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Kui H, Lei Y, Jia C, Xin Q, Tursun R, Zhong M, Liu C, Yuan R. Antithrombotic pharmacodynamics and metabolomics study in raw and processed products of Whitmania pigra Whitman. Heliyon 2024; 10:e27828. [PMID: 38596067 PMCID: PMC11002550 DOI: 10.1016/j.heliyon.2024.e27828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024] Open
Abstract
Objective As a traditional Chinese medicine, leech has obvious pharmacological activities in anticoagulantion and antithrombosis. Whitmania pigra Whitman (WP) is the most commonly used leech in the Chinese market. It is often used in clinical applications after high-temperature processing by talcum powder to remove the fishy taste and facilitate crushing. The anticoagulant and thrombolytic active ingredients are protein and polypeptide, which may denaturate and lose activity after high-temperature processing. The rationality of its processing has been questioned in recent years. This study aims to investigate the effect of talcum powder scalding on the antithrombotic activity of WP in vivo and to discuss its pharmacodynamic mechanism in vivo. Methods Raw and talcum-powdered processed WP were administered intragastrically for 14 days, and carrageenan was injected intraperitoneally to prepare a mouse model of tail vein thrombosis. The incidence rate of tail vein thrombosis and the thrombus area under pathological tissue sections were calculated to evaluate the antithrombotic effect between raw and processed WP. Non-targeted metabolomics was conducted using UPLC-Q-TOF/MS technology to analyze the changes of small molecule metabolites in the body after administration of WP. Results After intragastric administration, both the raw product and the processed product of WP could inhibit the thrombosis induced by carrageenan, and the processed product had a more apparent antithrombotic effect than the raw product. The administration of WP could regulate the changes of some small molecular metabolites, such as amino acids, lipids, and steroids, in Sphingolipid metabolism and Glycerophospholipid metabolism. Conclusions Based on the results of pharmacodynamics and metabolomics, processed WP will not reduce the antithrombotic activity of WP. This study provided a scientific basis for the rational use of leeches.
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Affiliation(s)
- Hongqian Kui
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, China
| | - Yan Lei
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, China
| | - Chunxue Jia
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, China
| | - Quancheng Xin
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, China
| | - Rustam Tursun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, China
| | - Miao Zhong
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, China
| | - Chuanxin Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, China
- Department of Metabolism and Endocrinology, Endocrine, and Metabolic Disease Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan, University of Science and Technology, Medical Key Laboratory of Hereditary Rare Diseases of Henan, Luoyang Sub-center of National Clinical Research Center for Metabolic Diseases, Luoyang, China
| | - Ruijuan Yuan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, China
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Balakrishnan N, Katkar R, Pham PV, Downey T, Kashyap P, Anastasiu DC, Ramasubramanian AK. Prospection of Peptide Inhibitors of Thrombin from Diverse Origins Using a Machine Learning Pipeline. Bioengineering (Basel) 2023; 10:1300. [PMID: 38002424 PMCID: PMC10669389 DOI: 10.3390/bioengineering10111300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/30/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Thrombin is a key enzyme involved in the development and progression of many cardiovascular diseases. Direct thrombin inhibitors (DTIs), with their minimum off-target effects and immediacy of action, have greatly improved the treatment of these diseases. However, the risk of bleeding, pharmacokinetic issues, and thrombotic complications remain major concerns. In an effort to increase the effectiveness of the DTI discovery pipeline, we developed a two-stage machine learning pipeline to identify and rank peptide sequences based on their effective thrombin inhibitory potential. The positive dataset for our model consisted of thrombin inhibitor peptides and their binding affinities (KI) curated from published literature, and the negative dataset consisted of peptides with no known thrombin inhibitory or related activity. The first stage of the model identified thrombin inhibitory sequences with Matthew's Correlation Coefficient (MCC) of 83.6%. The second stage of the model, which covers an eight-order of magnitude range in KI values, predicted the binding affinity of new sequences with a log room mean square error (RMSE) of 1.114. These models also revealed physicochemical and structural characteristics that are hidden but unique to thrombin inhibitor peptides. Using the model, we classified more than 10 million peptides from diverse sources and identified unique short peptide sequences (<15 aa) of interest, based on their predicted KI. Based on the binding energies of the interaction of the peptide with thrombin, we identified a promising set of putative DTI candidates. The prediction pipeline is available on a web server.
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Affiliation(s)
- Nivedha Balakrishnan
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Rahul Katkar
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Peter V. Pham
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Taylor Downey
- Department of Computer Science and Engineering, Santa Clara University, Santa Clara, CA 95053, USA (D.C.A.)
| | - Prarthna Kashyap
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - David C. Anastasiu
- Department of Computer Science and Engineering, Santa Clara University, Santa Clara, CA 95053, USA (D.C.A.)
| | - Anand K. Ramasubramanian
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
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In Vitro Antithrombotic, Hematological Toxicity, and Inhibitor Studies of Protocatechuic, Isovanillic, and p-Hydroxybenzoic Acids from Maclura Tricuspidata (Carr.) Bur. Molecules 2022; 27:molecules27113496. [PMID: 35684431 PMCID: PMC9181887 DOI: 10.3390/molecules27113496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/16/2022] [Accepted: 05/26/2022] [Indexed: 12/10/2022] Open
Abstract
In blood coagulation, circulating platelets and coagulation factors are crucial for the primary process because thrombi are generated by fibrin clotting with fibrinogen, thrombin, FXIIIa, and platelet activation. Therefore, strategies to reduce the activity of key coagulation factors, or interfere with their functions and delay the activation of platelets can be used as important tools to suppress excessive blood clot formation and platelet hyperactivation. This study examined the antithrombotic activity and hematological toxicity of PA, IVA, and 4-HA isolated from M. tricuspidata (Carr.) Bur in several in vitro experiments and inhibitor assays. We found that PA, IVA, and 4-HA attenuated the formation of fibrin polymers/clots and degraded the blood clots. These compounds inhibited the activities of procoagulant proteases and fibrinoligase, and prolonged the coagulation time. There was a significant reduction in platelet function and ATP or serotonin levels in thrombin-activated platelets. An inhibitor study showed that PA exhibited a mixed inhibition type for thrombin, an uncompetitive inhibition type for FXa, and a non-competitive inhibition type for FXIIIa and IVA, while 4-HA exhibited an uncompetitive inhibition type for thrombin and non-competitive inhibition type for FXa and FXIIIa. These three compounds (up to 50 μg/mL) were not toxic to blood cells.
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Novel Cysteine Protease Inhibitor Derived from the Haementeria vizottoi Leech: Recombinant Expression, Purification, and Characterization. Toxins (Basel) 2021; 13:toxins13120857. [PMID: 34941695 PMCID: PMC8705320 DOI: 10.3390/toxins13120857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Cathepsin L (CatL) is a lysosomal cysteine protease primarily involved in the terminal degradation of intracellular and endocytosed proteins. More specifically, in humans, CatL has been implicated in cancer progression and metastasis, as well as coronary artery diseases and others. Given this, the search for potent CatL inhibitors is of great importance. In the search for new molecules to perform proteolytic activity regulation, salivary secretions from hematophagous animals have been an important source, as they present protease inhibitors that evolved to disable host proteases. Based on the transcriptome of the Haementeria vizzotoi leech, the cDNA of Cystatin-Hv was selected for this study. Cystatin-Hv was expressed in Pichia pastoris and purified by two chromatographic steps. The kinetic results using human CatL indicated that Cystatin-Hv, in its recombinant form, is a potent inhibitor of this protease, with a Ki value of 7.9 nM. Consequently, the present study describes, for the first time, the attainment and the biochemical characterization of a recombinant cystatin from leeches as a potent CatL inhibitor. While searching out for new molecules of therapeutic interest, this leech cystatin opens up possibilities for the future use of this molecule in studies involving cellular and in vivo models.
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WPK5, a Novel Kunitz-Type Peptide from the Leech Whitmania pigra Inhibiting Factor XIa, and Its Loop-Replaced Mutant to Improve Potency. Biomedicines 2021; 9:biomedicines9121745. [PMID: 34944561 PMCID: PMC8698482 DOI: 10.3390/biomedicines9121745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022] Open
Abstract
Kunitz-type proteins or peptides have been found in many blood-sucking animals, but the identity of them in leeches remained elusive. In the present study, five Kunitz-type peptides named WPK1-WPK5 were identified from the leech Whitmania pigra. Recombinant WPK1-WPK5 were expressed in Pichia pastoris GS115, and their inhibitory activity against Factor XIa (FXIa) was tested. WPK5 showed inhibitory activity against FXIa with an IC50 value of 978.20 nM. To improve its potency, the loop replacement strategy was used. The loop 1 (TGPCRSNLER) and loop 2 (QYGGC) in WPK5 were replaced by loop 1 (TGPCRAMISR) and loop 2 (FYGGC) in PN2KPI, respectively, and the resulting peptide named WPK5-Mut showed an IC50 value of 8.34 nM to FXIa, which is about 100-fold the potency of FXIa compared to that of WPK5. WPK5-Mut was further evaluated for its extensive bioactivity in vitro and in vivo. It dose-dependently prolonged APTT on both murine plasma and human plasma, and potently inhibited FeCl3-induced carotid artery thrombosis in mice at a dose of 1.5 mg/kg. Additionally, WPK5-Mut did not show significant bleeding risk at a dose of 6 mg/kg. Together, these results showed that WPK5-Mut is a promising candidate for the development of an antithrombotic drug.
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Cheng S, Wang Y, Chen H, Liu H, Wang L, Battino M, Yao X, Zhu B, Du M. Anticoagulant Dodecapeptide Suppresses Thrombosis In Vivo by Inhibiting the Thrombin Exosite-I Binding Site. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10920-10931. [PMID: 34491753 DOI: 10.1021/acs.jafc.1c03414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Thrombin is a crucial regulatory serine protease in hemostasis and thrombosis and has been a therapeutic target of thrombotic events. A novel oyster-derived thrombin inhibitory dodecapeptide (IEELEELEAER, P-2-CG) was identified and characterized. P-2-CG prolonged thrombin time from 9.6 s to 23.3 s at 5 mg/mL in vitro. P-2-CG bound to thrombin Exosite-I domain spontaneously. The occupied Exosite-I blocked fibrinogen binding, which prolonged fibrinogen clotting time to 28 s from 18.5 s. Molecule dynamics demonstrated the interaction of P-2-CG and thrombin Exosite-I involved in eight hydrogen bonds and lots of electrostatic forces. The residue Tyr76 at thrombin Exosite-I is one critical amino acid for fibrinogen binding. The Glu11 in P-2-CG was bound with Tyr76 through strong hydrogen bonds and hydrophobic action. P-2-CG also significantly reduced the mortality of mice that suffered an acute pulmonary embolism induced by thrombin and inhibited mice tail thrombosis induced by κ-carrageenan. The thrombin inhibitory efficiency in vitro and antithrombosis in vivo of P-2-CG provided insight for further applications to serve as an antithrombotic agent.
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Affiliation(s)
- Shuzhen Cheng
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yuwei Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang 712046, China
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Hui Chen
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China
| | - Hanxiong Liu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China
| | - Lishu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee 53226, United States
| | - Maurizio Battino
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, University of Vigo-Vigo Campus, Vigo 36310, Spain
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Beiwei Zhu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China
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Iwama RE, Tessler M, Siddall ME, Kvist S. The Origin and Evolution of Antistasin-like Proteins in Leeches (Hirudinida, Clitellata). Genome Biol Evol 2021; 13:evaa242. [PMID: 33527140 PMCID: PMC7851590 DOI: 10.1093/gbe/evaa242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2020] [Indexed: 02/07/2023] Open
Abstract
Bloodfeeding is employed by many parasitic animals and requires specific innovations for efficient feeding. Some of these innovations are molecular features that are related to the inhibition of hemostasis. For example, bloodfeeding insects, bats, and leeches release proteins with anticoagulatory activity through their salivary secretions. The antistasin-like protein family, composed of serine protease inhibitors with one or more antistasin-like domains, is tightly linked to inhibition of hemostasis in leeches. However, this protein family has been recorded also in non-bloodfeeding invertebrates, such as cnidarians, mollusks, polychaetes, and oligochaetes. The present study aims to 1) root the antistasin-like gene tree and delimit the major orthologous groups, 2) identify potential independent origins of salivary proteins secreted by leeches, and 3) identify major changes in domain and/or motif structure within each orthologous group. Five clades containing leech antistasin-like proteins are distinguishable through rigorous phylogenetic analyses based on nine new transcriptomes and a diverse set of comparative data: the trypsin + leukocyte elastase inhibitors clade, the antistasin clade, the therostasin clade, and two additional, unnamed clades. The antistasin-like gene tree supports multiple origins of leech antistasin-like proteins due to the presence of both leech and non-leech sequences in one of the unnamed clades, but a single origin of factor Xa and trypsin + leukocyte elastase inhibitors. This is further supported by three sequence motifs that are exclusive to antistasins, the trypsin + leukocyte elastase inhibitor clade, and the therostasin clade, respectively. We discuss the implications of our findings for the evolution of this diverse family of leech anticoagulants.
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Affiliation(s)
- Rafael Eiji Iwama
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Michael Tessler
- Department of Biology, St. Francis College, Brooklyn, New York, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | | | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
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Characterization of thrombin/factor Xa inhibitors in Rhizoma Chuanxiong through UPLC-MS-based multivariate statistical analysis. Chin Med 2020; 15:93. [PMID: 32874198 PMCID: PMC7457533 DOI: 10.1186/s13020-020-00376-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
Background The dry root and rhizome of Ligusticum chuanxiong Hort., or Chuanxiong, has been used as a blood-activating and stasis-removing traditional Chinese medicine for 1000 years. Our previous studies have shown the inhibitory activity on platelet and thrombin (THR) of Chuanxiong. THR and factor Xa (FXa) play significant roles in the coagulation cascade and their inhibitors are of valuable in the treatment of thromboembolic diseases. The aim of the present study is to screen THR and FXa inhibitors from Chuanxiong. Methods Four extracts [ethyl acetate (EA), butanol (BA) and remained extract (RE) from 75% ethanol extract, and water extract (WE)] of Chuanxiong were prepared, and their THR/FXa inhibitory activities were assessed in vitro. Following silica-gel column chromatography (SC), the active EA extract and BA extract was further partitioned, respectively. Their active fractions (EA-SC1 to EA-SC5; BA-SC1 to BA-SC5) were obtained and analyzed by LC–MS. After modeling by the principal component analysis (PCA) and orthogonal partial least squares discriminate analysis (OPLS-DA), the specific marker compounds were predicted and identified. Their enzyme inhibitory was assessed in vitro and interactions with THR/FXa were investigated by molecular docking analysis. Results Chuanxiong EA extract showed strong activity against THR and BA extract was more effective in inhibiting FXa activity, and their fractions exhibited obvious difference in enzyme inhibitory activity. Furthermore, marker compounds a–h were predicted by PCA and OPLS-DA, and their chemical structures were identified. Among them, senkyunolide A, Z-ligustilide, ferulic acid and senkyunolide I (IC50 was determined as 0.77 mM) with potential THR inhibitory activity, as well as isochlorogenic acid A with FXa inhibitory activity were screened out. It was found that the four components could interact with the active site of THR, and the binding energy was lower than − 5 kcal/mol. Isochlorogenic acid A were bound to the active site of FXa, and the binding energy was − 9.39 kcal/mol. The IC50 was determined as 0.56 mM. Conclusions THR/FXa inhibitory components in different extracts of Chuanxiong were successfully characterized by the method of enzyme inhibition activity assays with ultra performance liquid chromatography-quadrupole time of flight mass spectrometry-based multivariate statistical analysis.
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Phillips AJ, Govedich FR, Moser WE. Leeches in the extreme: Morphological, physiological, and behavioral adaptations to inhospitable habitats. Int J Parasitol Parasites Wildl 2020; 12:318-325. [PMID: 33101909 PMCID: PMC7569739 DOI: 10.1016/j.ijppaw.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023]
Abstract
With more than 700 described species, leeches include morphological, physiological, and behavioral diversity and occur in terrestrial and aquatic habitats, including freshwater, estuarine, and marine ecosystems. Leeches inhabit a number of extreme environments, including extremes in temperature, moisture, salinity, pressure, light, and pollution. In some cases, leeches in extreme environments have specialized morphological, physiological, or behavioral adaptations to survive these conditions, yet unique adaptations are not apparent in some species. Leeches that inhabit inhospitable habitats occur in more than one branch or family of leech phylogeny suggesting that there have been independent invasions of environments with extreme conditions. Herein, we review examples of leeches that live in extreme conditions and the exceptional biology that has contributed to leeches being the most extreme annelids.
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Affiliation(s)
- Anna J. Phillips
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street and Constitution Avenue NW, Washington, DC, 20560, USA
| | - Fredric R. Govedich
- Biology Department, Southern Utah University, 351 W. University Blvd., Cedar City, UT, 84720, USA
| | - William E. Moser
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Museum Support Center–MRC 534, 4210 Silver Hill Road, Suitland, MD, 20746, USA
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Yang YY, Wu ZY, Zhang H, Yin SJ, Xia FB, Zhang Q, Wan JB, Gao JL, Yang FQ. LC-MS-based multivariate statistical analysis for the screening of potential thrombin/factor Xa inhibitors from Radix Salvia Miltiorrhiza. Chin Med 2020; 15:38. [PMID: 32351617 PMCID: PMC7183602 DOI: 10.1186/s13020-020-00320-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 04/20/2020] [Indexed: 02/03/2023] Open
Abstract
Background The dry root and rhizome of Salvia miltiorrhiza Bunge, or Danshen, is a well-known traditional Chinese medicine with anticoagulant activity. Taking into account that thrombin (THR) and factor Xa (FXa) play crucial roles in the coagulation cascade, it is reasonable and meaningful to screening THR and/or FXa inhibitors from Danshen. Methods Four extracts [butanol (BA), ethyl acetate (EA) and remained extract (RE) from 75% ethanol extract, and water extract (WE)] of Danshen were prepared, and their THR/FXa inhibitory activities were assessed in vitro. Then, the active EA extract was further separated by silica-gel column chromatography (SC), and its fractions (SC1–SC5) were analyzed by LC–MS. The principal component analysis (PCA) and orthogonal partial least squares discriminate analysis (OPLS-DA) were employed for predicting the specific marker compounds. The chemical structures of targeted compounds were identified by LC–MS/MS and their interactions with THR/FXa were analyzed by the molecular docking analysis. Results Danshen EA extract showed strong activity against THR and FXa, and its fractions (SC1–SC5) exhibited obvious difference in inhibitory activity against these two enzymes. Furthermore, four marker compounds with potential THR/FXa inhibitory activity were screened by PCA and OPLS-DA, and were identified as cryptotanshinone, tanshinone I, dihydrotanshinone I and tanshinone IIA. The molecular docking study showed that all these four tanshinones can interact with some key amino acid residues of the THR/FXa active cavities, such as HIS57 and SER195, which were considered to be promising candidates targeting THR and/or FXa with low binding energy (< − 7 kcal mol−1). Conclusions LC–MS combined with multivariate statistical analysis can effectively screen potential THR/FXa inhibitory components in Danshen.
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Affiliation(s)
- Yi-Yao Yang
- 1School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331 People's Republic of China
| | - Zhao-Yu Wu
- 1School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331 People's Republic of China
| | - Hao Zhang
- 1School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331 People's Republic of China
| | - Shi-Jun Yin
- 1School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331 People's Republic of China
| | - Fang-Bo Xia
- 3State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, People's Republic of China
| | - Qian Zhang
- 1School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331 People's Republic of China
| | - Jian-Bo Wan
- 3State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, People's Republic of China
| | - Jian-Li Gao
- 2Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053 People's Republic of China
| | - Feng-Qing Yang
- 1School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331 People's Republic of China
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Inhibitors of blood coagulation factor XIII. Anal Biochem 2020; 605:113708. [PMID: 32335064 DOI: 10.1016/j.ab.2020.113708] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
The blood coagulation factor XIII (FXIII) plays an essential role in the stabilization of fibrin clots. This factor, belonging to the class of transglutaminases, catalyzes the final step of secondary hemostasis, i.e. the crosslinking of fibrin polymers. These crosslinks protect the clots against premature fibrinolysis. Consequently, FXIII is an interesting target for the therapeutic treatment of cardiovascular diseases. In this context, inhibitors can influence FXIII in the activation process of the enzyme itself or in its catalytic activity. To date, there is no FXIII inhibitor in medical application, but several studies have been conducted in the past. These studies provided a better understanding of FXIII and identified new lead structures for FXIII inhibitors. Next to small molecule inhibitors, the most promising candidates for the development of clinically applicable FXIII inhibitors are the peptide inhibitors tridegin and transglutaminase-inhibiting Michael acceptors (TIMAs) due to their selectivity towards activated FXIII (FXIIIa). In this review, select FXIII inhibitors and their pharmacological potential are discussed.
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Müller C, Lukas P, Lemke S, Hildebrandt JP. Hirudin and Decorsins of the North American Medicinal Leech Macrobdella decora: Gene Structure Reveals Homology to Hirudins and Hirudin-Like Factors of Eurasian Medicinal Leeches. J Parasitol 2019. [DOI: 10.1645/18-117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Christian Müller
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Phil Lukas
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Sarah Lemke
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Jan-Peter Hildebrandt
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
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Cheng RM, Tang XP, Long AL, Mwangi J, Lai R, Sun RP, Long CB, Zhang ZQ. Purification and characterization of a novel anti-coagulant from the leech Hirudinaria manillensis. Zool Res 2019; 40:205-210. [PMID: 31011131 PMCID: PMC6591161 DOI: 10.24272/j.issn.2095-8137.2019.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Protease inhibitors have been reported rarely from the leech Hirudinaria manillensis. In this study, we purified a novel protease inhibitor (bdellin-HM-2) with anticoagulant properties from H. manillensis. With a molecular weight of 1.4x104, bdellin-HM-2 was also characterized with three intra-molecular disulfide bridges at the N-terminus and multiple HHXDD and HXDD motifs at the C-terminus. cDNA cloning revealed that the putative nucleotide-encoding protein of bdellin-HM-2 contained 132 amino acids and was encoded by a 399 bp open reading frame (ORF). Sequence alignment showed that bdellin-HM-2 shared similarity with the “non-classical” Kazal-type serine protease inhibitors, but had no inhibitory effect on trypsin, elastase, chymotrypsin, kallikrein, factor XIIa (FXIIa), factor XIa (FXIa), factor Xa (FXa), thrombin, or plasmin. Bdellin-HM-2 showed anticoagulant effects by prolonging the activated partial thromboplastin time (aPTT), indicating a role in enabling H. manillensis to obtain a blood meal from its host. Our results suggest that bdellin-HM-2 may play a crucial role in blood-sucking in this leech species and may be a potential candidate for the development of clinical anti-thrombotic drugs.
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Affiliation(s)
- Ruo-Mei Cheng
- Department of Pharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou Jiangsu 215123, China
| | - Xiao-Peng Tang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
| | - Ai-Lin Long
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
| | - James Mwangi
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming Yunnan 650223, China
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming Yunnan 650223, China
| | - Rui-Pu Sun
- Jiangxi Medical College, Nanchang University, Nanchang Jiangxi 330006, China
| | - Cheng-Bo Long
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming Yunnan 650223, China
| | - Zhen-Qing Zhang
- Department of Pharmaceutical Sciences, College of Pharmaceutical Sciences, Soochow University, Suzhou Jiangsu 215123, China
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Cheng S, Tu M, Liu H, Zhao G, Du M. Food-derived antithrombotic peptides: Preparation, identification, and interactions with thrombin. Crit Rev Food Sci Nutr 2019; 59:S81-S95. [PMID: 30740983 DOI: 10.1080/10408398.2018.1524363] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thromboembolism and its sequelae have been the leading causes of morbidity and mortality throughout the world. Food-derived antithrombotic peptides, as potential ingredients in health-promoting functional foods targeting thrombus, have attracted increasing attention because of their high biological activities, low toxicity, and ease of metabolism in the human body. This review presents the conventional workflow of preparation, isolation and identification of antithrombotic peptides from various kinds of food materials. More importantly, to analyze the antithrombotic effects and mechanism of antithrombotic peptides, methods for interaction of anticoagulant peptides and thrombin, the main participant in thrombosis, were analyzed from biochemistry, solution chemistry and crystal chemistry. The present study is intended to highlight the recent advances in research of food-derived antithrombotic peptide as a novel vehicle in the field of food science and nutrition. Future outlooks are highlighted with the aim to suggest a research line to be followed in further studies with the introduced research approach.
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Affiliation(s)
- Shuzheng Cheng
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Maolin Tu
- c Department of Food Science and Engineering , Harbin Institute of Technology , Harbin , Heilongjiang , China
| | - Hanxiong Liu
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China
| | - Guanghua Zhao
- b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Ming Du
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China
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Lu Z, Shi P, You H, Liu Y, Chen S. Transcriptomic analysis of the salivary gland of medicinal leech Hirudo nipponia. PLoS One 2018; 13:e0205875. [PMID: 30339694 PMCID: PMC6195274 DOI: 10.1371/journal.pone.0205875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022] Open
Abstract
Hirudo nipponia (known as Shui Zhi in Chinese) is a well-known Chinese medicine with numerous active ingredients in its body, especially in its saliva. This native Chinese blood-sucking leech has been used for therapeutic purposes since before 100 AD. Modern Chinese physicians use it for a wide range of diseases. Genomic data and molecular information about the pharmacologically active substances produced by this medicinal leech are presently unavailable despite this organism’s medicinal importance. In this study, we performed transcriptome profiling of the salivary glands of medicinal leech H. nipponia using the Illumina platform. In total, 84,657,362 clean reads were assembled into 50,535 unigenes. The obtained unigenes were compared to public databases. Furthermore, a unigene sequence similarity search and comparisons with the whole transcriptome of medical leech were performed to identify potential proteins. Finally, more than 21 genes were predicted to be involved in anticoagulatory, antithrombotic, antibacterial, anti-inflammatory and antitumor processes, which might play important roles in the treatment of various diseases. This study is the first analysis of a sialotranscriptome in H. nipponia. The transcriptome profile will shed light on its genetic background and provide a useful tool to deepen our understanding of the medical value of H. nipponia.
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Affiliation(s)
- Zenghui Lu
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Ping Shi
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Huajian You
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Yanqi Liu
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
| | - Shijiang Chen
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Sub-center of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine Resources, Chongqing, China
- * E-mail:
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Affiliation(s)
- Francesca L. Ware
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicester LE12 5RD, UK
| | - Martin R. Luck
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicester LE12 5RD, UK
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Amorim AMXP, de Oliveira UC, Faria F, Pasqualoto KFM, Junqueira-de-Azevedo IDLM, Chudzinski-Tavassi AM. Transcripts involved in hemostasis: Exploring salivary complexes from Haementeria vizottoi leeches through transcriptomics, phylogenetic studies and structural features. Toxicon 2015; 106:20-9. [PMID: 26363292 DOI: 10.1016/j.toxicon.2015.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/27/2015] [Accepted: 09/07/2015] [Indexed: 12/17/2022]
Abstract
Throughout evolution, parasites have adapted in order to successfully intervene in the host defense, producing specific peptides and proteins. Interestingly, these peptides and proteins have been exploited as potential drug candidates against several diseases. Furthermore, biotechnology studies and cDNA libraries have remarkably contributed to identify potentially bioactive molecules. In this regard, herein, a cDNA library of salivary complexes from Haementeria vizottoi leeches was constructed, the transcriptome was characterized and a phylogenetic analysis was performed considering antistasin-like and antiplatelet-like proteins. Hundred twenty three transcripts were identified coding for putative proteins involved in animal feeding (representing about 10% of the expression level). These sequences showed similarities with myohemerythrins, carbonic anhydrases, anticoagulants, antimicrobials, proteases and protease inhibitors. The phylogenetic analysis, regarding antistasin-like and antiplatetlet-like proteins, revealed two main clades in the Rhynchobdellida leeches. As expected, the sequences from H. vizottoi have presented high similarities with those types of proteins. Thus, our findings could be helpful not only to identify new coagulation inhibitors, but also to better understand the biological composition of the salivary complexes.
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Affiliation(s)
| | | | - Fernanda Faria
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, Av. Vital Brazil, 1500, CEP: 05.503-900, São Paulo, Brazil
| | | | | | - Ana Marisa Chudzinski-Tavassi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, Av. Vital Brazil, 1500, CEP: 05.503-900, São Paulo, Brazil; Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil.
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Zheng X, Li J, Chen Z, Liu Y, Chen K. Purification and characterization of an anticoagulant oligopeptide from Whitmania pigra Whitman. Pharmacogn Mag 2015; 11:444-8. [PMID: 26246717 PMCID: PMC4522828 DOI: 10.4103/0973-1296.160446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 05/27/2014] [Accepted: 07/10/2015] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Dried Whitmania pigra is used for the treatment of cardiovascular and cerebrovascular diseases in traditional Chinese medicine and hot water and alcohol extracts also have anticogulant activity. However, a lower molecular weight and more stable anticogulant is needed. OBJECTIVE The objective of the following study is to purify and characterize of an anticoagulant oligopeptide from Hirudo (Whitmania pigra Whitman). MATERIALS AND METHODS Gel filtration on Sephadex G-50, ion exchange on diethylaminoethyl-cellulose, and semi-prepared high-performance liquid chromatography were used to purify Hirudo. Automated coagulation analyzer was used for evaluating anticoagulant activity. Molecular weight was measured by Matrix-assisted laser desorption ionization time of flight mass spectrometry. Amino acid sequence of the oligopeptide was measured by amino acid sequence analyzer. RESULTS A new anticoagulant, named whitide, isolated from Hirudo was purified, with a molecular weight 1997.1 Da. Amino acid sequence of the oligopeptide was identified as Gly-Pro-ALa-Gly-Hyp-Val-Gly-Ala-Hyp-Gly-Gly-Hyp-Gly-Val-Arg-Gly-Leu-Hyp-Gly-Asp-Arg-Gly. The results revealed that its amino acid sequence had strong homology to various types of collagen. CONCLUSION Whitide might be an orally anticoagulant for its hot and trypsin stable.
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Affiliation(s)
- Xiaobei Zheng
- Department of Identification and Assessment of TCM, Hubei University of Traditional Chinese Medicine, Key Laboratory of TCM Resource and TCM Compound Co-constructed by Hubei province and Ministry of Education, New products of TCM Senile Diseases Co-Innovation Center of Hubei ; Department of Quality Control, Wuhan Institute of Biological Products Co., Ltd., China
| | - Juan Li
- Department of Identification and Assessment of TCM, Hubei University of Traditional Chinese Medicine, Key Laboratory of TCM Resource and TCM Compound Co-constructed by Hubei province and Ministry of Education, New products of TCM Senile Diseases Co-Innovation Center of Hubei
| | - Zhengwang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430065, China
| | - Yimei Liu
- Department of Identification and Assessment of TCM, Hubei University of Traditional Chinese Medicine, Key Laboratory of TCM Resource and TCM Compound Co-constructed by Hubei province and Ministry of Education, New products of TCM Senile Diseases Co-Innovation Center of Hubei
| | - Keli Chen
- Department of Identification and Assessment of TCM, Hubei University of Traditional Chinese Medicine, Key Laboratory of TCM Resource and TCM Compound Co-constructed by Hubei province and Ministry of Education, New products of TCM Senile Diseases Co-Innovation Center of Hubei
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Hibsh D, Schori H, Efroni S, Shefi O. De novo transcriptome assembly databases for the central nervous system of the medicinal leech. Sci Data 2015; 2:150015. [PMID: 25977819 PMCID: PMC4412018 DOI: 10.1038/sdata.2015.15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/03/2015] [Indexed: 01/17/2023] Open
Abstract
The study of non-model organisms stands to benefit greatly from genetic and genomic data. For a better understanding of the molecular mechanisms driving neuronal development, and to characterize the entire leech Hirudo medicinalis central nervous system (CNS) transcriptome we combined Trinity for de-novo assembly and Illumina HiSeq2000 for RNA-Seq. We present a set of 73,493 de-novo assembled transcripts for the leech, reconstructed from RNA collected, at a single ganglion resolution, from the CNS. This set of transcripts greatly enriches the available data for the leech. Here, we share two databases, such that each dataset allows a different type of search for candidate homologues. The first is the raw set of assembled transcripts. This set allows a sequence-based search. A comprehensive analysis of which revealed 22,604 contigs with high e-values, aligned versus the Swiss-Prot database. This analysis enabled the production of the second database, which includes correlated sequences to annotated transcript names, with the confidence of BLAST best hit.
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Affiliation(s)
- Dror Hibsh
- Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Hadas Schori
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Sol Efroni
- Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Orit Shefi
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
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Kong Y, Chen H, Wang YQ, Meng L, Wei JF. Direct thrombin inhibitors: patents 2002-2012 (Review). Mol Med Rep 2014; 9:1506-14. [PMID: 24604304 DOI: 10.3892/mmr.2014.2025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 01/21/2014] [Indexed: 11/06/2022] Open
Abstract
Acute vascular diseases and other thromboses of the blood system constitute major health risks in developing countries. Thrombin plays a central role in blood coagulation, which is a crucial process involved in thrombosis. Direct thrombin inhibitors (DTIs) such as argatroban, dabigatran, dabigatran etexilate, lepirudin, desirudin and bivalirudin, which bind to thrombin and block its enzymatic activity, are widely and effectively used in the treatment of thromboembolic diseases. DTIs appear to overcome the disadvantages of indirect thrombin inhibitors such as unfractionated heparins (UFH). Although these DTIs show specific advantages over indirect inhibitors, they still present limitations, such as a narrow therapeutic window, and bleeding and anaphylaxis as side-effects. Novel anticoagulant drugs need thus to be developed to overcome these limitations. In the search for additional candidate agents with improved efficacy, safety and high bioavailability in oral administration, a high number of compounds has been identified, such as those derived from the tripeptide template D-Phe-Pro-Arg, aptamers and peptides isolated from blood-sucking animals. These candidates may prove the new agents of choice for the treatment of cardiovascular diseases.
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Affiliation(s)
- Yi Kong
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, P.R. China
| | - Hao Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, P.R. China
| | - Yong-Qing Wang
- Research Division of Clinical Pharmacology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210009, P.R. China
| | - Ling Meng
- Research Division of Clinical Pharmacology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210009, P.R. China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210009, P.R. China
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Hibsh D, Schori H, Efroni S, Shefi O. Spatial regulation dominates gene function in the ganglia chain. ACTA ACUST UNITED AC 2013; 30:310-6. [PMID: 24085568 DOI: 10.1093/bioinformatics/btt570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MOTIVATION To understand the molecular mechanisms of neurons, it is imperative to identify genomic dissimilarities within the heterogeneity of the neural system. This is especially true for neuronal disorders in which spatial considerations are of critical nature. For this purpose, Hirudo medicinalis provides here an ideal system in which we are able to follow gene expression along the central nervous system, to affiliate location with gene behavior. RESULTS In all, 221.1 million high-quality short reads were sequenced on the Illumina Hiseq2000 platform at the single ganglion level. Thereafter, a de novo assembly was performed using two state-of-the-art assemblers, Trinity and Trans-ABySS, to reconstruct a comprehensive de novo transcriptome. Classification of Trinity and Trans-ABySS transcripts produced a non-redundant set of 76 845 and 268 355 transcripts (>200 bp), respectively. Remarkably, using Trinity, 82% of the published medicinal leech messenger RNAs was identified. For the innexin family, all of the 21 recently reported genes were identified. Spatial regulation analysis across three ganglia throughout the entire central nervous system revealed distinct patterns of gene expression. These transcriptome data were combined with expression distribution to produce a spatio-transcripto map along the ganglia chain. This study provides a resource for gene discovery and gene regulation in future studies.
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Affiliation(s)
- Dror Hibsh
- Faculty of Life Sciences, Faculty of Engineering and Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel 52900
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Hildebrandt JP, Lemke S. Small bite, large impact–saliva and salivary molecules in the medicinal leech, Hirudo medicinalis. Naturwissenschaften 2011; 98:995-1008. [DOI: 10.1007/s00114-011-0859-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/10/2011] [Accepted: 10/14/2011] [Indexed: 01/16/2023]
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Thrombin inhibitors from different animals. J Biomed Biotechnol 2010; 2010:641025. [PMID: 20976270 PMCID: PMC2953280 DOI: 10.1155/2010/641025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 06/16/2010] [Accepted: 08/02/2010] [Indexed: 11/18/2022] Open
Abstract
Venous and arterial thromboembolic diseases are still the most frequent causes of death and disability in high-income countries. Clinical anticoagulants are inhibitors of enzymes involved in the coagulation pathway, such as thrombin and factor X(a). Thrombin is a key enzyme of blood coagulation system, activating the platelets, converting the fibrinogen to the fibrin net, and amplifying its self-generation by the activation of factors V, VIII, and XI. Thrombin has long been a target for the development of oral anticoagulants. Furthermore, selective inhibitors of thrombin represent a new class of antithrombotic agents. For these reasons, a number of specific thrombin inhibitors are under evaluation for possible use as antithrombotic drugs. This paper summarizes old and new interests of specific thrombin inhibitors described in different animals.
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Macagno ER, Gaasterland T, Edsall L, Bafna V, Soares MB, Scheetz T, Casavant T, Da Silva C, Wincker P, Tasiemski A, Salzet M. Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics 2010; 11:407. [PMID: 20579359 PMCID: PMC2996935 DOI: 10.1186/1471-2164-11-407] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 06/25/2010] [Indexed: 11/17/2022] Open
Abstract
Background The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. Results A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions. Conclusions The sequences obtained for Hirudo transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of Helobdella robusta, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with Capitella capitata (a polychaete) and 56% with Aplysia californica (a mollusk), as well as 58% with Schistosoma mansoni (a platyhelminth). Phylogenetic comparisons of putative Hirudo innate immune response genes present within the Hirudo transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.
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Affiliation(s)
- Eduardo R Macagno
- Division of Biological Sciences, University of California, San Diego, CA, USA.
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Torres-Castillo JA, Mondragón Jacobo C, Blanco-Labra A. Characterization of a highly stable trypsin-like proteinase inhibitor from the seeds of Opuntia streptacantha (O. streptacantha Lemaire). PHYTOCHEMISTRY 2009; 70:1374-1381. [PMID: 19765785 DOI: 10.1016/j.phytochem.2009.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 05/29/2009] [Accepted: 08/18/2009] [Indexed: 05/28/2023]
Abstract
A trypsin inhibitor from Opuntia streptacantha Lemaire (Prickly pear) seeds was purified and characterized. Of several proteases tested, this inhibitor showed specificity to trypsin-like enzymes. The major inhibitor present in these seeds showed distinctive characteristics, most notably a low molecular weight of 4.19 kDa, as determined by MALDI TOF, and an unusually high thermal stability, retaining most of the activity after heating the sample 1h to 120 degrees C with a pressure of 1 kg/cm(2). Its complete amino acid sequence was obtained through mass spectrometry, this establishing presence a blocked N-terminal region. When comparing its sequence in the MEROPS database for peptidases and peptidase inhibitors, it showed 34.48% identity with a serine-proteinase inhibitor from the I15 family.
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Affiliation(s)
- J A Torres-Castillo
- Centro de Investigación y de Estudios Avanzados del I.P.N., Unidad Irapuato, Km. 9.6, Libramiento Norte Carr., Irapuato-León A. P. 629, Irapuato, Gto. 36821, Mexico
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Koh CY, Kazimirova M, Trimnell A, Takac P, Labuda M, Nuttall PA, Kini RM. Variegin, a novel fast and tight binding thrombin inhibitor from the tropical bont tick. J Biol Chem 2007; 282:29101-13. [PMID: 17684009 DOI: 10.1074/jbc.m705600200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tick saliva contains potent antihemostatic molecules that help ticks obtain their enormous blood meal during prolonged feeding. We isolated thrombin inhibitors present in the salivary gland extract from partially fed female Amblyomma variegatum, the tropical bont tick, and characterized the most potent, variegin, one of the smallest (32 residues) thrombin inhibitors found in nature. Full-length variegin and two truncated variants were chemically synthesized. Despite its small size and flexible structure, variegin binds thrombin with strong affinity (K(i) approximately 10.4 pM) and high specificity. Results using the truncated variants indicated that the seven residues at the N terminus affected the binding kinetics; when removed, the binding characteristics changed from fast to slow. Further, the thrombin active site binding moiety of variegin is in the region of residues 8-14, and the exosite-I binding moiety is within residues 15-32. Our results show that variegin is structurally and functionally similar to the rationally designed thrombin inhibitor, hirulog. However, compared with hirulog, variegin is a more potent inhibitor, and its inhibitory activity is largely retained after cleavage by thrombin.
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Affiliation(s)
- Cho Yeow Koh
- Protein Science Laboratory, Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
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Ricci-Silva ME, Konno K, Faria F, Rádis-Baptista G, Fontes W, Stöcklin R, Michalet S, Yamane T, Chudzinski-Tavassi AM. Protein mapping of the salivary complex from a hematophagous leech. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2005; 9:194-208. [PMID: 15969650 DOI: 10.1089/omi.2005.9.194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The salivary complex of leeches contains many components able to modulate physiological mechanisms, such as coagulation and fibrinolysis, and it is composed by the salivary glands and proboscis, encompassing two different proteomes. The bidimensional electrophoretic pattern of the salivary complex from the Haementeria depressa leech revealed a total of 352 spots, 103 in common with the muscular tissue and 249 exclusive from the salivary complex as detected by silver staining; these spots showed isoelectric points from 3.5 to 9.5 and covered an apparent molecular weight range from 10 to 105 kDa. The following isoforms of proteins were identified by mass spectrometry analysis: antiplatelet protein, myohemerythrin and carbonic anhydrase. Since the leeches were not fed for about 2-3 months to stimulate the secretion of proteins that facilitates the blood metabolism, these most abundant proteins in the salivary complex excised from leeches, are expected to play a role during feeding and might have some anti-hemostatic properties. Furthermore, by zymography, a gelatinolytic and a fibrinolytic protein were identified.
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Siddall ME, Budinoff RB, Borda E. Phylogenetic evaluation of systematics and biogeography of the leech family Glossiphoniidae. INVERTEBR SYST 2005. [DOI: 10.1071/is04034] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The phylogenetic relationships of Glossiphoniidae, a leech family characterised by its high degree of parental care, were investigated with the combined use of morphological data and three molecular datasets. There was strong support for monophyly of most accepted genera in the group, many of which are consistent with eyespot morphology. The genera Desserobdella Barta & Sawyer, 1990 and Oligobdella Moore, 1918 are suppressed as junior synonyms of Placobdella Blanchard, 1893 and thus recognising each of Placobdella picta (Verrill, 1872) Moore, 1906, Placobdella phalera (Graf, 1899) Moore, 1906, and Placobdella biannulata (Moore, 1900), comb. nov. The species Glossiphonia elegans (Verrill, 1872) Castle, 1900 and Helobdella modesta (Verrill, 1872), comb. nov. are resurrected for the North American counterparts to European non-sanguivorous species. Glossphonia baicalensis (Stschegolew, 1922), comb. nov. is removed from the genus Torix Blanchard 1898 and Alboglossiphonia quadrata (Moore, 1949) Sawyer, 1986 is removed from the genus Hemiclepsis Vejdovsky, 1884. The biogeographic implications of the phylogenetic hypothesis are evaluated in the context of what is already known for vertebrate hosts and Tertiary continental arrangements.
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Coin L, Bateman A, Durbin R. Enhanced protein domain discovery using taxonomy. BMC Bioinformatics 2004; 5:56. [PMID: 15137915 PMCID: PMC434490 DOI: 10.1186/1471-2105-5-56] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Accepted: 05/11/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids. RESULTS We show that by incorporating our understanding of the taxonomic distribution of specific protein domains, we can enhance domain recognition in protein sequences. We identify 4447 new instances of Pfam domains in the SP-TREMBL database using this technique, equivalent to the coverage increase given by the last 8.3% of Pfam families and to a 0.7% increase in the number of domain predictions. We use PSI-BLAST to cross-validate our new predictions. We also benchmark our approach using a SCOP test set of proteins of known structure, and demonstrate improvements relative to standard Hidden Markov model techniques. CONCLUSIONS Explicitly including knowledge about the taxonomic distribution of protein domains can enhance protein domain recognition. Our method can also incorporate other context-specific domain distributions - such as domain co-occurrence and protein localisation.
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Affiliation(s)
- Lachlan Coin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alex Bateman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Urata J, Shojo H, Kaneko Y. Inhibition mechanisms of hematophagous invertebrate compounds acting on the host blood coagulation and platelet aggregation pathways. Biochimie 2003; 85:493-500. [PMID: 12763308 DOI: 10.1016/s0300-9084(03)00071-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To facilitate blood feeding, hematophagous invertebrates have evolved a sophisticated array of physiological compounds that counteract homeostatic systems and inflammatory reactions of the vertebrate host. For this reason, hematophagous invertebrates possess a variety of anticoagulation components that are inhibitors of coagulant factors or antagonists of the platelet receptor. The examination of kinetic data and the crystal structure analysis have exposed the inhibition mechanisms for many of these anticoagulant reagents. Here, we attempt to classify the antihemostatic molecules and to focus on the kinetic approaches that have been instrumental in defining these mechanisms.
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Affiliation(s)
- Junko Urata
- Department of Epidemiology and Biostatics, Boston University School of Public Health, 715 Albany Street, Boston, MA 02118, USA
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Friedman M. Application of the S-pyridylethylation reaction to the elucidation of the structures and functions of proteins. JOURNAL OF PROTEIN CHEMISTRY 2001; 20:431-53. [PMID: 11760118 DOI: 10.1023/a:1012558530359] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Cysteine (Cys) and cystine residues in proteins are unstable under conditions used for acid hydrolysis of peptide bonds. To overcome this problem, we proposed the use of the S-pyridylethylation reaction to stabilize Cys residues as pyridylethyl-cysteine (PEC) protein derivatives. This suggestion was based on our observation that two synthetic derivatives formed by pyridylethylation of the SH group of Cys with either 2-vinylpyridine (2-VP) or 4-vinylpyridine (4-VP), designated as S-beta-(2-pyridylethyl)-L-cysteine (2-PEC) and S-beta-(4-pyridylethyl)-L-cysteine (4-PEC), were stable under acid conditions used to hydrolyze proteins. This was also the case for protein-bound PEC groups. Since their discovery over 30 years ago, pyridylethylation reactions have been widely modified and automated for the analysis of many structurally different proteins at levels as low as 20 picomoles, to determine the primary structures of proteins and to define the influence of SH groups and disulfide bonds on the structures and functional, enzymatic, medical, nutritional, pharmacological, and toxic properties of proteins isolated from plant, microbial, marine, animal, and human sources. Pyridylethylation has been accepted as the best method for the modification of Cys residues in proteins for subsequent analysis and sequence determination. The reaction has also been proposed to measure D-Cys, homocysteine, glutathione, tryptophan, dehydroalanine, and furanthiol food flavors. This integrated overview of the diverse literature on these reactions emphasizes general concepts. It is intended to serve as a resource and guide for further progress based on the reported application of pyridylethylation reactions to more than 150 proteins.
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Affiliation(s)
- M Friedman
- Western Regional Research Center, Agricultural Research Service, USDA, Albany, CA 94710, USA.
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Abstract
Increased life expectancy is associated with aging populations in the developed countries, and we can expect an increased incidence of cardiovascular and inflammatory diseases and cancers. A priority for medical research is to reduce such morbidity. Leeches have been demonstrated to be a useful source of drugs to treat cardiovascular diseases, as they have evolved highly specific mechanisms to feed on their hosts by blocking blood coagulation. Powerful molecules acting at different points in the coagulation cascade or in the inhibition of platelet aggregation have been purified from these animals. Moreover, clinical trials confirm their potential to treat cardiovascular diseases.
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Affiliation(s)
- M Salzet
- Laboratoire d'Endocrinologie et Immunité des Annélides, UPRESA CNRS 8017, Université des Sciences et Technologies de Lille, SN3, F-59655 Cedex, Villeneuve d'Ascq, France.
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Chopin V, Salzet M, Baert JL, Vandenbulcke F, Sautiére PE, Kerckaert JP, Malecha J. Therostasin, a novel clotting factor Xa inhibitor from the rhynchobdellid leech, Theromyzon tessulatum. J Biol Chem 2000; 275:32701-7. [PMID: 10852926 DOI: 10.1074/jbc.m909217199] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Therostasin is a potent naturally occurring tight-binding inhibitor of mammalian Factor Xa (K(i), 34 pm), isolated from the rhynchobdellid leech Theromyzon tessulatum. Therostasin is a cysteine-rich protein (8991 Da) consisting of 82 amino acid residues with 16 cysteine residues. Its amino acid sequence has been determined by a combination of techniques, including Edman degradation, enzymatic cleavage, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) on the native and s-beta-pyridylethylated compound. Sequence analysis reveals that it shares no significant homology with other Factor Xa inhibitors except for the putative reactive site. Moreover, it contains a signature pattern for proteins of the endothelin family, potent vasoconstrictors isolated in mammal and snake venom. Therostasin cDNA (825 bp) codes for a polypeptide of 82 amino acid residues preceded by 19 residues, representing a signal peptide sequence. As for the other known inhibitors of Factor Xa, therostasin is expressed and stored in the cells of the leech salivary glands.
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Affiliation(s)
- V Chopin
- Laboratoire d'Endocrinologie des Annélides, UPRES-A 8017 CNRS, SN3, Université des Sciences et Technologie de Lille, F-59655 Villeneuve d'Ascq Cédex, France
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