Article

Molecular Docking in Xin-Ke-Shu Preparation's Multi-Target Effect on Coronary Heart Disease

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Abstract

Xin-Ke-Shu (XKS), a traditional Chinese medicine (TCM) preparation, has been widely used for treatment of coronary heart disease (CHD) in China. However, the active constituents of XKS and their interactions with targets remain unclear. In this study, we assessed two docking programs, LibDock and AutoDock, by calculating the root-mean-square deviation (RMSD) of X-ray structure reproduction and the enrichment factor (EF) in virtual screening; both proved to be practical in our protein-ligand complex systems. Moreover, the combined use of the two programs yielded better EFs for each target. We therefore used a combination of the two programs to investigate the interactions of the 51 chemical constituents identified from XKS with five CHD targets, namely peroxisome proliferator activated receptor γ (PPAR-γ), angiotensin-converting enzyme (ACE), hydroxymethylglutaryl coenzyme A receptor (HMGR), cyclooxygenase-2 (COX2), and thrombin. The docking results suggest that pueroside A, pueroside B, salvianolic acid A, and salvianolic acid C can interact with two or more targets, and the other eight compounds may be potent for at least one of the five targets. In this research, we propose a strategy for studying TCM preparations, and suggest that XKS has a multi-target effect on CHD.

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... Emodin Monoamine oxidase B [145], Hypoxia-inducible factor 1a [121,158], Thymidine phosphorylase [136], Macrophage metalloelastase [123], Interleukin 8 [123], Tumor necrosis factor ligand superfamily member 5 [123] Rhein Monoamine oxidase B [145], Protein Tyrosine Phosphatase [141], Hypoxia-inducible factor 1a [137], Epidermal growth factor receptor [137] Chrysorphanol Monoamine oxidase B [145], Protein Tyrosine Phosphatase [141] Aloe-emodin Monoamine oxidase B [145] Physcion Monoamine oxidase B [145], Protein Tyrosine Phosphatase [141] Gallic Acid 3-O-b-D-Gluco-pyranoside Hypoxia-inducible factor 1a [159] Salvianolic acid B Tissue plasminogen activator [132], Plasminogen activator inhibitor-1 [132], Angiotensin converting enzyme [140] Tanshinone IIA Transforming growth factor beta 1 [134,160], Angiotensin converting enzyme [134], Peroxisome proliferatoractivated receptor [161,162] Calycosin Estrogen receptor [94] Formononetin Monoamine oxidase B [146], Mitogen-activated protein kinase 14 [135] Quercetin b2 adrenergic receptor [163], Interleukin 8 [139],Tumor necrosis factor ligand superfamily member 5 [138], C-C motif chemokine-2 [138], Nuclear factor NF-kB [139], Jun proto-oncogene [138] Curcumin b2 adrenergic receptor [164,165], Insulin receptor [92], C-C motif chemokine-2 [91], Interleukin 8 [91], Transforming growth factor beta 1 [92], Plasminogen activator inhibitor-1 [92], Fibronectin 1 [92] doi:10.1371/journal.pone.0089123.t004 proteins in multiple cellular pathways, which lead to changes at the individual cell level, the tissue level and, ultimately, the disease state. ...
... ACE is an important protein of the renin-angiotensin signal pathway. Salvianolic acid A can interact with angiotensinconverting enzyme (ACE) [140] and may reduce the arterial pressure, ventricular afterload and the blood volume. ...
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... Emodin Monoamine oxidase B [145], Hypoxia-inducible factor 1a [121,158], Thymidine phosphorylase [136], Macrophage metalloelastase [123], Interleukin 8 [123], Tumor necrosis factor ligand superfamily member 5 [123] Rhein Monoamine oxidase B [145], Protein Tyrosine Phosphatase [141], Hypoxia-inducible factor 1a [137], Epidermal growth factor receptor [137] Chrysorphanol Monoamine oxidase B [145], Protein Tyrosine Phosphatase [141] Aloe-emodin Monoamine oxidase B [145] Physcion Monoamine oxidase B [145], Protein Tyrosine Phosphatase [141] Gallic Acid 3-O-b-D-Gluco-pyranoside Hypoxia-inducible factor 1a [159] Salvianolic acid B Tissue plasminogen activator [132], Plasminogen activator inhibitor-1 [132], Angiotensin converting enzyme [140] Tanshinone IIA Transforming growth factor beta 1 [134,160], Angiotensin converting enzyme [134], Peroxisome proliferatoractivated receptor [161,162] Calycosin Estrogen receptor [94] Formononetin Monoamine oxidase B [146], Mitogen-activated protein kinase 14 [135] Quercetin b2 adrenergic receptor [163], Interleukin 8 [139],Tumor necrosis factor ligand superfamily member 5 [138], C-C motif chemokine-2 [138], Nuclear factor NF-kB [139], Jun proto-oncogene [138] Curcumin b2 adrenergic receptor [164,165], Insulin receptor [92], C-C motif chemokine-2 [91], Interleukin 8 [91], Transforming growth factor beta 1 [92], Plasminogen activator inhibitor-1 [92], Fibronectin 1 [92] doi:10.1371/journal.pone.0089123.t004 proteins in multiple cellular pathways, which lead to changes at the individual cell level, the tissue level and, ultimately, the disease state. ...
... ACE is an important protein of the renin-angiotensin signal pathway. Salvianolic acid A can interact with angiotensinconverting enzyme (ACE) [140] and may reduce the arterial pressure, ventricular afterload and the blood volume. ...
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... For the target protein with the original co-crystal ligand available, the cutoff value was the LibDock score of the protein and its corresponding original ligand (Rao et al., 2007). For the protein without original co-crystal ligand, the cutoff value was the LibDock score of the protein and its corresponding approved positive drug (Hu et al., 2012). Compounds with a higher LibDock score than the cutoff value were considered potential active ingredients of Hugan tablets. ...
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Atorvastatin is a widely used lipid-lowering drug in the clinic. Research shows that taking long-term atorvastatin has the risk of drug-induced liver injury (DILI) in most patients. Hugan tablets, a commonly used drug for liver disease, can effectively lower transaminase and protect the liver. However, the underlying mechanism of Hugan tablets alleviating atorvastatin-induced DILI remains unclear. To address this problem, comprehensive chemical profiling and network pharmacology methods were used in the study. First, the strategy of “compound−single herb−TCM prescription” was applied to characterize the ingredients of Hugan tablets. Then, active ingredients and potential targets of Hugan tablets in DILI treatment were screened using network pharmacology, molecular docking, and literature research. In the end, the mechanism of Hugan tablets in treating atorvastatin-induced DILI was elucidated. The results showed that Hugan tablets can effectively alleviate DILI induced by atorvastatin in model rats, and 71 compounds were characterized from Hugan tablets. Based on these compounds, 271 potential targets for the treatment of DILI were predicted, and 10 key targets were chosen by characterizing protein–protein interactions. Then, 30 potential active ingredients were screened through the molecular docking with these 10 key targets, and their biological activity was explained based on literature research. Finally, the major 19 active ingredients of Hugan tablets were discovered. In addition, further enrichment analysis of 271 targets indicated that the PI3K-Akt, TNF, HIF-1, Rap1, and FoxO signaling pathways may be the primary pathways regulated by Hugan tablets in treating DILI. This study proved that Hugan tablets could alleviate atorvastatin-induced DILI through multiple components, targets, and pathways.
... Therefore, these active compounds (e.g., naringenin, tangeretin, meranzin hydrate, and other structurally similar compounds) should be further isolated. Before entering the body, chemical compounds are hydrolyzed to metabolites in the gastrointestinal tract and then absorbed for their corresponding pharmacological effects [12]. Flavonoid glycosides of AF such as naringin, neohesperidin, and poncirin were hydrolyzed to naringenin, hesperetin, isosakuranetin, etc. ...
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New arylhydrazone derivatives and a series of 1,5-diphenyl pyrazoles were designed and synthesized from 1-(4-chlorophenyl)-4,4,4-trifuorobutane-1,3-dione 1. The newly synthesized compounds were investigated in vivo for their anti-inflammatory activities using carrageenan-induced rat paw oedema model. Moreover, they were tested for their inhibitory activity against ovine COX-1 and COX-2 using an in vitro cyclooxygenase (COX) inhibition assay. Some of the new compounds (2f, 6a and 6d) showed a reasonable in vitro COX-2 inhibitory activity, with IC₅₀ value of 0.45 μM and selectivity index of 111.1. A virtual screening was carried out through docking the designed compounds into the COX-2 binding site to predict if these compounds have analogous binding mode to the COX-2 inhibitors. Docking study of the synthesized compounds 2f, 6a and 6d into the active site of COX-2 revealed a similar binding mode to SC-558, a selective COX-2 inhibitor.
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Xin-Ke-Shu (XKS), a traditional Chinese medicine (TCM) preparation containing five herbal medicines, has been commonly used for the treatment of coronary heart disease in China. However, the chemical constituents in XKS have not been clarified yet. In order to quickly define the chemical profiles and control the quality of XKS preparations, liquid chromatography coupled with electrospray ionization hybrid linear trap quadrupole orbitrap (LC-LTQ-Orbitrap) mass spectrometry was applied for simultaneous identification and quantification of multi-constituent. A total of 51 compounds, including phenolic acids, isoflavone-C-glycosides, isoflavone-O-glycosides, flavonoids, and triterpenoid saponins, were identified or tentatively deduced on the base of their retention behaviors, MS and MS(n) data, or by comparing with reference substances and literatures. In addition, an optimized LC-ESI-MS method was established for quantitative determination of 15 marker compounds in XKS preparations from 7 independent pharmaceutical companies. The validation of the method, including spike recoveries, linearity, sensitivity (LOD and LOQ), precision, and repeatability, was carried out and demonstrated to be satisfied the requirements of quantitative analysis. This is the first report on the comprehensive determination of chemical constituents in XKS preparations by LC-LTQ-Orbitrap mass spectrometry. The results suggested that the established methods would be a powerful and reliable analytical tool for the characterization of multi-constituent in complex chemical system and quality control of TCM preparations.
Article
The synthesis of a novel series of 4-thiazolylpyrazolyl derivatives is described in the present report. All the newly synthesized compounds were examined for their anti-inflammatory activity using cotton pellet-induced granuloma and carrageenan-induced rat paw edema bioassays. Their inhibitory activities of cyclooxygenase-1 and cyclooxygenase-2 (COX-1 and COX-2), ulcerogenic effect and acute toxicity were also determined. Furthermore, all compounds were evaluated for their in vitro antimicrobial activity against Escherichia coli, Staphylococcus aureus and Candida albicans. A docking pose for compounds 8b, 10a and 10b separately in the active site of the human COX-2 enzyme and DNA-gyrase B was also obtained. The results revealed that compounds 8b, 10a and 10b exhibited good anti-inflammatory activity with no or minimal ulcerogenic effect and good safety margin. Compounds 10a and 10b were found to be the most potent anti-inflammatory agents in the present study. Meanwhile, 10a and 10b displayed higher selective inhibitory activity towards COX-2 compared to indomethacin. Moreover, compounds 10a and 10b exhibited promising antibacterial against both E. coli and S. aureus. Docking studies for 8b, 10a and 10b with COX-2 (PDB ID: 1CX2) and DNA-gyrase B (PDB ID: 1EI1) showed good binding profile.
Article
Salvianolic acid A (SAA), the water-soluble phenolic acids in Salvia miltiorrhiza, has shown the most potent bioactivities, including protection against cerebral lesion, defense from oxidative damage and improvement of remembrance. In the present study, we studied the antiplatelet and antithrombotic effects of a newly synthesized SAA with different methods both in vitro and in vivo. We tested the effect of antithrombotic activity of SAA in arterio-venous shunt model. The effects of SAA on adenosine diphosphate (ADP)-, Thrombin-, Arachidonic acid- induced rat platelets aggregation were tested both in vivo and in vitro. The activity of SAA on washed human platelet aggregation was determined by ADP stimulation. We also evaluated its property of modulation of hemorheology, assessed its bleeding side effect by measuring coagulation parameters after intravenous administration for 5 days and investigated the potential mechanisms underlying such activities. In vivo, SAA significantly reduced thrombus weight in the model of arterio-venous shunt. Meanwhile, SAA increased plasma cAMP level determined by radioimmunoassay in the same model. Intravenously administrated SAA (2.5-10 mg/kg) inhibited platelet aggregation induced by ADP in a dose-dependent manner. Notably, SAA did not affect coagulation parameters in rats after intravenous administration SAA for successive 5 days. In vitro, pretreatment with SAA on washed rat and human platelets significantly inhibited various agonists stimulated platelet aggregation and caused an increase in cAMP level in platelets activated by ADP. These findings support our hypothesis that SAA possesses antithrombotic activities. The antithrombotic effect might be related to its antiplatelet action and ability to modulate hemorheology without affecting coagulation system. The mechanisms underlying such activities may involve the induction of cAMP.
Article
The epidermal growth factor receptor (EGFR) represents a prognostic marker for short survival of patients and therapy resistance of tumors. Despite clinical usefulness of EGFR tyrosine kinase inhibitors, resistance can develop. Therefore, there is an urgent need for novel EGFR inhibitors. Camptothecins have been characterized as inhibitors of DNA topoisomerase I (TOP1), although a correlation between TOP1 expression and activity is not well established in clinical biopsies. Hence, other targets may also be relevant. By molecular docking, we found that camptothecin 20-N,N-glycinate (CPTg) and camptothecin (CPT) bind to the same pharmacophore at EGFR as erlotinib, albeit to partly different amino acids. To validate the in silico results, CPT and CPTg were evaluated for their cytotoxic activity and downstream signaling mechanisms in U87MG glioblastoma cell lines transduced with different expression vectors for EGFR. All transduced cell lines were more susceptible to CPTg or CPT than the non-transduced cells, indicating a preferential activity towards EGFR-expressing tumor cells. Microarray-based mRNA hybridizations were performed in treated a non-treated cell lines. Subsets of genes were commonly regulated between the cell lines. By pathway analyses, we ranked canonical pathways according to differential gene expression after drug treatment. The pathways for G2/M DNA damage checkpoint regulation, aryl hydrocarbon receptor signaling, and xenobiotic metabolism and endoplasmatic reticulum stress were top ranked. In conclusion, binding of CPTg and CPT to the erlotinib pharmacophore and preferential cytotoxicity towards EGFR-overexpressing cells indicate susceptibility towards erlotinib-resistant tumors. Multiple mechanisms may account for cytotoxicity of these camptothecins.
Article
A new group of 2,3-diarylquinoline derivatives possessing a methylsulfonyl COX-2 pharmacophore at the para-position of the C-2 phenyl ring were synthesized and evaluated as selective COX-2 inhibitors. In vitro COX-1/COX-2 structure-activity relationships were determined by varying the substituents on the C-4 quinoline ring. Among the 2,3-diarylquinolines, 2-(4-(methylsulfonyl) phenyl)-3-phenylquinoline-4-carboxylic acid (8) exhibited the highest potency and selectivity for COX-2 inhibitory activity (COX-2 IC(50)=0.07 microM; selectivity index=687.1) that was more selective than the reference drug celecoxib (COX-2 IC(50)=0.06 microM; selectivity index=405). A molecular modeling study where 8 was docked in the binding site of COX-2 indicated that the p-MeSO(2) COX-2 pharmacophore group on the C-2 phenyl ring is oriented in the vicinity of the COX-2 secondary pocket (Arg(513), Phe(518) and Val(523)) and the carboxylic acid substituent can interact with Ser(530). The structure activity data acquired indicate that the size and nature of the C-4 quinoline substituent are important for COX-2 inhibitory activity.
Article
We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique.
Article
Smilax china Linn. is extensively used in traditional Chinese medicine (TCM) as well as in Pakistan for several medicinal purposes including their use in inflammatory disorders. The aims of the current study were to validate and assess the folk use of Smilax china Linn. on pharmacological grounds using the isolated compound at molecular, in vivo and computational levels. Seiboldogenin was isolated from ethyl acetate fraction of the plant crude extract. In vitro lipoxygenase and in vivo carrageenan-induced hind paw oedema models were used in experimental studies while molecular docking technique was used to conduct computational study. Sieboldogenin showed significant lipoxygenase inhibition (IC50: 38 microM). It also exhibited significant inhibition (p<0.05) of carrageenan-induced hind paw oedema at the doses of 10 and 50mg/kg. Computational molecular docking showed its molecular interaction with important amino acid residues in the catalytic site of lipoxygenase, revealing its potential binding mode at molecular level. Sieboldogenin seems to be a potential new anti-inflammatory compound responsible for anti-inflammatory activities of Smilax china Linn. Its in vitro and in vivo inflammatory activities are in good agreement with the folk medicinal use of Smilax china Linn. in inflammatory disorders.
Article
Coronary heart disease (CHD) is the second leading cause of cardiovascular death in the Chinese population. It accounts for 22% of cardiovascular deaths in urban areas and 13% in rural areas. Although mortality from CHD in China is relatively low compared with Western levels, the burden of CHD has been increasing. This is partly because of a worsening profile of risk factors, such as an increased prevalence of hypertension, hyperlipidaemia, overweight/obesity, diabetes, etc and partly because of an increase in the aged population. Large-scale, randomised controlled trials on thrombolytic, blood-pressure-lowering, antiplatelet and blood-cholesterol-lowering treatment as well as cardiac intervention have been conducted for Chinese patients with myocardial infarction. The studies provide important information for the prevention and management of chronic CHD and acute myocardial infarction in the Chinese population.
Article
The interaction of a probe group with a protein of known structure is computed at sample positions throughout and around the macromolecule, giving an array of energy values. The probes include water, the methyl group, amine nitrogen, carboxy oxygen, and hydroxyl. Contour surfaces at appropriate energy levels are calculated for each probe and displayed by computer graphics together with the protein structure. Contours at negative energy levels delineate contours also enable other regions of attraction between probe and protein and are found at known ligand binding clefts in particular. The contours also enable other regions of attraction to be identified and facilitate the interpretation of protein-ligand energetics. They may, therefore, be of value for drug design.
Article
Thrombin, a serine protease, plays a central role in the initiation and propagation of thrombotic events. An extensive search for new thrombin inhibitors was performed, using an unconventional approach. Screening of small basic molecules for binding in the recognition pocket of thrombin led to the discovery of (aminoiminomethyl)piperidine (amidinopiperidine) as a weak, but intrinsically selective, thrombin inhibitor. Elaboration of this molecule provided compounds which inhibit thrombin with Ki's in the range of 20-50 nM and with selectivities of 1000-4000 against trypsin. These inhibitor compounds show a new and unexpected binding mode to thrombin. Modification of the central building block and then of one of the hydrophobic substituents led to the discovery of a new family of thrombin inhibitors which has reverted to the former binding mode to thrombin. This last class of compounds shows inhibitory activities in the picomolar range, low toxicity, and a short plasma half life which favors its use for an intravenous application. From this series of thrombin inhibitors, 19f(Ro 46-6240) was selected for clinical development as an antithrombotic agent for intravenous administration.
Article
Docking is a computational technique that samples conformations of small molecules in protein binding sites; scoring functions are used to assess which of these conformations best complements the protein binding site. An evaluation of 10 docking programs and 37 scoring functions was conducted against eight proteins of seven protein types for three tasks: binding mode prediction, virtual screening for lead identification, and rank-ordering by affinity for lead optimization. All of the docking programs were able to generate ligand conformations similar to crystallographically determined protein/ligand complex structures for at least one of the targets. However, scoring functions were less successful at distinguishing the crystallographic conformation from the set of docked poses. Docking programs identified active compounds from a pharmaceutically relevant pool of decoy compounds; however, no single program performed well for all of the targets. For prediction of compound affinity, none of the docking programs or scoring functions made a useful prediction of ligand binding affinity.
Article
Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98,266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40x40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/.
Article
In order to study the drug-like features of Xuefu Zhuyu Decoction (XFZYD), a Traditional Chinese Medicinal recipe, three different computational methods were introduced to characterize the molecules in XFZYD, including chemical space distribution, docking protocol, and ADME prediction. Chemical space compared between the compound sets from XFZYD and drug/drug-like shows XFZYD may have desired interaction with broader protein targets. And the docking results show that the XFZYD is a broad-spectrum recipe inhibiting many important target enzymes. Together with the predictions of ADME properties, clue of potential synergism of XFZYD was obtained.
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