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

Research Progress on the Material Basis of Traditional Chinese Medicines Based on Chemical Biology Methods

The chemical biology method is a cutting-edge technology that utilizes chemical research methods and ideas to study life and biomedicine at the molecular level. Recently, it has gradually been applied to screening chemical markers in traditional Chinese medicines. This article reviews the principles and applications of common chemical biology methods, including cell membrane chromatography, affinity ultrafiltration, magnetic bead enrichment, capillary electrophoresis, molecular exclusion chromatography, immobilized fusion target affinity chromatography, etc., in traditional Chinese medicines research. Applying chemical biology methods to screen chemical markers in traditional Chinese medicines has the advantages of simple and fast operation, strong specificity of results, good reproducibility, and high sensitivity, which can achieve high-throughput screening.

Screening of anti-inflammatory active components in Sabia schumanniana Diels by affinity ultrafiltration and UHPLC-Q-Exactive Orbitrap mass spectrometry

ETHNOPHARMACOLOGICAL RELEVANCE

Sabia schumanniana Diels is a traditional botanical used to treat lumbago and arthralgia. However, there has been limited research on the pharmacological effects of its chemical components.

AIM OF THE STUDY

This study aimed to rapidly screen for anti-inflammatory compounds in Sabia schumanniana Diels.

MATERIALS AND METHODS

An affinity ultrafiltration method based on UHPLC-Q-Exactive Orbitrap MS was established to rapidly screen and identify cyclooxygenase-2 (COX-2) receptor ligands. The reliability of this method was verified by molecular docking analysis and experiments with RAW264.7 cells.

RESULTS

Seventeen ligands were identified from Sabia schumanniana Diels using affinity ultrafiltration. Molecular docking results indicated that these ligands specifically docked with COX-2. Among them, N-nornuciferine exhibited notable anti-inflammatory activity.

CONCLUSIONS

The combination of affinity ultrafiltration and UHPLC-Q-Exactive Orbitrap MS is an effective and precise method for screening anti-inflammatory compounds. This study provides a foundation for further research on Sabia schumanniana Diels and offers guidance for its potential clinical applications.

Affinity Ultrafiltration Mass Spectrometry for Screening Active Ingredients in Traditional Chinese Medicine: A Review of the Past Decade (2014-2024)

Discovering targets in natural products is a critical and challenging task in new drug development. Rapid and efficient screening of active ingredients from complex systems like traditional Chinese medicine (TCM) is now crucial in drug research. Affinity ultrafiltration (AUF) technology is widely used to screen active ingredients in natural medicines. AUF-liquid chromatography-mass spectrometry (AUF-LC-MS) leverages the affinity between natural medicine extracts and targets to isolate active ingredients from complex matrices, employing LC-MS for detection and activity assessment. This review discusses the developments in employing AUF-LC-MS to analyze TCM and TCM compound preparations over the last decade. This review succinctly presents the advantages and limitations of AUF-LC-MS, illustrating its benefits through the example of screening for active ingredients in natural pharmaceuticals.

Screening of anticoagulant active components in Xuefu Zhuyu decoction via affinity-ultrafiltration coupled with mass spectrometry

This study aimed to establish an effective affinity-ultrafiltration coupled with mass spectrometry (AUF-MS) method to rapidly screen the active components of antithrombin in Xuefu Zhuyu decoction (XFZYD). The HPLC fingerprint of different batches of XFZYD was established to verify the stability of the compound ingredients. AUF-MS was established for the rapid screening of the active ingredients in XFZYD. Eight active ingredients were screened using AUF-MS: oxypaeoniflorin, chlorogenic acid, amygdalin, isoliquiritin, neohesperidin, hesperidin, glycyrrhizic acid and chikusetsu saponin IVa. Simultaneously, the anticoagulant effect of the active ingredients was verified by performing in vivo and in vitro experiments. The results of this study indicate that AUF-MS can be used for high-throughput screening of active components of traditional Chinese medicine compounds, thus providing a basis for the discovery of thrombin inhibitors and promoting the research progress of antithrombotic drugs. The compounds screened from XFZYD showed an inhibitory effect against thrombin and a certain antithrombotic effect.

Children of Nature: Thoughts on Targeted and Untargeted Analytical Approaches to Decipher Polyphenol Reactivity in Food Processing and Metabolism

Following 25 years of polyphenol research in our laboratory, the astonishing chemical and metabolic reactivity of polyphenols resulting in considerable chemical diversity has emerged as the most remarkable attribute of this class of natural products. To illustrate this concept, we will present selected data from black tea and coffee chemistry. In black tea chemistry, enzymatic fermentation converts six catechin derivatives into an estimated 30 000 different polyphenolic compounds via a process we have termed the oxidative cascade process. In coffee roasting, around 45 chlorogenic acids are converted into an estimated 250 novel derivatives following a series of diverse chemical transformations. Following ingestion by humans, these dietary polyphenols, whether genuine secondary metabolites or food processing products, encounter the microorganisms of the gut microbiota, converting them into a myriad of novel structures. In the case of coffee, only two out of 250 chlorogenic acids are absorbed intact, with most others being subject to gut microbial metabolism. Modern mass spectrometry (MS) has been key in unravelling the true complexity of polyphenols subjected to food processing and metabolism. We will accompany this assay with a short overview on analytical strategies developed, including ultrahigh-resolution MS, tandem MS, multivariate statistics, and molecular networking that allow an insight into the fascinating chemical processes surrounding dietary polyphenols. Finally, experimental results studying biological activity of polyphenols will be presented and discussed, highlighting a general promiscuity of this class of compounds associated with nonselective protein binding leading to loss of enzymatic function, another noteworthy general property of many dietary polyphenols frequently overlooked.

Bioaffinity Ultrafiltration Combined with HPLC-ESI-qTOF-MS/MS for Screening Potential Bioactive Components from the Stems of Dendrobium fimbriatum and In Silico Analysis

Dendrobium fimbriatum is a perennial herb, and its stems are high-grade tea and nourishing medicinal materials. Various solvent extracts of D. fimbriatum were evaluated for their anti-inflammatory, anti-acetylcholinesterase (AChE), antioxidant, and anti-α-glucosidase properties. Acetone and EtOAc extracts showed significant antioxidant effects. Acetone, n-hexane, and EtOAc extracts revealed potent inhibition against α-glucosidase. EtOAc, n-hexane, and dichloromethane extracts displayed significant anti-AChE activity. Among the isolated constituents, gigantol, moscatin, and dendrophenol showed potent antioxidant activities in FRAP, DPPH, and ABTS radical scavenging tests. Moscatin (IC50 = 161.86 ± 16.45 μM) and dendrophenol (IC50 = 165.19 ± 13.25 μM) displayed more potent anti-AChE activity than chlorogenic acid (IC50 = 236.24 ± 15.85 μM, positive control). Dendrophenol (IC50 = 14.31 ± 3.17 μM) revealed more efficient anti-NO activity than quercetin (positive control, IC50 = 23.09 ± 1.43 μM). Analysis of AChE and iNOS inhibitory components was performed using molecular docking and/or the bioaffinity ultrafiltration method. In bioaffinity ultrafiltration, the binding affinity of compounds to the enzyme (acetylcholinesterase and inducible nitric oxide synthase) was determined using the enrichment factor (EF). Among the main components of the EtOAc extract from D. fimbriatum stem, moscatin, dendrophenol, gigantol, and batatasin III with acetylcholinesterase exhibited the highest binding affinities, with affinity values of 66.31%, 59.48%, 54.60%, and 31.87%, respectively. Moreover, the affinity capacity of the identified compounds with inducible nitric oxide synthase can be ranked as moscatin (88.99%) > dendrophenol (65.11%) > gigantol (44.84%) > batatasin III (27.18%). This research suggests that the bioactive extracts and components of D. fimbriatum stem could be studied further as hopeful candidates for the prevention or treatment of hyperglycemia, oxidative stress-related diseases, and nervous disorders.

Revealing the anti-inflammatory ingredients in wine-processed Radix et Rhizoma Rhei using immobilized cysteinyl leukotriene receptor type 1 as the stationary phase

Despite the tremendous progress of wine-processed Radix et Rhizoma Rhei (Jiudahuang, JDH) in removing toxic heat from the blood in the upper portion of the body for hundreds of years, the deep understanding of its functional material basis of the anti-inflammatory ingredients remains unclear due to the lack of high specific and efficient methods. Herein, taking Cysteinyl leukotriene receptor type 1(CysLT1R) as the target protein, we established a chromatographic method based on the immobilized CysLT1R using haloalkane dehalogenases (Halo) at the C-terminus of the receptor in one step. After careful characterization by X-ray photoelectronic spectroscopy, immune-fluorometric analysis, and chromatographic investigations, the immobilized receptor was used to screen the anti-inflammatory ingredients in JDH. Aloe-emodin, rhein, emodin, chrysophanol, and physcion were identified as the main anthraquinone exerting anti-inflammatory effects in the drug. The association constants for the five compounds to bind with the receptor were calculated as (0.30 ± 0.06)× 105, (0.35 ± 0.03)× 105, (0.46 ± 0.05)× 105, (1.05 ± 0.14)× 105, and (1.66 ± 0.17)× 105 M-1 by injection amount-dependent method. Meanwhile, hydrogen bonds were identified as the main driving force for the five compounds to bind with CysLT1R by molecular docking. Based on these results, we believe that the immobilized receptor chromatography preserves historic significance in revealing the functional material basis of the complex matrices.

18Beta-Glycyrrhetinic Acid Attenuates H2O2-Induced Oxidative Damage and Apoptosis in Intestinal Epithelial Cells via Activating the PI3K/Akt Signaling Pathway

Oxidative stress causes gut dysfunction and is a contributing factor in several intestinal disorders. Intestinal epithelial cell survival is essential for maintaining human and animal health under oxidative stress. 18beta-Glycyrrhetinic acid (GA) is known to have multiple beneficial effects, including antioxidant activity; however, the underlying molecular mechanisms have not been well established. Thus, the present study evaluated the therapeutic effects of GA on H2O2-induced oxidative stress in intestinal porcine epithelial cells. The results showed that pretreatment with GA (100 nM for 16 h) significantly increased the levels of several antioxidant enzymes and reduced corresponding intracellular levels of reactive oxidative species and malondialdehyde. GA inhibited cell apoptosis via activating the phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) signaling pathway, as confirmed by RNA sequencing. Further analyses demonstrated that GA upregulated the phosphorylation levels of PI3K and Akt and the protein level of B cell lymphoma 2, whereas it downregulated Cytochrome c and tumor suppressor protein p53 levels. Moreover, molecular docking analysis predicted the binding of GA to Vasoactive intestinal peptide receptor 1, a primary membrane receptor, to activate the PI3K/Akt signaling pathway. Collectively, these results revealed that GA protected against H2O2-induced oxidative damage and cell apoptosis via activating the PI3K/Akt signaling pathway, suggesting the potential therapeutic use of GA to alleviate oxidative stress in humans/animals.

Targeted screening of multiple anti-inflammatory components from Chrysanthemi indici Flos by ligand fishing with affinity UF-LC/MS

Chrysanthemi indic Flos (CIF) has been commonly consumed for the treatment of inflammation and related skin diseases. However, the potential bioactive components responsible for its anti-inflammatory and sensitive skin (SS) improvement activities, and the correlated mechanisms of action still remain unknown. In this work, it was firstly found that the CIF extract (CIFE) displayed arrestive free radical scavenging activity on DPPH and ABTS radicals, with no significant difference with positive control Trolox (p > 0.05). Then, compared to the negative group, CIFE markedly decreased the productions of the pro-inflammatory cytokines (IL-1β, IL-6, PEG2, TNF-α, IFN-γ, NO) in LPS induced RAW264.7 cells in a dose-dependent manner (p < 0.01). Besides, CIFE strongly inhibited the COX-2 and hyaluronidase (HAase) with the IC50 values of 1.06 ± 0.01 μg/mL and 12.22 ± 0.39 μg/mL, indicating higher inhibitory effect than positive control of aspirin of 6.33 ± 0.05 μg/mL (p < 0.01), and comparable inhibitory effect with indometacin of 0.60 ± 0.03 μg/mL, and ascorbic acid of 11.03 ± 0.41 μg/mL (p > 0.05), respectively. Furthermore, kinetic assays with Lineweaver-Burk plot (Michaelis Menten equation) suggested that CIFE reversibly inhibited the COX-2 and HAase, with a mixed characteristics of competitive and non-competitive inhibition. Thereafter, multi-target affinity ultrafiltration liquid chromatography-mass spectrometry (UF-LC/MS) method was employed to fast fish out the potential COX-2 and HAase in CIFE. Herein, 13 components showed various affinity binding degrees to the COX-2 and HAase, while those components with relative binding affinity (RBA) value higher than 3.0, such as linarin and chlorogenic acid isomers, were deemed to be the most bioactive components for the anti-inflammatory and SS improvement activities of CIFE. Finally, the interaction mechanism, including binding energy, inhibition constant, docking sites, and the key amino acids involved in hydrogen bonds between the potential ligands and COX-2/HAase were simulated and confirmed with the molecule docking analysis. In summary, this study showcased the prominent anti-inflammatory and SS improvement activities of CIF, which would provide further insights on this functional medicinal plant to be a natural anti-SS remedy.

Screening and identification of potential hypoglycemic and hypolipidemic compounds from aqueous extract of Scutellaria baicalensis Georgi root combing affinity ultrafiltration with multiple drug targets and in silico analysis

INTRODUCTION

Scutellaria baicalensis Georgi, a traditional Chinese medicine, is widely applied to treat various diseases among people, especially in East Asia. However, the specific active compounds in S. baicalensis aqueous extracts (SBAEs) responsible for the hypoglycemic and hypolipidemic properties as well as their potential mechanisms of action remain unclear.

OBJECTIVES

This work aimed to explore the potential hypoglycemic and hypolipidemic compounds from SBAE and their potential mechanisms of action.

METHODOLOGY

The in vitro inhibitory tests against lipase and α-glucosidase, and the effects of SBAE on glucose consumption and total triglyceride content in HepG2 cells were first performed to evaluate the hypoglycemic and hypolipidemic effects. Then, affinity ultrafiltration liquid chromatography-mass spectrometry (LC-MS) screening strategy with five drug targets, including α-glucosidase, α-amylase, protein tyrosine phosphatase 1B (PTP1B), lipase and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) was developed to screen out the potential active constituents from SBAE, and some representative active compounds were further validated.

RESULTS

SBAE displayed noteworthy hypoglycemic and hypolipidemic properties, and 4, 10, 4, 8, and 8 potential bioactive components against α-amylase, α-glucosidase, PTP1B, HMGCR, and lipase were initially screened out, respectively. The interaction network was thus constructed between the potential bioactive compounds screened out and their corresponding drug targets. Among them, baicalein, wogonin, and wogonoside were revealed to possess remarkable hypoglycemic and hypolipidemic effects.

CONCLUSION

The potential hypolipidemic and hypoglycemic bioactive compounds in SBAE and their mode of action were initially explored through ligand-target interactions by combining affinity ultrafiltration LC-MS strategy with five drug targets.

Rapid screening and isolation of 5-lipoxygenase inhibitors in Inonotus obliquus and mechanism of action in the treatment of asthma

Accurate screening and targeted preparative isolation of active substances in natural medicines have long been two technical challenges in natural medicine research. This study outlines a new approach to improve the efficiency of natural product preparation, focusing on rapidly and accurately screening potential active ingredients in Inonotus obliquus as well as efficiently preparing 5-lipoxidase (5-LOX) inhibitors, to provide new ideas for the treatment of asthma with Inonotus obliquus. First, we used ultrafiltration (UF) mass spectrometry to screen for three potential inhibitors of 5-LOX in Inonotus obliquus. Subsequently, the inhibitory effect of the active ingredients screened in the UF assay on 5-LOX was verified using the molecular docking technique, and the potential role of the active compounds in Inonotus obliquus for the treatment of asthma was analyzed by network pharmacology. Finally, based on the above activity screening guidelines, we used semi-preparative liquid chromatography and consecutive high-speed countercurrent chromatography to isolate three high-purity 5-LOX inhibitors such as betulin, lanosterol, and quercetin. Obviously, through the above approach, we have seamlessly combined rapid discovery, screening, and centralized preparation of the active ingredient with molecular-level interactions between the active ingredient and the protease.

Identification of chemical compounds of Schizonepeta tenuifolia Briq. and screening of neuraminidase inhibitors based on AUF-MS and SPR technology

Schizonepeta tenuifolia Briq., as a traditional Chinese medicine, has the effect of treating influenza. There have been few comprehensive studies on the holistic chemical composition of Schizonepeta tenuifolia and the active substances acting on neuraminidase (NA) to treat influenza. In present study, a synthetic identification method including GC-MS and UPLC-Q-Orbitrap-MS combined with GNPS (Global Natural Product Social Molecular Network) technology was established and applied to identify the chemical constituents of Schizonepeta tenuifolia Briq. A total of 134 compounds were identified, including 42 volatile components and 92 non-volatile components. The potential NA inhibitors of Schizonepeta tenuifolia were explored by an affinity ultrafiltration - mass spectrometry - surface plasmon resonance (AUF-MS-SPR) strategy. Eleven compounds were screened out by AUF-MS and their binding forces to NA were detected by SPR. Among them, 5 compounds with excellent binding ability were further tested the KD value. Meanwhile, the NA inhibitory activities of the 11 compounds were verified in vitro. In conclusion, a holistic material base was established to provide a reference for further development of Schizonepeta tenuifolia and an AUF-MS-SPR strategy based on binding ability was selected to screen substances of interest from complex systems.

Screening, isolation, and activity evaluation of potential xanthine oxidase inhibitors in Poria Cum Radix Pini and mechanism of action in the treatment of gout disease

Poria Cum Radix Pini is a rare medicinal fungus that contains several potential therapeutic ingredients. On this basis, a particle swarm mathematical model was used to optimize the extraction process of total triterpenes from P. Cum Radix Pini, and xanthine oxidase inhibitors were screened using affinity ultrafiltration mass spectrometry. Meanwhile, the accuracy of the ultrafiltration assay was verified by molecular docking experiments and molecular dynamics analysis, and the mechanism of action of the active compounds for the treatment of gout was analyzed by enzymatic reaction kinetics and network pharmacology. A high-speed countercurrent chromatography method combined with the consecutive injection and the economical two-phase solvent system preparation using functional activity coefficient of universal quasichemical model (UNIFAC) mathematical model was developed for increasing the yield of target compound. In addition, dehydropachymic acid and pachymic acid were used as competitive inhibitors, and 3-O-acetyl-16alpha-hydroxydehydrotrametenolic acid and dehydrotrametenolic acid were used as mixed inhibitors. Then, activity-oriented separation and purification were performed by high-speed countercurrent chromatography combined with semi-preparative high-performance liquid chromatography and the purity of the four compounds isolated was higher than 90%. It will help to provide more opportunities to discover and develop new potential therapeutic remedies from health care food resources.

Target-guided isolation and purification of cyclooxygenase-2 inhibitors from Meconopsis integrifolia (Maxim.) Franch. by high-speed counter-current chromatography combined with ultrafiltration liquid chromatography

Meconopsis integrifolia (Maxim.) Franch. is used extensively in traditional Tibetan medicine for its potent anti-inflammatory properties. In this study, six cyclooxygenase-2 (COX-2) inhibitors were purified from M. integrifolia using high-speed counter-current chromatography guided by ultrafiltration liquid chromatography (ultrafiltration-LC). First, ultrafiltration-LC was performed to profile the COX-2 inhibitors in M. integrifolia. The reflux extraction conditions were further optimized using response surface methodology, and the results showed that the targeted COX-2 inhibitors could be well enriched under the optimized extraction conditions. Then the six target COX-2 inhibitors were separated by high-speed countercurrent chromatography with a solvent system composed of ethyl acetate/n-butanol/water (4:1:4, v/v/v. Finally, the six COX-2 inhibitors, including 21.2 mg of 8-hydroxyluteolin 7-sophoroside, 29.6 mg of 8-hydroxyluteolin 7-[6'''-acetylallosyl-(1→2)-glucoside], 42.5 mg of Sinocrassoside D3, 54.1 mg of Hypolaetin 7-[6'''-acetylallosyll-(l→2)-3''-acetylglucoside, 30.6 mg of Hypolaetin 7-[6'''-acetylallosyll-(l→2)-6''-acetylglucoside and 17.8 mg of Hypolaetin were obtained from 500 mg of sample. Their structures were elucidated by 1 H-NMR spectroscopy. This study reveals that ultrafiltration-LC combined with high-speed counter-current chromatography is a robust and efficient strategy for target-guided isolation and purification of bioactive molecules. It also enhances the scientific understanding of the anti-inflammatory properties of M. integrifolia but also paves the way for its further medicinal applications.

Screening and identification of neuraminidase inhibitors from Baphicacanthus cusia by a combination of affinity ultrafiltration, HPLC-MS/MS, molecular docking, and fluorescent techniques

Natural products provide a new opportunity for the discovery of neuraminidase (NA)inhibitors. In this study, an affinity ultrafiltration (AUF) coupled with HPLC-MS/MS method was firstly developed and optimized for screening of NA inhibitors from natural products. The critical factors influencing the interaction of enzyme-ligand (including sample concentration, enzyme concentration, incubation time and temperature, pH of the buffer, and dissociation solvents and time) were investigated and optimized by a one-factor-at-a-time design. The method was then applied to discover NA inhibitory compounds in stems and leaves of Baphicacanthus cusia. As a result, five active alkaloids were screened out and identifiedas 2,4(1H,3H)-quinazolinedione (1), 4(3H)-quinazolinone (2), 2(3H)-benzoxazolone (3), tryptanthrin (4), and indirubin (5) through analysis of their DAD profiles, MS/MS fragments, and comparison with reference substances. These active compounds were further evaluated for their NA inhibitory activity using a fluorescence-based NA inhibition assay. The result from the fluorescent assay revealed that all the five compounds(1-5) showed pronounced NA inhibitory activities with IC50values of 98.98, 64.69, 40.16, 69.44, and 144.73 μM, respectively. Finally, molecular docking of these five alkaloids with NA showed that hydrogen bond and π-cation interactions dominated within the binding sites with binding energies ranging between -5.7 to -7.9 kcal/mol, which was supported by the results of the AUF and the fluorescence-based enzyme assay. The developed AUF method is simple and efficient for screening potential NA inhibitors from stems and leaves of B. cusia.

Potent inhibition of human tyrosinase inhibitor by verproside from the whole plant of Pseudolysimachion rotundum var. subintegrum

Affinity-based ultrafiltration-mass spectrometry coupled with ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry was utilised for the structural identification of direct tyrosinase ligands from a crude Pseudolysimachion rotundum var. subintegrum extract. False positives were recognised by introducing time-dependent inhibition in the control for comparison. The P. rotundum extract contained nine main metabolites in the UPLC-QTOF-MS chromatogram. However, four metabolites were reduced after incubation with tyrosinase, indicating that these metabolites were bound to tyrosinase. The IC50 values of verproside (1) were 31.2 µM and 197.3 µM for mTyr and hTyr, respectively. Verproside showed 5.6-fold higher efficacy than that of its positive control (kojic acid in hTyr). The most potent tyrosinase inhibitor, verproside, features a 3,4-dihydroxybenzoic acid moiety on the iridoid glycoside and inhibits tyrosinase in a time-dependent and competitive manner. Among these three compounds, verproside is bound to the active site pocket with a docking energy of -6.9 kcal/mol and four hydrogen bonding interactions with HIS61 and HIS85.

Target Screen of Anti-Hyperuricemia Compounds from Cortex Fraxini In Vivo Based on ABCG2 and Bioaffinity Ultrafiltration Mass Spectrometry

The ATP-binding cassette (ABC) transporter ABCG2 is a significant urate transporter with a high capacity, and it plays a crucial role in the development of hyperuricemia and gout. Therefore, it has the potential to be targeted for therapeutic interventions. Cortex Fraxini, a traditional Chinese medicine (TCM), has been found to possess anti-hyperuricemia properties. However, the specific constituents of Cortex Fraxini responsible for this effect are still unknown, particularly the compound that is responsible for reducing uric acid levels in vivo. In this study, we propose a target screening protocol utilizing bio-affinity ultrafiltration mass spectrometry (BA-UF-MS) to expediently ascertain ABCG2 ligands from the plasma of rats administered with Cortex Fraxini. Our screening protocol successfully identified fraxin as a potential ligand that interacts with ABCG2 when it functions as the target protein. Subsequent investigations substantiated fraxin as an activated ligand of ABCG2. These findings imply that fraxin exhibits promise as a drug candidate for the treatment of hyperuricemia. Furthermore, the utilization of BA-UF-MS demonstrates its efficacy as a valuable methodology for identifying hit compounds that exhibit binding affinity towards ABCG2 within TCMs.

Potential antioxidative and anti-hyperuricemic components in Rodgersia podophylla A. Gray revealed by bio-affinity ultrafiltration with SOD and XOD

Rodgersia podophylla A. Gray (R. podophylla) is a traditional Chinese medicine with various pharmacological effects. However, its antioxidant and anti-hyperuricemia components and mechanisms of action have not been explored yet. In this study, we first assessed the antioxidant potential of R. podophylla with 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and ferric ion reducing antioxidant power (FRAP) assays. The results suggested that the ethyl acetate (EA) fraction of R. podophylla not only exhibited the strongest DPPH, ABTS radical scavenging and ferric-reducing activities, but also possessed the highest total phenolic and total flavonoid contents among the five fractions. After that, the potential superoxide dismutase (SOD) and xanthine oxidase (XOD) ligands from the EA fraction were quickly screened and identified through the bio-affinity ultrafiltration liquid chromatography-mass spectrometry (UF-LC-MS). Accordingly, norbergenin, catechin, procyanidin B2, 4-O-galloylbergenin, 11-O-galloylbergenin, and gallic acid were considered to be potential SOD ligands, while gallic acid, 11-O-galloylbergenin, catechin, bergenin, and procyanidin B2 were recognized as potential XOD ligands, respectively. Moreover, these six ligands effectively interacted with SOD in molecular docking simulation, with binding energies (BEs) ranging from -6.85 to -4.67 kcal/mol, and the inhibition constants (Ki) from 9.51 to 379.44 μM, which were better than the positive controls. Particularly, catechin exhibited a robust binding affinity towards XOD, with a BE value of -8.54 kcal/mol and Ki value of 0.55 μM, which surpassed the positive controls. In conclusion, our study revealed that R. podophylla possessed remarkable antioxidant and anti-hyperuricemia activities and that the UF-LC-MS method is suitable for screening potential ligands for SOD and XOD from medicinal plants.

Mining Xanthine Oxidase Inhibitors from an Edible Seaweed Pterocladiella capillacea by Using In Vitro Bioassays, Affinity Ultrafiltration LC-MS/MS, Metabolomics Tools, and In Silico Prediction

The prevalence of gout and the adverse effects of current synthetic anti-gout drugs call for new natural and effective xanthine oxidase (XOD) inhibitors to target this disease. Based on our previous finding that an edible seaweed Pterocladiella capillacea extract inhibits XOD, XOD-inhibitory and anti-inflammatory activities were used to evaluate the anti-gout potential of different P. capillacea extract fractions. Through affinity ultrafiltration coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS), feature-based molecular networking (FBMN), and database mining of multiple natural products, the extract's bioactive components were traced and annotated. Through molecular docking and ADMET analysis, the possibility and drug-likeness of the annotated XOD inhibitors were predicted. The results showed that fractions F4, F6, F4-2, and F4-3 exhibited strong XOD inhibition activity, among which F4-3 reached an inhibition ratio of 77.96% ± 4.91% to XOD at a concentration of 0.14 mg/mL. In addition, the P. capillacea extract and fractions also displayed anti-inflammatory activity. Affinity ultrafiltration LC-MS/MS analysis and molecular networking showed that out of the 20 annotated compounds, 8 compounds have been previously directly or indirectly reported from seaweeds, and 4 compounds have been reported to exhibit anti-gout activity. Molecular docking and ADMET showed that six seaweed-derived compounds can dock with the XOD activity pocket and follow the Lipinski drug-like rule. These results support the value of further investigating P. capillacea as part of the development of anti-gout drugs or related functional foods.

Identification of Xanthine Oxidase Inhibitors from Celery Seeds Using Affinity Ultrafiltration-Liquid Chromatography-Mass Spectrometry

Celery seeds have been used as an effective dietary supplement to manage hyperuricemia and diminish gout recurrence. Xanthine oxidase (XOD), the critical enzyme responsible for uric acid production, represents the most promising target for anti-hyperuricemia in clinical practice. In this study, we aimed to establish a method based on affinity ultrafiltration-liquid chromatography-mass spectrometry (UF-LC-MS) to directly and rapidly identify the bioactive compounds contributing to the XOD-inhibitory effects of celery seed crude extracts. Chemical profiling of celery seed extracts was performed using UPLC-TOF/MS. The structure was elucidated by matching the multistage fragment ion data to the database and publications of high-resolution natural product mass spectrometry. Thirty-two compounds, including fourteen flavonoids and six phenylpeptides, were identified from celery seed extracts. UF-LC-MS showed that luteolin-7-O-apinosyl glucoside, luteolin-7-O-glucoside, luteolin-7-O-malonyl apinoside, luteolin-7-O-6'-malonyl glucoside, luteolin, apigenin, and chrysoeriol were potential binding compounds of XOD. A further enzyme activity assay demonstrated that celery seed extract (IC50 = 1.98 mg/mL), luteolin-7-O-apinosyl glucoside (IC50 = 3140.51 μmol/L), luteolin-7-O-glucoside (IC50 = 975.83 μmol/L), luteolin-7-O-6'-malonyl glucoside (IC50 = 2018.37 μmol/L), luteolin (IC50 = 69.23 μmol/L), apigenin (IC50 = 92.56 μmol/L), and chrysoeriol (IC50 = 40.52 μmol/L) could dose-dependently inhibit XOD activities. This study highlighted UF-LC-MS as a useful platform for screening novel XOD inhibitors and revealed the chemical basis of celery seed as an anti-gout dietary supplement.

Licochalcone A inhibits the assembly function of β-barrel assembly machinery in Escherichia coli

Antimicrobial resistance (AMR) crisis urges the development of new antibiotics. In the present work, we for the first time used bio-affinity ultrafiltration combined with HPLC-MS (UF-HPLC-MS) to examine the interaction between the outer membrane β-barrel proteins and natural products. Our results showed that natural product licochalcone A from licorice interacts with BamA and BamD with the enrichment factor of 6.38 ± 1.46 and 4.80 ± 1.23, respectively. The interaction was further confirmed by use of biacore analysis, which demonstrated that the Kd value between BamA/D and licochalcone was 6.63/28.27 μM, suggesting a good affinity. To examine the effect of licochalcone A on BamA/D function, the developed versatile in vitro reconstitution assay was used and the results showed that 128 μg/mL licochalcone A could reduce the outer membrane protein A integration efficiency to 20%. Although licochalcone A alone can not inhibit the growth of E. coli, but it can affect the membrane permeability, suggesting that licochalcone A holds the potential to be used as a sensitizer to combat AMR.

Multi-target bioactive compound screening from the infructescence of Platycarya strobilacea Sieb. et Zucc. by affinity chromatography using immobilized β2 -adrenoceptor and muscarinic-3 acetylcholine receptor as the stationary phase

As a main source for the recognition and identification of lead compounds, traditional Chinese medicine plays a pivotal role in preventing diseases for years. However, screening bioactive compounds from traditional Chinese medicine remains challenging because of the complexity of the systems and the occurrence of the synergic effect of the compounds. The infructescence of Platycarya strobilacea Sieb. et Zucc is prescribed for allergic rhinitis treatment with unknown bioactive compounds and unclear mechanisms. Herein, we immobilized the β2 -adrenoceptor and muscarine-3 acetylcholine receptor onto the silica gel surface to prepare the stationary phase in a covalent bond through one step. The feasibility of the columns was investigated by the chromatographic method. Ellagic acid and catechin were identified as the bioactive compounds targeting the receptors. The binding constants of ellagic acid were calculated to be (1.56 ± 0.23)×107  M-1 for muscarine-3 acetylcholine receptor and (2.93 ± 0.15)×107  M-1 for β2 -adrenoceptor by frontal analysis. While catechin can bind with muscarine-3 acetylcholine receptor with an affinity of (3.21 ± 0.05)×105  M-1 . Hydrogen bonds and van der Waals' force were the main driving forces for the two compounds with the receptors. The established method provides an alternative for multi-target bioactive compound screening in complex matrices.

Identification of pancreatic lipase inhibitors from Eucommia ulmoides tea by affinity-ultrafiltration combined UPLC-Orbitrap MS and in vitro validation

Pancreatic lipase inhibitors can reduce blood lipids by inactivating the catalytic activity of human pancreatic lipase, a key enzyme involved in triglyceride hydrolysis, which helps control some dyslipidemic diseases. The ability of Eucommia ulmoides tea to improve fat-related diseases is closely related to the natural inhibitory components of pancreatic lipase contained in the tea. In this study, fifteen pancreatic lipase inhibitors were screened and identified from Eucommia ulmoides tea by affinity-ultrafiltration combined UPLC-Q-Exactive Orbitrap/MS. Four representative components of geniposidic acid, quercetin-3-O-sambuboside, isochlorogenic acid A, and quercetin with high binding degrees were further verified by nanoscale differential scanning fluorimetry (nanoDSF) and enzyme inhibitory assays. The results of flow cytometry showed that they could significantly reduce the activity of pancreatic lipase in AR42J cells induced by palmitic acid in a concentration-dependent manner. Our findings suggest that Eucommia ulmoides tea may be a promising resource for pancreatic lipase inhibitors of natural origin.

Inhibition mechanism of α-glucosidase inhibitors screened from Tartary buckwheat and synergistic effect with acarbose

Tartary buckwheat has been shown to provide a good antihyperglycemic effect. However, it is unclear which active compounds play a key role in attenuating postprandial hyperglycemia. Presently, acetone extract from the hull of Tartary buckwheat had the best effect for α-glucosidase inhibition (IC₅₀ = 0.02 mg/mL). Twelve potential α-glucosidase inhibitors from Tartary buckwheat were screened and identified by the combination of ultrafiltration and high-performance liquid chromatography coupled with mass spectrometry. Myricetin and quercetin exhibited the highest anti-α-glucosidase activity with IC₅₀ values of 0.02 and 0.06 mg/mL, respectively. These inhibitors manifested different types of inhibition manners against α-glucosidase via direct interaction with the amino acid residues. The results of structure-activity relationships indicated that an increase in the number of -OH on the B-ring greatly strengthened α-glucosidase inhibitory activity, but glucoside and rutinoside replacement on the C-ring obviously weakened this influence. Furthermore, a synergistic effect was observed between inhibitors with different inhibition manners.

Fast and efficient identification of hyaluronidase specific inhibitors from Chrysanthemum morifolium Ramat. using UF-LC-MS technique and their anti-inflammation effect in macrophages

The purpose of the study was to establish a rapid analytical strategy to screen potential anti-inflammatory compounds from Flos Chrysanthemum flower. The enzyme assay was conducted to prescreen botanical extracts, in which Chrysanthemum morifolium aqueous extract (CME) displayed hyaluronidase (HAase) inhibitory activity in a dose-dependent manner with the values of 8.31, 24.25, and 66.51% at concentrations of 1.00, 2.00, and 4 0.00 mg/mL, respectively. Eight potential compounds targeting HAase (compounds 9, 10, 11, 13, 15, 17, 20 and 21) from CME were screened using ultrafiltration affinity liquid chromatography coupled with mass spectrometry (UF-LC-MS) technology. The well-known inhibitor, dipotassium glycyrrhizinate (DG), was used as a positive control and competitive ligand to eliminate false positives. Then, four of these potential components (compounds 9, 10, 17, and 21), namely eriodictyol-7-O-glucoside, luteoloside, apigenin-7-O-glucoside and diosmetin-7-O-glucoside, were distinguished as potent HAase specific inhibitor candidates with high BD and CBD values. The enzyme inhibitory activities of candidate compounds were verified using enzyme inhibition assay. At a concentration of 1000 μM, compounds 9, 10, 17, and 21 showed 40.15, 44.85, 18.04, and 24.15% inhibition of HAase, respectively. Furthermore, all the four compounds significantly decreased the production of nitric oxide (NO) and IL-6, and significantly suppressed the mRNA expression of inducible NO synthase (iNOS) and IL-1β in both murine and human macrophages.

Bioaffinity ultrafiltration coupled with HPLC-ESI-MS/MS for screening potential α-glucosidase inhibitors from pomegranate peel

Pomegranate peel (PoP) contains plenty of bioactive compounds and exhibits strong activity to prevent postprandial hyperglycaemia and improve diabetes mellitus. Presently, bioaffinity ultrafiltration coupled with high performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-ESI-MS/MS) is employed to screen and identify the efficient α-glucosidase inhibitors in PoP and the detailed inhibitory mechanisms are further investigated. The results show that many substances, including ellagic acid, kaempferol, gallic acid, and resveratrol in PoP reveal strong activity to inhibit α-glucosidase and ellagic acid (EA) is screened as the most effective compound. Further research indicates that EA plays a competitive and reversible inhibition role against α-glucosidase with the value of Ki was 6.24 × 105 mol/L. EA also directly interacts with the amino acids of α-glucosidase mainly via van der Waals forces and hydrogen bonds, thereby, influencing the secondary structure and stability of α-glucosidase. Finally, the α-glucosidase inhibitory activity of EA is further confirmed to significantly reduce postprandial blood glucose in vivo.

Progress of isolation, chemical synthesis and biological activities of natural chalcones bearing 2-hydroxy-3-methyl-3-butenyl group

Chalcones have a three-carbon α,β-unsaturated carbonyl system composed of two phenolic rings. Many chalcones have shown broad spectrum of biological activities with clinical potentials against various diseases. They are usually abundant in seeds, fruit skin, bark and flowers of most edible plants. Among them, chalcones bearing 2-hydroxy-3-methyl-3-butenyl (HMB) group have been reported several times in the past few decades due to their novel scaffolds and numerous interesting biological activities. In this paper, we reviewed the isolation of twelve natural chalcones and a natural chalcone-type compound bearing 2-hydroxy-3-methyl-3-butenyl group discovered so far, and reviewed their synthesis methods and biological activities reported in the literature. We anticipate that this review will inspire further research of natural chalcones.

Recent advances on discovery of enzyme inhibitors from natural products using bioactivity screening

The essence of enzymes is to keep the homeostasis and balance of human by catalyzing metabolic responses and modulating cell. Suppression of enzyme slows the progress of some diseases, making it a therapeutic target. Therefore, it is important to develop enzyme inhibitors by proper bioactivity screening strategies for the future treatment of some major diseases. In this review, we summarized the recent (2015-2020) applications of several screening strategies (electrophoretically mediated microanalysis, enzyme immobilization, affinity chromatography, and affinity ultrafiltration) in finding enzyme inhibitors from certain species of bioactive natural compounds of plant origin (flavonoids, alkaloids, phenolic acids, saponins, anthraquinones, coumarins). At the same time, the advantages and disadvantages of each strategy were also discussed, and the future possible development direction in enzyme inhibitor screening has prospected. To sum up, it is expected to help readers select suitable screening strategies for enzyme inhibitors and provide useful information for the study of the biological of specific kinds of natural products. This article is protected by copyright. All rights reserved.

Screening and characterization of potential α-glucosidase inhibitors from Cercis chinensis Bunge fruits using ultrafiltration coupled with HPLC-ESI-MS/MS

A more accurate HPLC-MS screening method combining functional enzyme assay and affinity ultrafiltration screening assay was developed and applied for the screening of natural product inhibitors of α-glucosidase from Cercis chinensis Bunge fruits. The enzyme assay was conducted to prescreen botanical extracts, in which maltose was used as the substrate and detection object. That showed the Cercis chinensis Bunge fruits demonstrated higher α-glucosidase inhibitory activity (IC₅₀ = 11.94 ± 1.23 μg/mL) than acarbose (IC₅₀ = 44.03 ± 4.37 μg/mL) (n = 3, p < 0.05). Subsequently, twelve bioactive components targeting α-glucosidase were screened out and identified using affinity ultrafiltration coupled to liquid chromatography-mass spectrometry. The known inhibitor, acarbose, was used as a positive control and competitive ligand to eliminate false positives. Moreover, bindings of the twelve components to the active site of α-glucosidase were investigated via molecular docking, which further confirmed the results of the screening assay.

Screening and characterisation of potential antioxidant, hypoglycemic and hypolipidemic components revealed in Portulaca oleracea via multi-target affinity ultrafiltration LC-MS and molecular docking

INTRODUCTION

Portulaca oleracea is a commonly used nutritional vegetable and traditional herbal medicine with plenty of nutrients and manifold pharmacological activities. However, the potential active ingredients for its remarkable antioxidant, hypoglycemic and hypolipidemic activities remain unexplored.

OBJECTIVES

The present study aims to systematically evaluate the antioxidant activities of different extracts of P. oleracea and screen bioactive ligands that can interact with α-glucosidase, pancreatic lipase, and superoxide dismutase (SOD).

METHODS

In this research, the antioxidant activities of different parts of P. oleracea and their corresponding total phenolic content (TPC) and total flavonoid content (TFC) were systematically determined. Subsequently, a multi-target affinity ultrafiltration method was developed using affinity ultrafiltration with SOD, α-glucosidase, and pancreatic lipase coupled to liquid chromatography-mass spectrometry (UF-LC-MS). Later, molecular docking was used to further investigate the possible interaction mechanism between these ligands and target enzymes.

RESULTS

Among them, the ethyl acetate (EA) fraction showed the highest antioxidant activity along with the highest TPC and TFC, and four compounds in the EA fraction were quickly retrieved as potential SOD, α-glucosidase, and pancreatic lipase ligands, respectively. Molecular docking revealed that these potential ligands exhibited strong binding ability and inhibitory activities on SOD, α-glucosidase, and pancreatic lipase.

CONCLUSION

The present study revealed that P. oleracea can be used as a functional food with excellent antioxidant, hypoglycemic and hypolipidemic effects. Meanwhile, the integrated strategy based on multi-target UF-LC-MS and molecular docking also provided a powerful tool and a multidimensional perspective for further exploration of active ingredients in P. oleracea responsible for the antioxidant, hypoglycemic and hypolipidemic activities.

Efficient discovery of potential inhibitors for SARS-CoV-2 3C-like protease from herbal extracts using a native MS-based affinity-selection method

The 3C-like protease (3CLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to the virus life cycle and is supposed to be a potential target for the treatment of coronaviral infection. Traditional Chinese medicines (TCMs) have played an impressive role in the treatment of COVID-19 in China. The effectiveness of TCM formulations prompts scientists to take continuous effort on searching for bioactive small molecules from the ancient resources. Herein, we developed a native mass spectrometry-based affinity-selection method for rapid screening of active small molecules from crude herbal extracts applied for COVID-19 therapy. Six common herbs named Lonicera japonica, Scutellaria baicalensis, Forsythia suspensa, Glycyrrhiza uralensis, Cirsium japonicum, and Andrographis paniculata were investigated. After preliminary separation of the crude extracts, the fractions were incubated with 3CLpro. A native MS-based affinity screening assay was then conducted to search for the protein-ligand complexes. A UHPLC-Q/TOF-MS with UNIFI data acquisition and data processing software was applied to identify the hit compounds. Standard compounds were used to verify the outcomes. Among the 16 hits, three flavonoids, baicalein, scutellarein and ganhuangenin, were identified as potential noncovalent inhibitors against 3CLpro with IC₅₀ values of 0.94, 3.02, and 0.84 μM, respectively. Their binding affinities were further characterized by native MS, with K_d values being 1.43, 3.85, and 1.09 μM, respectively. Overall, we established an efficient native MS-based strategy for discovering 3CLpro ligands from crude mixtures, which supplies a potential strategy of small molecule lead discovery from TCMs.

Development of a method to screen and isolate xanthine oxidase inhibitors from black bean in a single step: Hyphenation of semipreparative liquid chromatography and stepwise flow rate countercurrent chromatography

Black bean, in which isoflavones are the main active constituent, also contains saponins and monoterpenes. Soybean isoflavone is a secondary metabolite that is formed during the growth of soybean; it exhibits antioxidant and cardiovascular activities and traces estrogen-like effects. In this study, black bean isoflavones were extracted with n-butanol, and ultrafiltration-liquid chromatography-mass spectrometry was used to screen their activity. Subsequently, the inhibitors were isolated and purified using semipreparative liquid chromatography and stepwise flow rate countercurrent chromatography. Thereafter, five active compounds were identified using mass spectrometry and nuclear magnetic resonance experiments. Finally, the inhibition types of the xanthine oxidase inhibitors were determined using enzymatic kinetic studies. The IC₅₀ values of daidzin, glycitein-7-O-glucoside, genistin, daidzein, and genistein were determined to be 35.08, 56.22, 30.76, 68.79, and 95.37 μg/mL, respectively. Daidzin, genistin, and daidzein exhibited reversible inhibition, whereas glycitein-7-O-glucoside and genistein presented irreversible inhibition. This novel approach, which was based on ultrafiltration-liquid chromatography-mass spectrometry and stepwise flow rate countercurrent chromatography, is a powerful method for screening and isolating xanthine oxidase inhibitors from complex matrices. The study of enzyme inhibition types is helpful for understanding the underlying inhibition mechanism. Therefore, a beneficial platform was developed for the large-scale production of bioactive and nutraceutical ingredients.

Ligand fishing based on bioaffinity ultrafiltration for screening xanthine oxidase inhibitors from citrus plants

Citrus plants are valuable medicinal plants with abundant flavonoids content in the parts of fruits and peels, which exhibit potential hypouricemic effect. In the present study, a ligand fishing assay was performed based on bio-affinity ultrafiltration for rapidly screening and identifying xanthine oxidase inhibitors from citrus plants. Under the optimal experimental conditions, five potential ligands were fished out when xanthine oxidase acted as the targeted protein. Subsequently, the chemical structures of all five compounds were identified by quadrupole time-of-flight mass spectrometry. Among them, hesperidin and naringin were confirmed as high-efficiency xanthine oxidase inhibitors. The half maximal inhibitory concentration values of hesperidin and naringin were 0.15 and 1.82 μM, respectively. Compared with the clinical antigout drug, allopurinol (half maximal inhibitory concentration = 8.03 μM), lower half maximal inhibitory concentration values indicated higher enzyme inhibitory activity. The Lineweaver-Burk plots indicated that the two compounds inhibited xanthine oxidase in a noncompetitive manner. The results demonstrate that the bioaffinity ultrafiltration method is a powerful tool for screening out xanthine oxidase inhibitors from natural products.

LABEL-FREE BIO-AFFINITY MASS SPECTROMETRY FOR SCREENING AND LOCATING BIOACTIVE MOLECULES

Despite the recent increase in the development of bioactive molecules in the drug industry, the enormous chemical space and lack of productivity are still important issues. Additional alternative approaches to screen and locate bioactive molecules are urgently needed. Label-free bio-affinity mass spectrometry (BA-MS) provides opportunities for the discovery and development of innovative drugs. This review provides a comprehensive portrayal of BA-MS techniques and of their applications in screening and locating bioactive molecules. After introducing the basic principles, alongside some application notes, the current state-of-the-art of BA-MS-assisted drug discovery is discussed, including native MS, size-exclusion chromatography-MS, ultrafiltration-MS, solid-phase micro-extraction-MS, and cell membrane chromatography-MS. Finally, several challenges and limitations of the current methods are summarized, with a view to potential future directions for BA-MS-assisted drug discovery. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.

Techniques and Strategies for Potential Protein Target Discovery and Active Pharmaceutical Molecule Screening in a Pandemic

Viruses remain a major challenge in the fierce fight against diseases. There have been many pandemics caused by various viruses throughout the world over the years. Recently, the global outbreak of COVID-19 has had a catastrophic impact on human health and the world economy. Antiviral drug treatment has become another essential means to overcome pandemics in addition to vaccine development. How to quickly find effective drugs that can control the development of a pandemic is a hot issue that still needs to be resolved in medical research today. To accelerate the development of drugs, it is necessary to target the key target proteins in the development of the pandemic, screen active molecules, and develop reliable methods for the identification and characterization of target proteins based on the active ingredients of drugs. This article discusses key target proteins and their biological mechanisms in the progression of COVID-19 and other major epidemics. We propose a model based on these foundations, which includes identifying potential core targets, screening potential active molecules of core targets, and verifying active molecules. This article summarizes the related innovative technologies and methods. We hope to provide a reference for the screening of drugs related to pandemics and the development of new drugs.

Recent Advances in Molecular Docking for the Research and Discovery of Potential Marine Drugs

Marine drugs have long been used and exhibit unique advantages in clinical practices. Among the marine drugs that have been approved by the Food and Drug Administration (FDA), the protein–ligand interactions, such as cytarabine–DNA polymerase, vidarabine–adenylyl cyclase, and eribulin–tubulin complexes, are the important mechanisms of action for their efficacy. However, the complex and multi-targeted components in marine medicinal resources, their bio-active chemical basis, and mechanisms of action have posed huge challenges in the discovery and development of marine drugs so far, which need to be systematically investigated in-depth. Molecular docking could effectively predict the binding mode and binding energy of the protein–ligand complexes and has become a major method of computer-aided drug design (CADD), hence this powerful tool has been widely used in many aspects of the research on marine drugs. This review introduces the basic principles and software of the molecular docking and further summarizes the applications of this method in marine drug discovery and design, including the early virtual screening in the drug discovery stage, drug target discovery, potential mechanisms of action, and the prediction of drug metabolism. In addition, this review would also discuss and prospect the problems of molecular docking, in order to provide more theoretical basis for clinical practices and new marine drug research and development.

Integrated metabolomics and ligand fishing approaches to screen the hypoglycemic ingredients from four Coptis medicines

Rhizoma Coptidis, which is mainly originated from the rhizomes of Coptis chinensis, C. deltoidea, C. omeiensis and C. teeta, has been proved to possess a superior anti-diabetic effect in clinic. However, the metabolic characterization and the hypoglycemic ingredients among these Coptis species remain unclear. In this study, we employed an integrated strategy to screen the bioactive ingredients based on metabolomics and ligand fishing approaches. First, the ultra high-performance liquid chromatography coupled to quadruple time-of-flight tandem mass spectrometry (UHPLC-Q-TOF-MS/MS) was used for qualitative identification of four Coptis rhizomes. After prescreening by α-glucosidase inhibition assay, an affinity ultrafiltration system was constructed to fish out hypoglycemic ingredients from the fractions with superior activity, and verified by molecular docking on a virtual platform. The distribution of major compounds suggested the four Coptis rhizomes possess similar metabolic profiles, mainly including alkaloids and phenylpropanoids. Besides, eight compounds (magnoflorine, groenlandicine, jatrorrhizine, epiberberine, columbamine, coptisine, palmatine and berberine) from the n-butanol fraction were specifically bound to α-glucosidase, and considered as hypoglycemic ingredients of Rhizoma Coptidis. Molecular docking revealed that the inhibitors bound to α-glucosidase mainly by hydrophobic interaction, hydrogen bond interaction and π-π interaction. Summary, this research leads a more systematic and comprehensive study on metabolic characterization and hypoglycemic ingredients of Rhizoma Coptidis, which can provide a theoretical basis for the further clinical application.

Hypoglycemic and hypolipidemic effects of Moringa oleifera leaves and their functional chemical constituents

Moringa oleifera Lam. (M. oleifera) leaves have long been consumed as both nutritive vegetable and popular folk medicine for hyperglycemia and hyperlipidemia in Kenya communities. In the current study, in vitro inhibition by M. oleifera leaf extract (MOLE, 90% (v/v) ethanol) of α-glucosidase and pancreatic lipase was demonstrated, followed by determination of the effects of MOLE on both glucose consumption and lipid levels (TC, TG, HDL-C and LDL-C) in 3T3-L1 cells. Potential ligands in MOLE were fast screened using affinity ultrafiltration LC-MS, and 14 and 10 components displayed certain binding affinity to α-glucosidase and pancreatic lipase, respectively. Docking studies revealed the binding energies and hydrogen bonds between potential ligands and enzymes. This study suggests that M. oleifera leaves may be a promising natural source for the prevention and treatment of hyperglycemia and hyperlipidemia as well as a functional food or other product for health care in the near future.

In Vitro Antibacterial and Antiproliferative Potential of Echinops lanceolatus Mattf. (Asteraceae) and Identification of Potential Bioactive Compounds

Many species belonging to the genus Echinops are widely used in traditional medicine to treat infectious diseases and cancers. The present study aimed to evaluate the antibacterial and antiproliferative properties of Echinops lanceolatus Mattf. (Asteraceae). The activity of the methanolic extract and subsequent partition fractions was investigated against drug-resistant bacteria (Gram-negative and Gram-positive) and human tumor cell lines using broth microdilution and sulforhodamine B (SRB) assay, respectively. Our findings revealed weak to moderate antibacterial activities of tested extracts, with the recorded minimal inhibitory concentrations ranging from 256 to 1024 µg/mL. The ethyl acetate fraction (EL-EA) was found to be the most effective. Likewise, that fraction displayed strong antiproliferative potential with recorded IC50 of 8.27 µg/mL and 28.27 µg/mL on A549 and HeLa cells, respectively. An analysis based on the ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) of the EL-EA fraction allowed the identification of 32 compounds, of which quinic acid and derivatives, cinnamic acid derivatives, dihydrokaempferol, naringenin-7-O-glucoside, apigenin-7-O-d-glucoside, naringin, apigenin, rhoifolin, coniferyl aldehyde, and secoisolariciresinol are well-known compounds of biological importance. This study is first to report on the biological activity and phytochemical profile of E. lanceolatus. We provide a baseline to consider E. lanceolatus as a valuable source of anti-infective and antiproliferative agents.

Screening Immunoactive Compounds of Ganoderma lucidum Spores by Mass Spectrometry Molecular Networking Combined With in vivo Zebrafish Assays

Ganoderma lucidum is a well-known herbal remedy widely used for treating various chronic diseases. Traditionally, the fruiting body is regarded as the medicinal part of this fungus, while recently, the therapeutic potentials of Ganoderma lucidum spore (GLS) is gaining increasing interests. However, detailed knowledge of chemical compositions and biological activities of the spore is still lacking. In this study, high-resolution mass spectrometry and molecular networking were employed for in-depth chemical profiling of GLS, sporoderm-broken GLS (BGLS) and sporoderm-removed GLS (RGLS), leading to the characterization of 109 constituents. The result also showed that RGLS contained more triterpenoids with much higher contents than BGLS and GLS. Moreover, the immunomodulatory activities of BGLS and RGLS were investigated in the zebrafish models of neutropenia or macrophage deficiency. RGLS exhibited more potent activities in alleviating vinorelbine-induced neutropenia or macrophage deficiency, and significantly enhanced phagocytic function of macrophages, which indicated the immunomodulatory activity of GLS was positively correlated with the content of triterpenoids. Further correlation analysis of chemical profiles of GLS and corresponding bioactivities by partial least squares regression identified the potential immunoactive compounds of GLS, including 20-hydroxylganoderic acid G, elfvingic acid A and ganohainanic acid C. Our findings suggest that combining mass spectrometry molecular networking with zebrafish-based bioassays and chemometrics is a feasible strategy to reveal complex chemical compositions of herbal medicines, as well as to discover their potential active constituents.

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.