High-throughput detection of drugs binding to proteins using desorption electrospray ionization mass spectrometry

Potential Multifunctional Bioactive Compounds from Dysosma versipellis Explored by Bioaffinity Ultrafiltration-HPLC/MS with Topo I, Topo II, COX-2 and ACE2

Background

Dysosma versipellis (D. versipellis) has been traditionally used as a folk medicine for ages. However, the specific phytochemicals responsible for their correlated anti-inflammatory, anti-proliferative and antiviral activities remain unknown.

Purpose

This study aimed to explore the specific active components in D. versipellis responsible for its potential anti-inflammatory, anti-proliferative, and antiviral effects, and further elucidate the corresponding mechanisms of action.

Methods

Bioaffinity ultrafiltration coupled to liquid chromatography–mass spectrometry (UF-LC/MS) was firstly hired to fast screen for the anti-inflammatory, anti-proliferative and antiviral compounds from rhizomes of D. versipellis, and then further validation was conducted using in vitro inhibition assays and molecular docking.

Results

A total of 12, 12, 9 and 12 phytochemicals with considerable affinities to Topo I, Topo II, COX-2 and ACE2 were fished out, respectively. The anti-proliferative assay in vitro indicated that podophyllotoxin and quercetin exhibited comparably strong inhibitory rates on A549 and HT-29 cells compared with 5-FU and etoposide. Meanwhile, kaempferol displayed prominent dose-dependent inhibition against COX-2 with IC₅₀ value at 0.36 ± 0.02 μM lower than indomethacin at 0.73 ± 0.07 μM. Furthermore, quercetin exerted stronger inhibitory effect against ACE2 with IC₅₀ value at 104.79 ± 8.26 μM comparable to quercetin 3-O-glucoside at 135.25 ± 6.54 μM.

Conclusion

We firstly showcased an experimental investigation on the correlations between bioactive phytochemicals of D. versipellis and their multiple drug targets reflecting its potential pharmacological activities, and further constructed a multi-target and multi-component network to decipher its empirical traditional applications. It could not only offer a reliable and valuable experimental basis to better comprehend the curative effects of D. versipellis but also provide more new insights and strategies for other traditional medicinal plants.

Exploring Multifunctional Bioactive Components from Podophyllum sinense Using Multi-Target Ultrafiltration

Podophyllum sinense (P. sinense) has been used as a traditional herbal medicine for ages due to its extensive pharmaceutical activities, including antiproliferative, anti-inflammatory, antiviral, insecticidal effects, etc. Nevertheless, the specific bioactive constituents responsible for its antiproliferative, anti-inflammatory, and antiviral activities remain elusive, owing to its complicated and diversified chemical components. In order to explore these specific bioactive components and their potential interaction targets, affinity ultrafiltration with multiple drug targets coupled with high performance liquid chromatography/mass spectrometry (UF–HPLC/MS) strategy was developed to rapidly screen out and identify bioactive compounds against four well-known drug targets that are correlated to the application of P. sinense as a traditional medicine, namely, Topo I, Topo II, COX-2, and ACE2. As a result, 7, 10, 6, and 7 phytochemicals were screened out as the potential Topo I, Topo II, COX-2, and ACE2 ligands, respectively. Further confirmation of these potential bioactive components with antiproliferative and COX-2 inhibitory assays in vitro was also implemented. Herein, diphyllin and podophyllotoxin with higher EF values demonstrated higher inhibitory rates against A549 and HT-29 cells as compared with those of 5-FU and etoposide. The IC₅₀ values of diphyllin were calculated at 6.46 ± 1.79 and 30.73 ± 0.56 μM on A549 and HT-29 cells, respectively. Moreover, diphyllin exhibited good COX-2 inhibitory activity with the IC₅₀ value at 1.29 ± 0.14 μM, whereas indomethacin was 1.22 ± 0.08 μM. In addition, those representative constituents with good affinity on Topo I, Topo II, COX-2, or ACE2, such as diphyllin, podophyllotoxin, and diphyllin O-glucoside, were further validated with molecular docking analysis. Above all, the integrated method of UF–HPLC/MS with multiple drug targets rapidly singled out multi-target bioactive components and partly elucidated their action mechanisms regarding its multiple pharmacological effects from P. sinense, which could provide valuable information about its further development for the new multi-target drug discovery from natural medicines.

Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques

The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.

Current advances in screening for bioactive components from medicinal plants by affinity ultrafiltration mass spectrometry

INTRODUCTION

Medicinal plants have played an important role in maintaining human health for thousands of years. However, the interactions between the active components in medicinal plants and some certain biological targets during a disease are still unclear in most cases.

OBJECTIVE

To conduct the high-throughput screening for small active molecules that can interact with biological targets, which is of great theoretical significance and practical value.

METHODOLOGY

The ultrafiltration mass spectrometry (UF-LC/MS) is a powerful bio-analytical method by combining affinity ultrafiltration and liquid chromatography-mass spectrometry (LC/MS), which could rapidly screen and identify small active molecules that bind to biological targets of interest at the same time. Compared with other analytical methods, affinity UF-LC/MS has the characteristics of fast, sensitive and high throughput, and is especially suitable for the complicated extracts of medicinal plants.

RESULTS

In this review, the basic principle, characteristics and some most recent challenges in UF-LC/MS have been demonstrated. Meanwhile, the progress and applications of affinity UF-LC/MS in the discovery of the active components from natural medicinal plants and the interactions between small molecules and biological target proteins are also briefly summarised. In addition, the future directions for UF-LC/MS are also prospected.

CONCLUSION

Affinity UF-LC/MS is a powerful tool in studies on the interactions between small active molecules and biological protein targets, especially in the high-throughput screening of active components from the natural medicinal plants.

Antiproliferative activities of Amaryllidaceae alkaloids from Lycoris radiata targeting DNA topoisomerase I

Crude Amaryllidaceae alkaloids (AAs) extracted from Lycoris radiata are reported to exhibit significant anti-cancer activity. However, the specific alkaloids responsible for the pharmacodynamic activity and their targets still remain elusive. In this context, we strived to combine affinity ultrafiltration with topoisomerase I (Top I) as a target enzyme aiming to fish out specific bioactive AAs from Lycoris radiata. 11 AAs from Lycoris radiata were thus screened out, among which hippeastrine (peak 5) with the highest Enrichment factor (EF) against Top I exhibited good dose-dependent inhibition with IC₅₀ at 7.25 ± 0.20 μg/mL comparable to camptothecin (positive control) at 6.72 ± 0.23 μg/mL. The molecular docking simulation further indicated the inhibitory mechanism between Top I and hippeastrine. The in vitro antiproliferation assays finally revealed that hippeastrine strongly inhibited the proliferation of HT-29 and Hep G2 cells in an intuitive dose-dependent manner with the IC₅₀ values at 3.98 ± 0.29 μg/mL and 11.85 ± 0.20 μg/mL, respectively, and also induced significant cellular morphological changes, which further validated our screening method and the potent antineoplastic effects. Collectively, these results suggested that hippeastrine could be a very promising anticancer candidate for the therapy of cancer in the near future.

Screening for inhibitors of topoisomerase I from Lycoris radiata by combining ultrafiltration with liquid chromatography/mass spectrometry

RATIONALE

Although crude Amaryllidaceae alkaloids (AAs) extracted from Lycoris radiata are reported to exhibit significant anti-cancer activity, both the specific responsible alkaloid(s) and their targets remain elusive. Screening anti-cancer AAs targeted on topoisomerase I from crude AAs could be very helpful in tackling these two challenging questions.

METHODS

An ultrafiltration method combined with liquid chromatography/electrospray ionization mass spectrometry (UF-LC/MS) was developed to screen for the inhibitors of topoisomerase I, which has been reported to mediate DNA unwinding during carcinoma proliferation. Enrichment factors (EFs) of different AAs were used to evaluate the binding affinity between AAs and topoisomerase I, and the AAs with higher EFs were further tested to validate the method.

RESULTS

Eleven AAs from Lycoris radiata (ten of which were identified) were screened using UF-LC/MS, and a glaring discrepancy in EFs was revealed for the first time. One of the AAs, hippeastrine, with the highest EF at 49.3%, was further tested against topoisomerase I, and the IC50 value of hippeastrine was determined to be 23.0 μmol/L, which is comparable with the well-known anti-cancer drug camptothecin at 19.3 μmol/L.

CONCLUSIONS

A simple, rapid and effective screening method using UF-LC/MS was developed and successfully applied to screen candidate inhibitors of topoisomerase I from crude AAs in Lycoris radiata, which may pave the way to further understand the potential anti-cancer constituents and mechanisms of Lycoris radiata. Copyright © 2016 John Wiley & Sons, Ltd.

Screening of the binding of small molecules to proteins by desorption electrospray ionization mass spectrometry combined with protein microarray

The interaction between bioactive small molecule ligands and proteins is one of the important research areas in proteomics. Herein, a simple and rapid method is established to screen small ligands that bind to proteins. We designed an agarose slide to immobilize different proteins. The protein microarrays were allowed to interact with different small ligands, and after washing, the microarrays were screened by desorption electrospray ionization mass spectrometry (DESI MS). This method can be applied to screen specific protein binding ligands and was shown for seven proteins and 34 known ligands for these proteins. In addition, a high-throughput screening was achieved, with the analysis requiring approximately 4 s for one sample spot. We then applied this method to determine the binding between the important protein matrix metalloproteinase-9 (MMP-9) and 88 small compounds. The molecular docking results confirmed the MS results, demonstrating that this method is suitable for the rapid and accurate screening of ligands binding to proteins. Graphical Abstract ᅟ.

Direct analysis of quaternary alkaloids by in situ reactive desorption corona beam ionization MS

The direct detection of quaternary alkaloids by atmospheric pressure chemical ionization (APCI)-base ambient MS is difficult because of their poor volatility. In this study, a reactive protocol was developed for the in situ determination of quaternary alkaloids using desorption corona beam ionization (DCBI) mass spectrometry (MS). The model compounds of 8 quaternary alkaloids including sanguinarine, chelerythrine, cyclanoline, nitidine, coptisine, jatrorrhizine, berberine, palmatine and 2 tertiary alkaloids including protopine and allocryptopine were investigated in different states such as on a polytetrafluoroethylene (PTFE) plate, in raw herbal materials, and in silica gel. After various reactive reagents were studied, the mixture of saturated aqueous NaOH solution and CH3OH solvent (3 : 7, v/v) was selected as the optimized reactive reagent for the reactive DCBI-MS detection. All the target molecules can be detected with high sensitivity. On a PTFE plate the limits of detection were 0.0795, 0.1060, 0.4860, 0.9665, 0.8879, 0.3987, 0.5557, 0.4591, 0.0889, and 0.1929 mg L(-1) for sanguinarine, chelerythrine, cyclanoline, nitidine, coptisine, jatrorrhizine, berberine, palmatine, protopine, and allocryptopine, respectively. The reactive protocol was also applied to the direct detection of raw herbal materials and thin layer chromatography successfully.