Open Access Article
Zhiqiang Wang
ab,
Seung Hwan Hwangb,
Guanglei Zuob,
Set Byeol Kimb and
Soon Sung Lim
*bcd
aCollege of Public Health, Hebei University, Baoding, 071002, China
bDepartment of Food Science and Nutrition, Hallym University, 1 Hallymdeahak-gil, Chuncheon, 24252, Republic of Korea. E-mail: limss@hallym.ac.kr; Fax: +82-33-251-0663; Tel: +82-33-248-2144
cInstitute of Korea Nutrition, Hallym University, 1 Hallymdeahak-gil, Chuncheon, 24252, Republic of Korea
dInstitute of Natural Medicine, Hallym University, 1 Hallymdeahak-gil, Chuncheon, 24252, Republic of Korea
First published on 28th February 2018
A novel in vitro strategy for affinity-based ultrafiltration-high performance liquid chromatography (HPLC) was developed for the direct identification of cytochrome P450 (CYP) 1A2, 3A4, and 2C9 specific ligands from Danshen extracts, in which human liver microsome (HLM) was used as the source of CYP enzymes. The Danshen extract was incubated without HLM, with HLM, or with HLM where the active site of the target enzyme was blocked with a specific competitive probe before ultrafiltration to isolate ligand–enzyme complexes from unbound compounds. Subsequently, HPLC analysis was performed on the released ligands from the complexes. α-Naphthoflavone, ketoconazole, and sulfaphenazole were used as specific competitive probes for CYP1A2, 3A4, and 2C9, respectively. The signal-to-noise ratio (S/N) and specific-signal-to-noise ratio (S-S/N) of each compound were calculated using the obtained peak areas. Finally, two criteria were applied to select putative ligands for each specific target: (1) S/N > 1; (2) S-S/N > 0. Finally, dihydrotanshinone was identified as a specific ligand for CYP1A2 and tanshinone I, cryptotanshinone, and tanshinone IIA were identified as specific ligands for CYP1A2, 2C9, and 3A4. It was demonstrated that the newly developed method can be used to rapidly and directly detect specific ligands from natural product extracts in multi-target systems.
Affinity-based ultrafiltration-high performance liquid chromatography (HPLC) has emerged as a rapid and convenient approach for protein–ligand interaction studies, and has been widely applied for the screening and identification of ligands of enzymes, proteins, or receptors from natural product matrices, in which small molecules from natural product extracts bound to selected targets (enzymes, proteins, or receptors) can be separated from unbound small molecules by ultrafiltration and subsequently identified.5 Thus, examination of the HPLC profile of certain peaks can be used to identify “hits”. Affinity-based ultrafiltration-HPLC has significant advantages including rapid and convenient operation, low cost, high hit ratio, and lack of immobilization of screening targets on a carrier as in other active molecular screening methods such as bioassay-guided fractionation, biochromatography, magnetic separation, microdialysis, hollow fiber adsorption etc.6–8 Even though the disadvantages of affinity-based ultrafiltration-HPLC such as false positive results and false negative results can be avoided,9 high concentrations of pure screening targets (enzymes, proteins, or receptors) are required.10 To our knowledge, only a small proportion of commercially available pure targets (enzymes, proteins, or receptors) are cheap and stable, and most are expensive; many targets cannot be prepared easily and are not commercially available. The use of tissue products (i.e., microsomes, extracts etc.) or cell lysates is more feasible and cost effective. Nevertheless, previous studies have only described multi-ligand screening in single-target systems on affinity-based ultrafiltration-HPLC platforms, and using this method for screening in a multi-target system is still a challenge.
Herein, we propose a novel strategy for affinity-based ultrafiltration-HPLC for the detection of specific ligands of multiple targets from natural product extracts using label-free competitive probes. As a proof-of-concept, the specific ligands of cytochrome P450 (CYP) 1A2, 2C9, and 3A4 were directly identified from Danshen (Salvia miltiorrhiza) ethanol extracts (DEE), in which human liver microsome (HLM) was used as the source of CYP enzymes instead of pure recombinant human enzymes. The CYP superfamily is an important drug-metabolizing enzyme system and is involved in the biotransformation of a number of exogenous (drugs, toxic chemicals, organic solvents, carcinogens, and environmental pollutants) and endogenous compounds (steroids hormones, fatty acids, bile acids, and prostaglandins). It is almost universally accepted that over 90% of drug metabolism in humans is mediated by CYP enzymes.11 Moreover, among the CYPs identified to date, enzymes from CYP1, CYP2, and CYP3 families catalyse the biotransformations of the majority of drugs used in clinics today. Danshen is the dried root and rhizome of Salvia miltiorrhiza and is a widely used medicinal plant for the treatment of cardiovascular disease in China and serves as a complementary medicine in the West.12 Among the major active constituents of Danshen that have been isolated and characterized, tanshinones have been reported to exhibit anti-platelet, cardio-protective, anti-inflammatory, hepato-protective, and anti-HIV effects in preclinical studies.13 Moreover, a number of herb–drug interactions leading to adverse outcomes were reported to involve Danshen when it was co-administered with certain therapeutic agents.14,15 As the pharmacokinetics of Danshen have been well studied, it was selected to validate the proposed method.
As a proof-of-concept, a case study was carried out as described previously to directly identify the specific ligands of CYP1A2, 3A4, and 2C9 from DEE, in which HLM was used as the source of CYP enzymes instead of pure recombinant human enzymes. As mentioned previously, Danshen is a popular herbal medicine and is widely used for promoting blood circulation to remove blood stasis, clearing away heat, relieving vexation, nourishing blood, and tranquilizing the mind and cooling blood to relieve carbuncles. Among the major active isolated and characterized constituents of Danshen, tanshinones, a series of abietane diterpenes, have been reported to exhibit anti-platelet, cardio-protective, anti-inflammatory, hepatoprotective, and anti-HIV effects in preclinical studies. The four major tanshinones in Danshen are dihydrotanshinone, tanshinone I, cryptotanshinone, and tanshinone IIA. Numerous studies have demonstrated the potential applications of these tanshinones in a broad spectrum of maladies such as atherosclerosis, cardiac arrhythmias, hypertension, obesity, metabolic syndromes, and cancer. Thus, the potential herb–drug interactions between tanshinones, including dihydrotanshinone, tanshinone I, cryptotanshinone, and tanshinone IIA, with therapeutic agents have been evaluated.16 In the present study, α-naphthoflavone, ketoconazole, and sulfaphenazole were selected as competitive probes for CYP1A2, 3A4, and 2C9, respectively (Fig. 2f). According to Fig. 2a–e, the S/Ns and S-S/Ns of compounds from DEE were measured (Table 1), and the S/N and S-S/N plots are shown in Fig. 3. Although a number of compounds from DEE showed binding affinities towards HLM (Fig. 2a and b), only compound 1 (S/N = 1.16; S-S/N1A2 = 0.09) was identified as a specific ligand of CYP1A2; compound 2 (S/N = 1.88; S-S/N1A2 = 0.04; S-S/N2C9 = 0.16; S-S/N3A4 = 0.13), compound 3 (S/N = 1.33; S-S/N1A2 = 0.51; S-S/N2C9 = 0.47; S-S/N3A4 = 0.54), and compound 4 (S/N = 2.34; S-S/N1A2 = 0.62; S-S/N2C9 = 0.62; S-S/N3A4 = 0.39) were identified as specific ligands of CYP1A2, 2C9, 3A4. The four compounds were identified as dihydrotanshinone (1), tanshinone I (2), cryptotanshinone (3), and tanshinone IIA (4) (Fig. 2f).
| CYP isoform | Danshen componentsa | S/Nb | S-S/Nc | IC50d (μM) | Kid (μM) | Mode of inhibitiond |
|---|---|---|---|---|---|---|
| a Asterisk indicated the specific ligands identified by ultrafiltration-HPLC with probes.b S/N is the signal-noise ratio.c S-S/N is the specific signal-noise ratio.d IC50, Ki, and mode of inhibition were cited from Wang et al.16; Ki is the inhibitory constant. | ||||||
| 1A2 | Dihydrotanshinone (1)* | 1.16 | 0.09 | 0.50 | 0.53 | Competitive |
| Tanshinone I (2)* | 1.88 | 0.04 | 1.70 | 2.16 | Competitive | |
| Cryptotanshinone (3)* | 1.33 | 0.51 | 3.06 | 1.88 | Competitive | |
| Tanshinone IIA (4)* | 2.34 | 0.62 | 2.01 | 1.45 | Competitive | |
| 3A4 | Dihydrotanshinone (1) | 1.16 | −0.21 | 3.22 | 2.11 | Non-competitive |
| Tanshinone I (2)* | 1.88 | 0.13 | >100 | 86.9 | Competitive | |
| Cryptotanshinone (3)* | 1.33 | 0.54 | >100 | 120.4 | Competitive | |
| Tanshinone IIA (4)* | 2.34 | 0.39 | >100 | 218.7 | Competitive | |
| 2C9 | Dihydrotanshinone (1) | 1.16 | −0.07 | 7.48 | 1.92 | Competitive |
| Tanshinone I (2)* | 1.88 | 0.16 | >100 | 51.2 | Competitive | |
| Cryptotanshinone (3)* | 1.33 | 0.47 | 23.86 | 22.9 | Competitive | |
| Tanshinone IIA (4)* | 2.34 | 0.62 | >100 | 61.6 | Competitive | |
To validate our results, we summarized the data obtained in this and previous studies using traditional inhibition methods (Table 1). The results revealed that these tanshinones are ligands (inhibitors) of CYP1A2, 3A4 and 2C9. However, these results do not exactly match those obtained with our newly developed approach of ultrafiltration-HPLC with competitive probes, where dihydrotanshinone was not identified as a specific ligand of CYP3A4 and CYP2C9. Originally, competitive binding experiments were used to verify and screening results,17 but Chen et al. first used competitive binding experiments in ultrafiltration-HPLC to eliminate false positives.18 In fact, not only false positive, but also ligands with different binding sites from competitive binding compounds will be eliminated by such competitive binding experiments. Thus, Song et al. and Wang et al. proposed that competitive binding experiments could be used to identify selective and specific enzyme inhibitors from natural products.9,19 Recently, Wang et al. concluded that competitive binding experiments could reduce the false positive results of affinity-based ultrafiltration-HPLC.20 Alternatively, in multi-target systems, all ligands binding to unexpected targets can be considered false positive results, and the specific ligand of the expected target enzyme might be distinguished by competitive binding experiments by adding a specific competitive probe compound. We proposed the developed method under this assumption. However, one limitation of competitive binding experiments is that not all false positives can be eliminated and some ligand candidates may be excluded, similar to the results obtained herein. Wang et al. indicated that this limitation is due to the properties of the competitive binding compounds, including binding site and affinity differences between ligands and competitive probes.20 Put simply, the developed strategy will only work when binding site of the ligand, which has a similar or lower binding affinity than the competitive binding probe. Thus, selecting an appropriate competitive probe is critical. Dihydrotanshinone was not identified as a specific ligand for CYP3A4 and CYP2C9 perhaps because dihydrotanshinone has a different binding site than the probes or has a relatively high binding affinity towards the target enzyme.
To confirm our hypothesis, the results of the in vitro kinetic analysis and in silico computer simulation of docking model are presented in Table 1 and Fig. 4. The kinetic results (Table 1) revealed that dihydrotanshinone is a competitive inhibitor of CYP1A2 (Ki = 0.53 μM) and CYP2C9 (Ki = 1.92 μM) and is a non-competitive inhibitor of CYP3A4 (Ki = 2.11 μM); tanshinone I is a competitive inhibitor of CYP1A2 (Ki = 2.16 μM), CYP2C9 (Ki = 51.20 μM), and CYP3A4 (Ki = 86.90 μM); cryptotanshinone is a competitive inhibitor of CYP1A2 (Ki = 1.88 μM), CYP2C9 (Ki = 22.90 μM), and CYP3A4 (Ki = 120.40 μM); tanshinone IIA is a competitive inhibitor of CYP1A2 (Ki = 1.45 μM), CYP2C9 (Ki = 61.60 μM), and CYP3A4 (Ki = 218.70 μM). These results suggested that (1) dihydrotanshinone might be a specific, high affinity ligand of CYP2C9 because it exhibited competitive inhibition and a much lower Ki value than the other three compounds; (2) dihydrotanshinone might be a non-specific, high affinity ligand of CYP3A4 because it showed non-competitive inhibition and a much lower Ki value than the other three compounds. The computer simulation results (Fig. 4) revealed that all tanshinones had the same binding site as the probes except dihydrotanshinone and ketoconazole for CYP3A4, indicating that dihydrotanshinone is not a specific ligand of CYP3A4. These results demonstrated that the developed method can be used to rapidly and directly identify specific ligands from natural product extracts in multi-target systems, and the selection of appropriate competitive probes is critical in this method.
The DEE was dissolved in DMSO to prepare the extract sample solution (1 mg mL−1) for further assays. The HLM was dissolved in potassium phosphate buffer (0.5 M, pH 7.4) to prepare HLM potassium phosphate buffer stock solution (5 mg mL−1) for further assays. The probes including α-naphthoflavone, ketoconazole, and sulfaphenazole were dissolved in 20% methanol (v/v) to prepare the probe stock solutions (5 Mm) for the competitive binding experiments.
000 MW cut-off membrane (Millipore) by centrifugation at 6350 × g for 30 min at 4 °C, followed by two washes with potassium phosphate buffer to remove unbound compounds. Meanwhile, the protein complexes retained on the membrane of the ultrafiltration unit were transferred to a new centrifugal tube. The ligands were dissociated from the protein complexes with 50% methanol (v/v) and were separated from the denatured proteins by centrifugation, and were subsequently washed with 50% methanol (v/v). The released bound ligands were combined and dried under nitrogen gas for 3 h. Next, the dried bound compounds were reconstituted in 50% methanol (v/v, 100 μL) and the reconstituted bound fractions were subjected to HPLC analysis using the methods described in Section “HPLC conditions”. The blank experiment was carried out similarly, but without the addition of probe pre-incubated HLM, which was prepared following the methods described in Section “Competitive binding experiments”. To rank the binding affinities of the ligands to HLM, the S/N was calculated using eqn (1):| S/N = Aa/Ab | (1) |
| S-S/N = (Aa − Ac)/Ab | (2) |
Footnotes |
| † This research was presented at Experimental Biology 2017, 22–26 April 2017, Chicago, USA. |
| ‡ Electronic supplementary information (ESI) available. See DOI: 10.1039/c7ra12161j |
| This journal is © The Royal Society of Chemistry 2018 |