophotometer. The blank was prepared by using DMSO instead of a sample. The sample procedure was repeated for gallic acid at different concentrations, i.e., 0.00, 0.25, 0.50, 0.75 and 1 mg; the results were used to produce a calibration curve. Total phenolic content was calculated as the milligrams of gallic acid equivalent (GAE) per gram of sample (mg GAE/g) by using the gallic acid calibration curve, y = 0.0016× + 0.0295, R² = 0.9548. V79 fibroblast cultures. V79-4 cells were grown in tissue culture flasks using DMEM as the growth medium at 37 °C in a humidified atmosphere of 5% carbon dioxide and 95% air. Cultures were examined daily to ensure they remained healthy. The confluent monolayer was removed by trypsinization, and the number of viable cells was calculated. Cells were seeded into a 96-well plate at a seeding density of 10 000 cells/well and incubated at 37 °C. The test substance was prepared by dilution with an appropriate volume of complete growth medium (DMEM) supplemented with 10% foetal bovine serum (FBS) to obtain the highest working concentration of 100 µg/ml (weight/volume). Procedures were performed aseptically.

In vitro
The test substance was tested in triplicate at concentrations of 3.125, 6.25, 12.5, 25, 50 and 100 µg/ml. Growth medium from each well of a 96-well plate containing healthy culture was replaced with 200 µl of the test substance and controls respectively. The cultures were then incubated for 24 hours at 37 °C in a humidified atmosphere of 5% carbon dioxide and 95% air.
In vitro cytotoxicity assay. Cells were plated in 96-well microplates and cultured for 24 h. The test compounds were dissolved in DMSO and added at different concentrations (100, 50, 25, 12.5, 6.25, 3.13 µg/ml) to the plate in triplicate. The cytotoxicities against K-562 and H1299 cell lines were measured using a colorimetric MTT (3-(4,5-dimethylthiazol-2-yl)−2,5-diphenyltetrazolium bromide) assay. Exponentially growing cells were harvested and suspended in DMEM, and a 100 µl cell suspension was added to a 96-well plate. After 24 h incubation at 37 °C with 5% CO 2 , the cells were treated with varying concentrations of the test compounds (100 µl). The medium was removed, and cells in each well were incubated with PBS containing 1 mg/ml MTT for 24 h at 37 °C with 5% CO 2 . DMSO (100 µl) was added to each well to dissolve the insoluble formazan crystal, and plates were incubated for 4 h at 37 °C for complete solubilization of formazan. The level of coloured formazan derivative was analysed on a microplate reader using the results at wavelengths of 570 nm and 630 nm as references 45 . The percent viability of cells was calculated using the following equation: Absorbance of treated cells Absorbance of cells in solvent 100 Percent viability was plotted versus compound concentration, and IC 50 values at which the compound showed 50% inhibition of tumour cell proliferation were calculated using Microsoft Excel. The compound was tested at each concentration in triplicate.
HIV-1 protease fluorogenic assay. The HIV-1 Protease Inhibitor Screening Kit (Fluorometric) from Biovision Incorporated (Milpitas, CA, USA) was used to measure the inhibitory effect of each sample on HIV-1 protease activity. Pepstatin A (1 mM) was used as a known standard for HIV-1 protease inhibition, and 1% DMSO was used as a solvent control. The assay was performed according to the manufacturer's instructions. Briefly, each sample (1 mg/ml) was incubated with HIV-1 protease enzyme at room temperature for 15 minutes. Then, the HIV-1 protease fluorescent substrate was added. The fluorescence (excitation/emission = 330/450 nm) in kinetic mode over a period of 90 minutes at 37 °C was determined using a PerkinElmer EnSpire plate reader.
Statistical analysis. One-way ANOVA at 95% confidence level was used for statistical analysis followed by Dunnett's test in relation to control and standard. Molecular docking. The structure of wild-type HIV-1 protease (PDB ID: 3OXC) was downloaded from the protein databank for molecular docking. The protein model was prepared by removing all non-standard residues that included antiviral drug saquinavir, sulfate ion and formic acid in their structure. Water molecules were removed from the structure and hydrogen atoms added using AutoDockTools-1.5.6 prior to conversion of the file format to PDBQT for docking analysis. A grid box with dimensions of 50 × 40 × 40 A 3 was generated with HIV-1 protease as the centroid using AutoDockTools-1.5.6. Vanicoside, pepstatin, and polygonuminss were docked in the HIV-1 protease using AutoDockVina 1.1.2 46 . Docking of the molecules was repeated in three independent runs. Structures were visualized and hydrogen bond interactions were further analysed using UCSF Chimera version 1.11 47 .