Study on Structure Activity Relationship of Natural Flavonoids against Thrombin by Molecular Docking Virtual Screening Combined with Activity Evaluation In Vitro

Thrombin-targeted screening of anticoagulant active components from Polygonum amplexicaule D. Don var. sinense Forb by affinity ultrafiltration coupled with UPLC-Q-TOF-MS

INTRODUCTION

Polygonum amplexicaule D. Don var. sinense Forb (PAF), a medicinal plant, has the effect of promoting blood circulation and removing blood stasis. However, the active compounds and targets of its anticoagulant effect are still unclear.

OBJECTIVES

This study aims to establish an effective reversely thrombin-targeted screening method for anticoagulant active components in PAF by affinity ultrafiltration (AUF) coupled with ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectroscopy (UPLC-Q-TOF-MS).

METHODS

Different polar parts of PAF were screened for potential thrombin ligands by AUF-HPLC and identified by UPLC-Q-TOF-MS. After studying the affinity between ligands and thrombin by molecular docking, the antithrombotic activity of ligands was detected in vivo by zebrafish thrombus model, and in vitro by chromogenic substrate method. The mechanism of such ligands on thrombin was further studied by coagulation factor assay.

RESULTS

Eleven potential thrombin ligands from PAF were screened by the AUF-UPLC-Q-TOF-MS method, and two compounds (butyl gallate and β-sitosterol) with significant anticoagulant activity were discovered via in vitro and in vivo activity testing.

CONCLUSION

A method system based on AUF-UPLC-Q-TOF-MS, molecular docking and in vivo and in vitro experiments also provided a powerful tool for further exploration of anticoagulant active components in PAF.

Pharmacological Activities of Lonicerae japonicae flos and Its Derivative-"Chrysoeriol" in Skin Diseases

Chrysoeriol is an active ingredient derived from the Chinese medicinal herb (CMH) "Lonicerae japonicae flos" in the dried flower bud or bloomed flower of Lonicera japonica Thunberg. Dermatoses are the most common diseases in humans, including eczema, acne, psoriasis, moles, and fungal infections, which are temporary or permanent and may be painless or painful. Topical corticosteroids are widely used in Western medicine, but there are some side effects when it is continuously and regularly utilized in a large dosage. Chrysoeriol is a natural active ingredient, nontoxic, and without any adverse reactions in the treatment of dermatological conditions.

METHODS

Nine electronic databases were searched, including WanFang Data, PubMed, Science Direct, Scopus, Web of Science, Springer Link, SciFinder, and China National Knowledge Infrastructure (CNKI), without regard to language constraints. The pharmacological activities of chrysoeriol from Lonicerae japonicae flos to fight against skin diseases were explained and evaluated through the literature review of either in vitro or in vivo studies.

RESULTS

Chrysoeriol decreased the mRNA levels of proinflammatory cytokines IL-6, IL-1β, and TNF-α. These were transcriptionally regulated by NF-κB and STAT3 to combat skin inflammation. It also showed promising actions in treating many skin ailments including wound healing, depigmentation, photoprotection, and antiaging.

CONCLUSION

The cutaneous route is the best delivery approach to chrysoeriol across the skin barrier. However, toxicity, dosage, and safety assessments of chrysoeriol in a formulation or nanochrysoeriol on the human epidermis for application in skin diseases must be further investigated.

Bioassay-guided identification of antithrombotic compounds from Cnidoscolus aconitifolius (Mill.) I. M. Jhonst.: molecular docking, bioavailability, and toxicity prediction

Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Conventional antithrombotic therapy has reported hemorrhagic accidents. Ethnobotanical and scientific reports point to Cnidoscolus aconitifolius as an antithrombotic adjuvant. Previously, C. aconitifolius leaves ethanolic extract displayed antiplatelet, anticoagulant, and fibrinolytic activities. This work aimed to identify compounds from C. aconitifolius with in vitro antithrombotic activity through a bioassay-guided study. Antiplatelet, anticoagulant, and fibrinolytic tests guided the fractionation. Ethanolic extract was subjected to a liquid-liquid partitioning, followed by vacuum liquid, and size exclusion chromatography to obtain the bioactive JP10B fraction. The compounds were identified through UHPLC-QTOF-MS, and their molecular docking, bioavailability, and toxicological parameters were determined computationally. Kaempferol-3-O-glucorhamnoside and 15(S)-HPETE were identified; both showed affinity for antithrombotic targets, low absorption, and safety for human consumption. Further in vitro and in vivo evaluations will better understand their antithrombotic mechanism. This bioassay-guided fractionation demonstrated that C. aconitifolius ethanolic extract has antithrombotic compounds.Communicated by Ramaswamy H. Sarma.

A metabolomics discrimination-based strategy for screening the antithrombin active markers of perilla seeds: A natural oil crop

Natural crops oil with high nutritional value has gradually attracted attention. Perilla seeds are regarded as a source of functional edible oil in America, Asia and European countries due to its abundant nutrients. In this research, samples were extracted by different polarity solvents and evaluated their thrombin inhibition activities in vitro. Metabolomics combined with chemometrics revealed the antithrombin active markers of perilla seeds. The enzyme kinetics and molecular docking results were useful in clarifying their inhibition of thrombin. The orthogonal experimental design was applied to optimize the extraction process of six antithrombin active markers from perilla seeds. The results showed that rosmarinic acid, luteolin, luteolin-7-O-glucoside, α-linolenic acid, linoleic acid, and oleic acid were screened out as functional and active markers. Besides, perilla seeds as a natural oil crop had the potential of antithrombin. It can also be applied in the food field because of its nutraceutical functions. Metabolomics combined with chemometrics will facilitate the discovery of functional, active markers in perilla seeds, which is conducive to accurate quality control.

Virtual screening and biological activity evaluation of novel efflux pump inhibitors targeting AdeB

The AdeABC efflux pump is an important mechanism causing multidrug resistance in Acinetobacter baumannii, and its main component AdeB can recognize carbapenems, aminoglycosides, and other multi-class antibiotics and efflux them intracellularly, which is an ideal target for the development of anti-multidrug resistant bacteria drugs. Here, we combined multiple computer-aided drug design methods to target AdeB to identify promising novel structural inhibitors. Virtual screening was performed by molecular docking and molecular dynamics simulation (MD) and 12 potential compounds were identified from the databases. Meanwhile, their biological activities were validated by in vitro activity assays, and ChemDiv L676-2179 (γ-IFN), ChemDiv L676-1461, and Chembridge 53717615 were confirmed to suppress efflux effects and restore antibiotic susceptibility of resistant bacteria, which are expected to be developed as adjuvant drugs for the treatment of multi-drug resistant Acinetobacter baumannii clinical infections.

Lipid-Based Delivery Systems for Flavonoids and Flavonolignans: Liposomes, Nanoemulsions, and Solid Lipid Nanoparticles

Herbal chemicals with a long history in medicine have attracted a lot of attention. Flavonolignans and flavonoids are considered as two classes of the above-mentioned compounds with different functional groups which exhibit several therapeutic capabilities such as antimicrobial, anti-inflammatory, antioxidant, antidiabetic, and anticancer activities. Based on the studies, high hydrophobic properties of the aforementioned compounds limit their bioavailability inside the human body and restrict their wide application. Nanoscale formulations such as solid lipid nanoparticles, liposomes, and other types of lipid-based delivery systems have been introduced to overcome the above-mentioned challenges. This approach allows the aforementioned hydrophobic therapeutic compounds to be encapsulated between hydrophobic structures, resulting in improving their bioavailability. The above-mentioned enhanced delivery system improves delivery to the targeted sites and reduces the daily required dosage. Lowering the required daily dose improves the performance of the drug by diminishing its side effects on non-targeted tissues. The present study aims to highlight the recent improvements in implementing lipid-based nanocarriers to deliver flavonolignans and flavonoids.

Flavonoids as a therapeutical option for the treatment of thrombotic complications associated with COVID-19

The SARS-CoV-2 outbreak has been one of the largest public health crises globally, while thrombotic complications have emerged as an important factor contributing to mortality. Therefore, compounds that regulate the processes involved in thrombosis could represent a dietary strategy to prevent thrombotic complications involved in COVID-19. In August 2022, various databases were consulted using the keywords "flavonoids", "antiplatelet", "anticoagulant", "fibrinolytic", and "nitric oxide". Studies conducted between 2019 and 2022 were chosen. Flavonoids, at concentrations mainly between 2 and 300 μM, are capable of regulating platelet aggregation, blood coagulation, fibrinolysis, and nitric oxide production due to their action on multiple receptors and enzymes. Most of the studies have been carried out through in vitro and in silico models, and limited studies have reported the in vivo and clinical effect of flavonoids. Currently, quercetin has been the only flavonoid evaluated clinically in patients with COVID-19 for its effect on D-dimer levels. Therefore, clinical studies in COVID-19 patients analyzing the effect on platelet, coagulant, fibrinolytic, and nitric oxide parameters are required. In addition, further high-quality studies that consider cytotoxic safety and bioavailability are required to firmly propose flavonoids as a treatment for the thrombotic complications implicated in COVID-19.

MILCDock: Machine Learning Enhanced Consensus Docking for Virtual Screening in Drug Discovery

Molecular docking tools are regularly used to computationally identify new molecules in virtual screening for drug discovery. However, docking tools suffer from inaccurate scoring functions with widely varying performance on different proteins. To enable more accurate ranking of active over inactive ligands in virtual screening, we created a machine learning consensus docking tool, MILCDock, that uses predictions from five traditional molecular docking tools to predict the probability a ligand binds to a protein. MILCDock was trained and tested on data from both the DUD-E and LIT-PCBA docking datasets and shows improved performance over traditional molecular docking tools and other consensus docking methods on the DUD-E dataset. LIT-PCBA targets proved to be difficult for all methods tested. We also find that DUD-E data, although biased, can be effective in training machine learning tools if care is taken to avoid DUD-E's biases during training.

Ecological roles of secondary metabolites of Saposhnikovia divaricata in adaptation to drought stress

Saposhnikovia divaricata is a traditional Chinese herb that mainly grows in arid grasslands and strongly adapts to various stresses. Drought is not only a major abiotic stress factor but also a typical feature conducive to producing high-quality medicinal material. The present study investigated by treating S. divaricata plants with polyethylene glycol (PEG-6000). Ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) identified 146 compounds from the roots of S. divaricata, among which seven primary metabolites and 28 secondary metabolites showed significant changes after drought treatment. UV-Vis spectrophotometer detected the activity of antioxidant enzymes and the content of superoxide anion (O2 -.) and malondialdehyde (MDA). The differential primary metabolites revealed that drought promotes glycolysis, reducing primary metabolism and enhancing secondary metabolism. Meanwhile, the differential secondary metabolites showed an increase in the content of compounds upstream of the secondary metabolic pathway, and other glycosides and increased that of the corresponding aglycones. The activities of antioxidant enzymes and the content of O2 -. and MDA shown different changes duing the drought treatment. These observations indicate that drought promotes the biosynthesis and transformation of the secondary metabolites and activity of antioxidant enzymes, improving plant adaptability. The present study also analyzed a few primary and secondary metabolites of S. divaricata under different degrees and durations of drought and speculated on the metabolic pathways in an arid environment. The findings indicate the biological nature, diversity, and complexity of secondary metabolites and the mechanisms of plant adaptation to ecological stress.

Phytochemical Analysis of the Methanolic Extract and Essential Oil from Leaves of Industrial Hemp Futura 75 Cultivar: Isolation of a New Cannabinoid Derivative and Biological Profile Using Computational Approaches

Cannabis sativa L. is a plant belonging to the Cannabaceae family, cultivated for its psychoactive cannabinoid (Δ⁹-THC) concentration or for its fiber and nutrient content in industrial use. Industrial hemp shows a low Δ⁹-THC level and is a valuable source of phytochemicals, mainly represented by cannabinoids, flavones, terpenes, and alkaloids, with health-promoting effects. In the present study, we investigated the phytochemical composition of leaves of the industrial hemp cultivar Futura 75, a monoecious cultivar commercially used for food preparations or cosmetic purposes. Leaves are generally discarded, and represent waste products. We analyzed the methanol extract of Futura 75 leaves by HPLC and NMR spectroscopy and the essential oil by GC-MS. In addition, in order to compare the chemical constituents, we prepared the water infusion. One new cannabinoid derivative (1) and seven known components, namely, cannabidiol (2), cannabidiolic acid (3), β-cannabispirol (4), β-cannabispirol (5), canniprene (6), cannabiripsol (7), and cannflavin B (8) were identified. The content of CBD was highest in all preparations. In addition, we present the outcomes of a computational study focused on elucidating the role of 2α-hydroxy-Δ^3,7-cannabitriol (1), CBD (2), and CBDA (3) in inflammation and thrombogenesis.

A combined application of molecular docking technology and indirect ELISA for the serodiagnosis of bovine tuberculosis

BACKGROUND

There is an urgent need to find reliable and rapid bovine tuberculosis (bTB) diagnostics in response to the rising prevalence of bTB worldwide. Toll-like receptor 2 (TLR2) recognizes components of bTB and initiates antigen-presenting cells to mediate humoral immunity. Evaluating the affinity of antigens with TLR2 can form the basis of a new method for the diagnosis of bTB based on humoral immunity.

OBJECTIVES

To develop a reliable and rapid strategy to improve diagnostic tools for bTB.

METHODS

In this study, we expressed and purified the sixteen bTB-specific recombinant proteins in Escherichia coli. The two antigenic proteins, MPT70 and MPT83, which were most valuable for serological diagnosis of bTB were screened. Molecular docking technology was used to analyze the affinity of MPT70, MPT83, dominant epitope peptide of MPT70 (M1), and dominant epitope peptide MPT83 (M2) with TLR2, combined with the detection results of enzyme-linked immunosorbent assay to evaluate the molecular docking effect.

RESULTS

The results showed that interaction surface Cα-atom root mean square deviation of proteins (M1, M2, MPT70, MPT83)-TLR2 protein are less than 2.5 A, showing a high affinity. It is verified by clinical serum samples that MPT70, MPT83, MPT70-MPT83 showed good diagnostic potential for the detection of anti-bTB IgG and M1, M2 can replace the whole protein as the detection antigen.

CONCLUSIONS

Molecular docking to evaluate the affinity of bTB protein and TLR2 combined with ELISA provides new insights for the diagnosis of bTB.

An integration strategy combined progressive multivariate statistics with anticoagulant activity evaluation for screening anticoagulant quality markers in Chinese patent medicine

ETHNOPHARMACOLOGICAL RELEVANCE

The cardiovascular and cerebrovascular diseases affect human health globally. Naoxintong capsules (NXTs), a famous Chinese Patent Medicine, has been especially applied to treat cerebral infarction and coronary heart disease in clinical practice. The anticoagulant activity of this prescription plays an important role in this course of treatment.

AIM OF THE STUDY

Thrombin and factor Xa (FXa) are two key targets considering the anticoagulant activity. The purpose of this investigation is to screen the quanlity markers as key thrombin and FXa inhibitors for the anticoagulant activity oriented quality control of Chinese patent medicine.

MATERIALS AND METHODS

Simple multi-polar solvent extraction processes using various proportions of solvents were conducted and their thrombin/FXa inhibitory activities were evaluated in vitro. Bivariate correlation analysis (BCA), grey correlation analysis (GCA), and orthogonal partial least squares discriminate analysis (OPLS-DA) were adopted for screening the potential active markers related to the anticoagulant activity. The chemical structures of these active compounds were identified by UHPLC-Q-TOF-MS/MS and their thrombin/FXa inhibitory activity was determined. The molecular docking technology was applied to explore the interaction between the compounds and targets. The contribution of these anticoagulant active ingredients in NXT was also investigated. Last but not the least, the contents of these markers in NXT were determined by liquid chromatography-electrospray ionization tandem triple quadrupole mass spectrometry (HPLC-ESI-MS/MS) method.

RESULTS

The results showed that the NXT extract exhibited great activity against thrombin and FXa, especially extracted by 75% methanol (v/v). Six marker compounds with potential anticoagulant activity were screened out. Therein, four of the active compounds owing thrombin inhibitory activity (paeoniflorin, lithospermic acid, salvianolic acid B, Z-ligustilide) and five of the active compounds owing FXa inhibitory activity (3,5-dicaffeoylquinic acid, rosmarinic acid, lithospermic acid, salvianolic acid B and Z-ligustilide). In addition, these active compounds accounted for a large proportion of thrombin/FXa inhibitory activity of NXTs. The binding energy also showed the strong interaction formed by close connection of the compounds to the residues of targets.

CONCLUSIONS

The proposed integrated stategy could be an efficient strategy to screen potential thrombin/FXa inhibitors for the bioactivity related quanlity control of Chinese patent medicine.

The Effects of Sorbus aucuparia L. Fruit Extracts on Oxidative/Nitrative Modifications of Human Fibrinogen, Impact on Enzymatic Properties of Thrombin, and Hyaluronidase Activity In Vitro

Sorbus aucuparia L. fruits (rowanberries) are food products with acknowledged nutritional value, high phenolic content, and traditional application in diabetes. In this study, the effects of rowanberry extracts (phytochemically standardised, i.a., by LC-MS/MS) on some aspects of plasma haemostasis and vascular conditions were evaluated in vitro as possible mechanisms connected with cardiovascular complications of diabetes. The analyses of structural modifications of human fibrinogen under oxidative stress conditions (C-ELISA, SDS-PAGE and Western blot) revealed that the extracts (at a concentration of 1-5 µg/mL) considerably reduced the nitration of tyrosine residues and formation of high-molecular-weight aggregates. Moreover, they inhibited the enzymatic activity of thrombin (both amidolytic and proteolytic). Additionally, some promising outcomes might be expected regarding endothelial functions from the extracts ability to inhibit hyaluronidase. Parallel experiments on model polyphenols and correlation studies formed the basis for determining the contribution of different compounds, including hydroxycinnamic acid derivatives, flavonols, and low- or high-molecular-weight flavan-3-ols derivatives (proanthocyanidins), to the observed effects. The possible synergistic activity of individual constituents was also noticed. These results broaden the knowledge on the biological activity of rowanberries, partly confirming their health-promoting properties, and indicating that their functional applications might be promising.

Bioactive Natural Compounds with Antiplatelet and Anticoagulant Activity and Their Potential Role in the Treatment of Thrombotic Disorders

Natural anticoagulant drugs can be obtained from plants, rich in secondary bioactive metabolites which, in addition to being effective antioxidants, also possess anticoagulant and antiplatelet properties and, for this reason, can be excellent candidates for the treatment of thrombotic diseases. This review reports an overview of the hemostatic process and thrombotic disorders together with data on plants, more and less common from around the world, containing bioactive compounds characterized by antiplatelet and anticoagulant activity. The reported literature was obtained from Medline, PubMed, Elsevier, Web of Science, Google Scholar considering only articles in the English language, published in peer-reviewed journals. The number of citations of the articles and the impact factor of the journals were other parameters used to select the scientific papers to be included in the review. The analysis of the literature data selected demonstrates that many plants’ bioactive compounds show antiplatelet and anticoagulant activity that make them potential candidates to be used as new natural compounds able to interfere with both primary and secondary hemostasis. Moreover, they could be used together with anticoagulants currently administered in clinical practice to increase their efficacy and to reduce complications in the treatment of thrombotic disorders.

Food Containing Bioactive Flavonoids and Other Phenolic or Sulfur Phytochemicals With Antiviral Effect: Can We Design a Promising Diet Against COVID-19?

Since in late 2019, when the coronavirus 2 (SARS-CoV-2) pathogen of coronavirus disease 2019 (COVID-19) started to spread all over the world, causing the awful global pandemic we are still experiencing, an impressive number of biologists, infectious disease scientists, virologists, pharmacologists, molecular biologists, immunologists, and other researchers working in laboratories of all the advanced countries focused their research on the setting up of biotechnological tools, namely vaccines and monoclonal antibodies, as well as of rational design of drugs for therapeutic approaches. While vaccines have been quickly obtained, no satisfactory anti-Covid-19 preventive, or therapeutic approach has so far been discovered and approved. However, among the possible ways to achieve the goal of COVID-19 prevention or mitigation, there is one route, i.e., the diet, which until now has had little consideration. In fact, in the edible parts of plants supplying our food, there are a fair number of secondary metabolites mainly belonging to the large class of the flavonoids, endowed with antiviral or other health beneficial activities such as immunostimulating or anti-inflammatory action that could play a role in contributing to some extent to prevent or alleviate the viral infection and/or counteract the development of SARS induced by the novel coronavirus. In this review, a number of bioactive phytochemicals, in particular flavonoids, proven to be capable of providing some degree of protection against COVID-19, are browsed, illustrating their beneficial properties and mechanisms of action as well as their distribution in cultivated plant species which supply food for the human diet. Furthermore, room is also given to information regarding the amount in food, the resistance to cooking processes and, as a very important feature, the degree of bioavailability of these compounds. Concluding, remarks and perspectives for future studies aimed at increasing and improving knowledge and the possibility of using this natural complementary therapy to counteract COVID-19 and other viral pathologies are discussed.

Flavonoids: A complementary approach to conventional therapy of COVID-19?

COVID-19, the highly contagious novel disease caused by SARS-CoV-2, has become a major international concern as it has spread quickly all over the globe. However, scientific knowledge and therapeutic treatment options for this new coronavirus remain limited. Although previous outbreaks of human coronaviruses (CoVs) such as SARS and MERS stimulated research, there are, to date, no antiviral therapeutics available that specifically target these kinds of viruses. Natural compounds with a great diversity of chemical structures may provide an alternative approach for the discovery of new antivirals. In fact, numerous flavonoids were found to have antiviral effects against SARS-and MERS-CoV by mainly inhibiting the enzymes 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). In this review, we specifically focused on the search for flavonoids, polyphenolic compounds, which are proven to be effective against human CoVs. We therefore summarized and analyzed the latest progress in research to identify flavonoids for antiviral therapy and proposed strategies for future work on medicinal plants against coronaviruses such as SARS-CoV-2. We discovered quercetin, herbacetin, and isobavachalcone as the most promising flavonoids with anti-CoV potential.

Complexity of active medicinal ingredients in radix scutellariae with sodium hydrosulfite exposure

Both plants and animals are living things made up of similar cells as well as organelles, and their essence of life is the same. However, plants face more environmental stress than animals and generate excessive reactive oxygen species (ROS), a group of small molecules that can harm proteins, necessitating distinctive metabolic processes. Secondary metabolites in plants are a group of chemical components that can eliminate ROS and can also exhibit medicinal properties; therefore, herbal medicines are often closely linked to the ecological significance of secondary metabolites. Why plants contain so many, not few, active medicinal ingredients is unknown. The root of Scutellaria baicalensis, a popular herbal medicine, is rich in various flavonoids with diverse structural features. Sodium hydrosulfite (Na₂S₂O₄) can produce O˙^-₂ radicals and induce physical conditions under environmental stress. Using UHPLC-ESI-Q-TOF-MS/MS analysis, a total of 25 different compounds were identified in the roots of S. baicalensis between the Na₂S₂O₄ groups and suitable conditions. Based on the results of the t-test (P<0.05) performed for the groups and ions with values of VIP ≥ 2, the most significantly different chemical markers with Na₂S₂O₄ treatment were shikimic acid, citric acid, baicalin, wogonoside, baicalein, wogonin, 3,5,7,2',6'-pentahydroxyflavanone, 5,2',6'-trihydroxy-7,8-dimethoxy flavone, chrysin, eriodictyol, 5,8-dihydroxy-6,7 -dimethoxy flavone, skullcapflavone Ⅱ, and 5,7-dihydroxy-6,8,2',3'-tetrame thoxyflavone, and most of them were free flavonoids with many phenolic hydroxyl or methoxyl groups and characteristically high antioxidant activities. S. baicalensis roots modified their ability to eliminate ROS and maintained the equilibrium of ROS through the multitudinous biosynthesis and conversion of flavonoids, which is similar to the equilibrium established by an intricate buffer solution and perfectly explains the diversity and complexity of medicinal plant ingredients.