Screening of Potential Thrombin and Factor Xa Inhibitors from the Danshen-Chuanxiong Herbal Pair through a Spectrum-Effect Relationship Analysis.

In this study; a spectrum-effect relationship analysis combined with a high-performance liquid chromatography-mass spectrometry (LC-MS) analysis was established to screen and identify active components that can inhibit thrombin and factor Xa (THR and FXa) in Salviae Miltiorrhizae Radix et Rhizoma-Chuanxiong Rhizoma (Danshen-Chuanxiong) herbal pair. Ten potential active compounds were predicted through a canonical correlation analysis (CCA), and eight of them were tentatively identified through an LC-MS analysis. Furthermore; the enzyme inhibitory activity of six available compounds; chlorogenic acid; Z-ligustilide; caffeic acid; ferulic acid; tanshinone I and tanshinone IIA; were tested to verify the feasibility of the method. Among them; chlorogenic acid was validated to possess a good THR inhibitory activity with IC50 of 185.08 µM. Tanshinone I and tanshinone IIA are potential FXa inhibitors with IC50 of 112.59 µM and 138.19 µM; respectively. Meanwhile; molecular docking results show that tanshinone I and tanshinone IIA; which both have binding energies of less than -7.0 kcal·mol-1; can interact with FXa by forming H-bonds with residues of SER214; GLY219 and GLN192. In short; the THR and FXa inhibitors in the Danshen-Chuanxiong herbal pair have been successfully characterized through a spectrum-effect relationship analysis and an LC-MS analysis.

Aqueous Extract of Taegeuk Ginseng Inhibits Platelet Aggregation and Thrombus Formation.

The inhibitory effects of taegeuk ginseng extract (TGE) on platelet aggregation and thrombus formation were investigated. The TGE significantly inhibited collagen- and adenosine 5'-diphosphate (ADP)-induced platelet aggregation in vitro in a dose-dependent manner. Also oral administration of TGE to rats significantly prevented ADP- and collagen-induced platelet aggregation ex vivo, but it did not affect the plasma coagulation system. The oral administration of TGE significantly delayed the occlusion of the carotid artery in ferrous chloride-treated rats in vivo. These results suggest that in vivo antithrombotic effect of TGE may be due to its inhibitory activity on platelet aggregation rather than on plasma coagulation.

[Effect of ingestion on antithrombin activity in different tissues of Whitmania pigra].

To study the effects of ingestion on antithrombin activities in different tissues of Whitmania pigra, the salivary glands, ingluvies, intestine and muscle of adult leeches were weighted on the 1st d, 3rd d, 5th d, 7th d and 11th d after feeding, respectively, and meanwhile antithrombin activity was measured by antithrombin titration method. The results showed that the antithrombin activity of salivary glands in different stages was significantly higher than that in other tissues (P<0.05). The activity of antithrombin in muscle tissue increased initially and then decreased with the prolongation of the time after feeding, and the peak was observed on the 5th day after feeding (P<0.05). The activity of antithrombin in the salivary glands, gluvies and intestine were found the highest on the 1st day after feeding(P<0.05), and then gradually decreased with the prolongation of the time of stopping the diet. The total amount of antithrombin activity on the 5th day was increased by 49.5%, 73.5%, 69.1% and 126.0% comparing with the 1st, 3rd, 7th and 11th day after feeding, respectively (P<0.05). In summary, both the feeding behavior and the food can induce the secretion of anticoagulant substances in the salivary glands and the digestive tract. The total amount of antithrombin activity was the highest on the 5th day after feeding and the 5th day after feeding was suggested as harvesting time.

An ultrafiltration and high performance liquid chromatography coupled with diode array detector and mass spectrometry approach for screening and characterizing thrombin inhibitors from Rhizoma Chuanxiong.

Thrombin (THR) plays a significant role in thromboembolic diseases, direct THR inhibitors are a class of important clinical anticoagulant drugs. This study established a THR in-solution based biospecific extraction combined with ultrafiltration and high performance liquid chromatography coupled with diode array detector and mass spectrometry analysis (TUA) method to screen and identify ligands for THR in Rhizoma Chuanxiong. After evaluating the reliability of the present TUA method using positive (argatroban) and negative (adenosine, tirofiban, ticagrelor) control drugs, this method was successfully applied to detect eight potential active compounds in Rhizoma Chuanxiong. Two new THR-targeted compounds isochlorogenic acid C and senkyunolide I with high THR inhibitory activity (IC50 206.48 and 197.23µM, respectively) were identified by liquid chromatography/mass spectrometry and enzyme inhibitory activity test finally. They were reported with direct THR inhibition activity for the first time and their ligand-THR interactions were explored by in silico molecular docking research. In addition, based on the TUA screening result, four compounds gained similar structure with the two hit compounds were also investigated as promising candidates targeting THR with high binding energy (>5.0kcal/mol). These results may prove that the proposed method could effectively screen THR inhibitors in complex mixtures.

RETRACTED: In vivo and in vitro antithrombus activities of depolymerized holothurian polysaccharides.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of authors. The authors have recently found a serious mistake in Table 1 of the article, where the molecular ratio of different monosaccharides is inconsistent with their previously published work. This error flaws the paper and so the authors wish it to be retracted to avoid misunderstanding and misinterpretation of their research work. The authors apologise for any concern or confusion that might have resulted in publishing this article.

Screening of thrombin inhibitors from phenolic acids using enzyme-immobilized magnetic beads through direct covalent binding by ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry.

Thrombin was immobilized on dynabeads®M-270 epoxy by direct covalent binding method for the first time. The enzyme coated magnetic beads were combined with ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry technique to establish a simple, rapid and reliable approach for screening thrombin inhibitors from Danshen preparation. The conjugation of thrombin to the magnetic beads was characterized using scanning electron microscope, transmission electron microscope and infrared spectroscopy, and the enzyme activity was determined by the analysis of enzyme-bead ratio and peak areas of target compounds. Several factors including amount of magnetic beads, type of elution solvent, incubation temperature and time were optimized. Additionally, two thrombin-bound compounds (protocatechuic aldehyde and salvianolic acid C) in Danshen injection were validated by conventional inhibitory assay and the IC50 values were 286.11 and 66.09µg/mL, respectively. Our findings suggested that the proposed method was efficient in screening active compounds from medicinal plants.

A chemical family-based strategy for uncovering hidden bioactive molecules and multicomponent interactions in herbal medicines.

Two concepts involving natural products were proposed and demonstrated in this paper. (1) Natural product libraries (e.g. herbal extract) are not perfect for bioactivity screening because of the vast complexity of compound compositions, and thus a library reconstruction procedure is necessary before screening. (2) The traditional mode of "screening single compound" could be improved to "screening single compound, drug combination and multicomponent interaction" due to the fact that herbal medicines work by integrative effects of multi-components rather than single effective constituents. Based on the two concepts, we established a novel strategy aiming to make screening easier and deeper. Using thrombin as the model enzyme, we firstly uncovered the minor lead compounds, potential drug combinations and multicomponent interactions in an herbal medicine of Dan-Qi pair, showing a significant advantage over previous methods. This strategy was expected to be a new and promising mode for investigation of herbal medicines.

Discovery of non-competitive thrombin inhibitor derived from competitive tryptase inhibitor skeleton: Shift in molecular recognition resulted from skeletal conversion of carboxylate into phosphonate.

A novel series of terminal and internal phosphonate esters based on our previously developed aryl carboxylate-type tryptase selective inhibitor 1 was synthesized. The potency of these synthesized compounds was assessed in vitro with an enzyme inhibition assay using three available serine proteases, that is, tryptase, trypsin, and thrombin. The internal phosphonate derivative 6 showed potent thrombin inhibitory activity with an IC50 value of 1.0 µM, whereas it exhibited no or only weak tryptase and trypsin inhibition at 10 µM. The Lineweaver-Burk plot analysis indicates that the inhibition pattern of thrombin with 6 is non-competitive in spite of the fact that the lead carboxylate compound 1 is competitive inhibitor. Therefore, the skeletal conversion of the carboxylate into a phosphonate alters the mode of molecular recognition of these inhibitors by thrombin.

Screening of direct thrombin inhibitors from Radix Salviae Miltiorrhizae by a peak fractionation approach.

Thrombin plays a significant role in thromboembolic disease. In this work, a peak fractionation approach combined with an activity assay method was used to screen direct thrombin inhibitors from Radix Salviae Miltiorrhizae (RSM), a famous herbal remedy for the treatment of cardiovascular diseases in China. A total of 91 fractions were collected from the RSM extract, and 19 fractions out of them showed thrombin inhibitory effects with dose-effect relationship. Among them, three compounds were unambiguously identified as 15, 16-dihydrotanshinone I, cryptotanshinone and tanshinone IIA with IC50 values of 29.39, 81.11 and 66.60µM, respectively. The three compounds were reported with direct thrombin inhibition activities for the first time and their ligand-thrombin interactions were explored by a molecular docking research. These results may contribute to explain the medical benefit of RSM for the prevention and treatment of cardiovascular diseases.

Anti-thrombotic effect of rutin isolated from Dendropanax morbifera Leveille.

Dendropanax morbifera H. Lev. is well known in Korean traditional medicine for improvement of blood circulation. In this study, rutin, a bioflavonoid having anti-thrombotic and anticoagulant activities was isolated from a traditional medicinal plant, D. morbifera H. Lev. The chemical characteristics of rutin was studied to be quercetin 3-O-α-l-rhamnopyranosyl-(1-6)-ß-d-glucopyranoside using high performance liquid chromatography mass spectrometry (HPLC-MS), proton nuclear magnetic resonance ((1)H NMR) and carbon-13 nuclear magnetic resonance ((13)C NMR). Turbidity and fibrin clotting studies revealed that rutin reduces fibrin clot in concentration dependent manner. Rutin was found to prolong activated partial thromboplastin time (aPTT), prothrombin time (PT) and closure time (CT). Furthermore, it decreased the activity of pro-coagulant protein, thrombin. In vivo study showed that rutin exerted a significant protective effect against collagen and epinephrine (or thrombin) induced acute thromboembolism in mice. These results suggest that rutin has a potent to be an anti-thrombotic agent for cardiovascular diseases.

Virtual screening using combinatorial cyclic peptide libraries reveals protein interfaces readily targetable by cyclic peptides.

Protein-protein and protein-peptide interactions are responsible for the vast majority of biological functions in vivo, but targeting these interactions with small molecules has historically been difficult. What is required are efficient combined computational and experimental screening methods to choose among a number of potential protein interfaces worthy of targeting lead macrocyclic compounds for further investigation. To achieve this, we have generated combinatorial 3D virtual libraries of short disulfide-bonded peptides and compared them to pharmacophore models of important protein-protein and protein-peptide structures, including short linear motifs (SLiMs), protein-binding peptides, and turn structures at protein-protein interfaces, built from 3D models available in the Protein Data Bank. We prepared a total of 372 reference pharmacophores, which were matched against 108,659 multiconformer cyclic peptides. After normalization to exclude nonspecific cyclic peptides, the top hits notably are enriched for mimetics of turn structures, including a turn at the interaction surface of human α thrombin, and also feature several protein-binding peptides. The top cyclic peptide hits also cover the critical "hot spot" interaction sites predicted from the interaction crystal structure. We have validated our method by testing cyclic peptides predicted to inhibit thrombin, a key protein in the blood coagulation pathway of important therapeutic interest, identifying a cyclic peptide inhibitor with lead-like activity. We conclude that protein interfaces most readily targetable by cyclic peptides and related macrocyclic drugs may be identified computationally among a set of candidate interfaces, accelerating the choice of interfaces against which lead compounds may be screened.

[Study on antiplatelet and antithrombin activitives and effective components variation of Puhuang-Wulingzhi before and after compatibility].

The changes of bioactive constituents were analyzed for Puhuang-Wulingzhi before and after compatibility and the antiplatelet and antithrombin activitives were evaluated in order to elucidate the scientific and reasonable of Puhuang-Wulingzhi compatibility. UPLC-QTOF-MA-Markerlynx, principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis were used for data analysis and tracking changes of chemical composition during the decocting process. In vitro platelet aggregation induced by ADP, thrombin time(TT) and prothrombin time (PT) were investigated for Puhuang-Wulingzhi before and after compatibility. The results showed that significant differences were found between the mixed decoction and codecoction of Wulingzhi and Puhuang. Five compounds changed obviously were identified as typhaneoside, naringenin, isorhamnetin-3-O-ruinoside, quercetin-3-O-neohesperidoside, kaempferol-3-O-neohesperidoside. The codecoction, comparing with the single decoction, was more significant in antiplatelet aggregation and could prolong thrombin time. In the same crude drug dose, the thrombin time (TT) elongation were greater. These data could provide references for elucidation of bioactive components for this herb pair.

Conformational activation of antithrombin by heparin involves an altered exosite interaction with protease.

Heparin allosterically activates antithrombin as an inhibitor of factors Xa and IXa by enhancing the initial Michaelis complex interaction of inhibitor with protease through exosites. Here, we investigate the mechanism of this enhancement by analyzing the effects of alanine mutations of six putative antithrombin exosite residues and three complementary protease exosite residues on antithrombin reactivity with these proteases in unactivated and heparin-activated states. Mutations of antithrombin Tyr(253) and His(319) exosite residues produced massive 10-200-fold losses in reactivity with factors Xa and IXa in both unactivated and heparin-activated states, indicating that these residues made critical attractive interactions with protease independent of heparin activation. By contrast, mutations of Asn(233), Arg(235), Glu(237), and Glu(255) exosite residues showed that these residues made both repulsive and attractive interactions with protease that depended on the activation state and whether the critical Tyr(253)/His(319) residues were mutated. Mutation of factor Xa Arg(143), Lys(148), and Arg(150) residues that interact with the exosite in the x-ray structure of the Michaelis complex confirmed the importance of all residues for heparin-activated antithrombin reactivity and Arg(150) for native serpin reactivity. These results demonstrate that the exosite is a key determinant of antithrombin reactivity with factors Xa and IXa in the native as well as the heparin-activated state and support a new model of allosteric activation we recently proposed in which a balance between attractive and repulsive exosite interactions in the native state is shifted to favor the attractive interactions in the activated state through core conformational changes induced by heparin binding.

Evaluation of antithrombotic activity of thrombin DNA aptamers by a murine thrombosis model.

Aptamers are nucleic acid based molecular recognition elements with a high potential for the theranostics. Some of the aptamers are under development for therapeutic applications as promising antithrombotic agents; and G-quadruplex DNA aptamers, which directly inhibit the thrombin activity, are among them. RA-36, the 31-meric DNA aptamer, consists of two thrombin binding pharmacophores joined with the thymine linker. It has been shown earlier that RA-36 directly inhibits thrombin in the reaction of fibrinogen hydrolysis, and also it inhibits plasma and blood coagulation. Studies of both inhibitory and anticoagulation effects had indicated rather high species specificity of the aptamer. Further R&D of RA-36 requires exploring its efficiency in vivo. Therefore the development of a robust and adequate animal model for effective physiological studies of aptamers is in high current demand. This work is devoted to in vivo study of the antithrombotic effect of RA-36 aptamer. A murine model of thrombosis has been applied to reveal a lag and even prevention of thrombus formation when RA-36 was intravenous bolus injected in high doses of 1.4-7.1 µmol/kg (14-70 mg/kg). A comparative study of RA-36 aptamer and bivalirudin reveals that both direct thrombin inhibitors have similar antithrombotic effects for the murine model of thrombosis; though in vitro bivalirudin has anticoagulation activity several times higher compared to RA-36. The results indicate that both RA-36 aptamer and bivalirudin are direct thrombin inhibitors of different potency, but possible interactions of the thrombin-inhibitor complex with other components of blood coagulation cascade level the physiological effects for both inhibitors.

Prothrombin complex concentrates as reversal agents for new oral anticoagulants: lessons from preclinical studies with Beriplex.

Although new oral anticoagulants (NOACs) represent an advance in anticoagulant therapy over vitamin K antagonists (VKAs), they nevertheless have a low, but significant risk for bleeding complications. Reversal agents for VKAs, such as prothrombin complex concentrates (PCCs), are currently being evaluated in preclinical studies for NOAC reversal. This article reviews the preclinical data for the most extensively studied PCC for NOAC reversal, Beriplex, a 4-factor PCC. The results from the Beriplex studies are also compared with those obtained with other reversal agents, including different nonactivated PCCs, activated PCCs, and recombinant activated factor VII.

GpIbα interacts exclusively with exosite II of thrombin.

Activation of platelets by the serine protease thrombin is a critical event in haemostasis. This process involves the binding of thrombin to glycoprotein Ibα (GpIbα) and cleavage of protease-activated receptors (PARs). The N-terminal extracellular domain of GpIbα contains an acidic peptide stretch that has been identified as the main thrombin binding site, and both anion binding exosites of thrombin have been implicated in GpIbα binding, but it remains unclear how they are involved. This issue is of critical importance for the mechanism of platelet activation by thrombin. If both exosites bind to GpIbα, thrombin could potentially act as a platelet adhesion molecule or receptor dimerisation trigger. Alternatively, if only a single site is involved, GpIbα may serve as a cofactor for PAR-1 activation by thrombin. To determine the involvement of thrombin's two exosites in GpIbα binding, we employed the complementary methods of mutational analysis, binding studies, X-ray crystallography and NMR spectroscopy. Our results indicate that the peptide corresponding to the C-terminal portion of GpIbα and the entire extracellular domain bind exclusively to thrombin's exosite II. The interaction of thrombin with GpIbα thus serves to recruit thrombin activity to the platelet surface while leaving exosite I free for PAR-1 recognition.

Antithrombin effect of polyphenol-rich extracts from black chokeberry and grape seeds.

Thrombin is a serine protease that cleaves the peptide bonds in proteins located on the carboxyl side of arginine. Thrombin plays a central role in thromboembolic diseases, which are the major cause of mortality. The aim of the study was to estimate the effects of plant extracts on proteolytic properties of thrombin. Thrombin was incubated with polyphenol-rich extracts from berries of Aronia melanocarpa or seeds of Vitis vinifera (0.5, 5, 50 µg/mL) and with polyphenols ((+)-catechin, (-)-epicatechin, gallic acid, chlorogenic acid, procyanidin B1, cyanidin, cyanidin 3-glucoside, quercetin). The in vitro experiments showed that both extracts in all used concentrations inhibited proteolytic activity of thrombin observed as inhibition of thrombin-induced fibrinogen polymerization, stabilized fibrin formation, and platelet aggregation. Moreover, thrombin amidolytic activity was inhibited by polyphenols belonging to the flavonoid class. Results presented in this study indicate that polyphenol-rich extracts from berries of A. melanocarpa and seeds of V. vinifera may become promising dietary supplements in the prevention of thrombotic states.

Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector.

Anopheles mosquitoes are vectors of malaria, a potentially fatal blood disease affecting half a billion humans worldwide. These blood-feeding insects include in their antihemostatic arsenal a potent thrombin inhibitor, the flexible and cysteine-less anophelin. Here, we present a thorough structure-and-function analysis of thrombin inhibition by anophelin, including the 2.3-Å crystal structure of the human thrombin·anophelin complex. Anophelin residues 32-61 are well-defined by electron density, completely occupying the long cleft between the active site and exosite I. However, in striking contrast to substrates, the D50-R53 anophelin tetrapeptide occupies the active site cleft of the enzyme, whereas the upstream residues A35-P45 shield the regulatory exosite I, defining a unique reverse-binding mode of an inhibitor to the target proteinase. The extensive interactions established, the disruption of thrombin's active site charge-relay system, and the insertion of residue R53 into the proteinase S(1) pocket in an orientation opposed to productive substrates explain anophelin's remarkable specificity and resistance to proteolysis by thrombin. Complementary biophysical and functional characterization of point mutants and truncated versions of anophelin unambiguously establish the molecular mechanism of action of this family of serine proteinase inhibitors (I77). These findings have implications for the design of novel antithrombotics.

In silico discovery of a compound with nanomolar affinity to antithrombin causing partial activation and increased heparin affinity.

The medical and socioeconomic relevance of thromboembolic disorders promotes an ongoing effort to develop new anticoagulants. Heparin is widely used as activator of antithrombin but incurs side effects. We screened a large database in silico to find alternative molecules and predicted d-myo-inositol 3,4,5,6-tetrakisphosphate (TMI) to strongly interact with antithrombin. Isothermal titration calorimetry confirmed a TMI affinity of 45 nM, higher than the heparin affinity (273 nM). Functional studies, fluorescence analysis, and citrullination experiments revealed that TMI induced a partial activation of antithrombin that facilitated the interaction with heparin and low affinity heparins. TMI improved antithrombin inhibitory function of plasma from homozygous patients with antithrombin deficiency with a heparin binding defect and also in a model with endothelial cells. Our in silico screen identified a new, non-polysaccharide scaffold able to interact with the heparin binding domain of antithrombin. The functional consequences of this interaction were experimentally characterized and suggest potential anticoagulant therapeutic applications.