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Ghosh U, Kumar V, Singh G, Kanti Chakraborty T. Conformation Based in silico Studies of Cyclic Tetrapeptides with βγ Fused Turns as Thrombin Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Uttam Ghosh
- Department of Organic Chemistry Indian Institute of Science Bengaluru 560012 India
| | - Vikash Kumar
- CSIR-Central Drug Research Institute Lucknow 226031 India
| | - Gajendra Singh
- CSIR-Central Drug Research Institute Lucknow 226031 India
- School of Life Sciences Central University of Rajasthan Bandar Sindri Ajmer 305817 Rajasthan India
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2
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Zhou S, Zhao W, Hu J, Mao C, Zhou M. Application of Nanotechnology in Thrombus Therapy. Adv Healthc Mater 2023; 12:e2202578. [PMID: 36507827 DOI: 10.1002/adhm.202202578] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/26/2022] [Indexed: 12/14/2022]
Abstract
A thrombus is a blood clot that forms in the lumen of an artery or vein, restricting blood flow and causing clinical symptoms. Thrombosis is associated with many life-threatening cardiovascular diseases. However, current clinical therapeutic technologies still have many problems in targeting, enrichment, penetration, and safety to meet the thrombosis treatment needs. Therefore, researchers devote themselves to developing nanosystems loaded with antithrombotic drugs to address this paradox in recent years. Herein, the existing thrombosis treatment technologies are first reviewed; and then, their advantages and disadvantages are outlined based on a brief discussion of thrombosis's definition and formation mechanism. Furthermore, the need and application cases for introducing nanotechnology are discussed, focusing on thrombus-specific targeted ligand modification technology and microenvironment-triggered responsive drug release technology. Then, nanomaterials that can be used to design antithrombotic nanotherapeutic systems are summarized. Moreover, a variety of drug delivery technologies driven by nanomotors in thrombosis therapy is also introduced. Last of all, a prospective discussion on the future development of nanotechnology for thrombosis therapy is highlighted.
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Affiliation(s)
- Shuyin Zhou
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China.,Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Wenbo Zhao
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jinglei Hu
- Kuang Yaming Honors School, Nanjing University, Nanjing, 210023, China
| | - Chun Mao
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Min Zhou
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
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3
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A combined computational and experimental approach predicts thrombin adsorption to zeolites. Colloids Surf B Biointerfaces 2023; 221:113007. [DOI: 10.1016/j.colsurfb.2022.113007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/08/2022]
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4
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Lukas P, Melikian G, Hildebrandt JP, Müller C. Make it double: identification and characterization of a Tandem-Hirudin from the Asian medicinal leech Hirudinaria manillensis. Parasitol Res 2022; 121:2995-3006. [PMID: 36006484 PMCID: PMC9464118 DOI: 10.1007/s00436-022-07634-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022]
Abstract
Haematophagous leeches express a broad variety of secretory proteins in their salivary glands, among them are hirudins and hirudin-like factors. Here, we describe the identification, molecular and initial functional characterization of Tandem-Hirudin (TH), a novel salivary gland derived factor identified in the Asian medicinal leech, Hirudinaria manillensis. In contrast to the typical structure of hirudins, TH comprises two globular domains arranged in a tandem-like orientation and lacks the elongated C-terminal tail. Similar structures of thrombin inhibitors have so far been identified only in kissing bugs and ticks. Expression of TH was performed in both cell-based and cell-free bacterial systems. A subsequent functional characterization revealed no evidence for a thrombin-inhibitory potency of TH.
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Affiliation(s)
- Phil Lukas
- Animal Physiology, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, D-17489, Greifswald, Germany
| | - Georgij Melikian
- Animal Physiology, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, D-17489, Greifswald, Germany
| | - Jan-Peter Hildebrandt
- Animal Physiology, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, D-17489, Greifswald, Germany
| | - Christian Müller
- Animal Physiology, Zoological Institute and Museum, University of Greifswald, Felix-Hausdorff-Str. 1, D-17489, Greifswald, Germany.
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5
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Modrzycka S, Kołt S, Polderdijk SGI, Adams TE, Potoczek S, Huntington JA, Kasperkiewicz P, Drąg M. Parallel imaging of coagulation pathway proteases activated protein C, thrombin, and factor Xa in human plasma. Chem Sci 2022; 13:6813-6829. [PMID: 35774156 PMCID: PMC9200056 DOI: 10.1039/d2sc01108e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022] Open
Abstract
Activated protein C (APC), thrombin, and factor (f) Xa are vitamin K-dependent serine proteases that are key factors in blood coagulation. Moreover, they play important roles in inflammation, apoptosis, fibrosis, angiogenesis, and viral infections. Abnormal activity of these coagulation factors has been related to multiple conditions, such as bleeding and thrombosis, Alzheimer's disease, sepsis, multiple sclerosis, and COVID-19. The individual activities of APC, thrombin, and fXa in coagulation and in various diseases are difficult to establish since these proteases are related and have similar substrate preferences. Therefore, the development of selective chemical tools that enable imaging and discrimination between coagulation factors in biological samples may provide better insight into their roles in various conditions and potentially aid in the establishment of novel diagnostic tests. In our study, we used a large collection of unnatural amino acids, and this enabled us to extensively explore the binding pockets of the enzymes' active sites. Based on the specificity profiles obtained, we designed highly selective substrates, inhibitors, and fluorescent activity-based probes (ABPs) that were used for fast, direct, and simultaneous detection of APC, thrombin, and fXa in human plasma. Using a collection of natural and unnatural amino acids, we synthesized a set of fluorescent activity-based probes for the fast, direct, and simultaneous detection of coagulation factors in human plasma.![]()
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Affiliation(s)
- Sylwia Modrzycka
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Stéphanie G I Polderdijk
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Ty E Adams
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Stanisław Potoczek
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Wrocław Medical University Pasteura 1 50-367 Wrocław Poland
| | - James A Huntington
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
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6
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Mechanistic and Predictive QSAR Analysis of Diverse Molecules to Capture Salient and Hidden Pharmacophores for Anti-Thrombotic Activity. Int J Mol Sci 2021; 22:ijms22158352. [PMID: 34361118 PMCID: PMC8348508 DOI: 10.3390/ijms22158352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/24/2021] [Accepted: 07/31/2021] [Indexed: 12/02/2022] Open
Abstract
Thrombosis is a life-threatening disease with a high mortality rate in many countries. Even though anti-thrombotic drugs are available, their serious side effects compel the search for safer drugs. In search of a safer anti-thrombotic drug, Quantitative Structure-Activity Relationship (QSAR) could be useful to identify crucial pharmacophoric features. The present work is based on a larger data set comprising 1121 diverse compounds to develop a QSAR model having a balance of acceptable predictive ability (Predictive QSAR) and mechanistic interpretation (Mechanistic QSAR). The developed six parametric model fulfils the recommended values for internal and external validation along with Y-randomization parameters such as R2tr = 0.831, Q2LMO = 0.828, R2ex = 0.783. The present analysis reveals that anti-thrombotic activity is found to be correlated with concealed structural traits such as positively charged ring carbon atoms, specific combination of aromatic Nitrogen and sp2-hybridized carbon atoms, etc. Thus, the model captured reported as well as novel pharmacophoric features. The results of QSAR analysis are further vindicated by reported crystal structures of compounds with factor Xa. The analysis led to the identification of useful novel pharmacophoric features, which could be used for future optimization of lead compounds.
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Fredenburgh JC, Weitz JI. New anticoagulants: Moving beyond the direct oral anticoagulants. J Thromb Haemost 2021; 19:20-29. [PMID: 33047462 DOI: 10.1111/jth.15126] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 01/23/2023]
Abstract
Although anticoagulants have been in use for more than 80 years, heparin and vitamin K antagonists were the sole available options until recently. Although these agents revolutionized the prevention and treatment of thrombotic diseases, their use has been hampered by the necessity for coagulation monitoring and by bleeding complications resulting in part from their multiple sites of action. Owing to advances in basic science, animal models, and epidemiology, the arsenal of available anticoagulants has expanded in the past two decades. This evolution has yielded many novel compounds that target single coagulation enzymes. Initially, thrombin and factor Xa were targeted because of their critical roles in coagulation. However, attention has now shifted to compounds that target upstream reactions, particularly those catalyzed by factors XIIa and XIa, which are part of the contact system. This shift is predicated on epidemiological and experimental evidence suggesting that these factors are more important for thrombosis than for hemostasis. With the goal of developing a new class of anticoagulants associated with a lower risk of bleeding than currently available agents, dozens of drugs targeting the contact system are now in development. This article focuses on the rationale, development, and testing of these new agents with a concentration on those that have reached or completed phase 2 evaluation for at least one indication.
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Affiliation(s)
- James C Fredenburgh
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
- Departments of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jeffrey I Weitz
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
- Departments of Medicine, McMaster University, Hamilton, ON, Canada
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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8
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Burley SK. Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. J Biol Chem 2021; 296:100559. [PMID: 33744282 PMCID: PMC8059052 DOI: 10.1016/j.jbc.2021.100559] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/02/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
The Protein Data Bank (PDB) is an international core data resource central to fundamental biology, biomedicine, bioenergy, and biotechnology/bioengineering. Now celebrating its 50th anniversary, the PDB houses >175,000 experimentally determined atomic structures of proteins, nucleic acids, and their complexes with one another and small molecules and drugs. The importance of three-dimensional (3D) biostructure information for research and education obtains from the intimate link between molecular form and function evident throughout biology. Among the most prolific consumers of PDB data are biomedical researchers, who rely on the open access resource as the authoritative source of well-validated, expertly curated biostructures. This review recounts how the PDB grew from just seven protein structures to contain more than 49,000 structures of human proteins that have proven critical for understanding their roles in human health and disease. It then describes how these structures are used in academe and industry to validate drug targets, assess target druggability, characterize how tool compounds and other small-molecules bind to drug targets, guide medicinal chemistry optimization of binding affinity and selectivity, and overcome challenges during preclinical drug development. Three case studies drawn from oncology exemplify how structural biologists and open access to PDB structures impacted recent regulatory approvals of antineoplastic drugs.
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Affiliation(s)
- Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA.
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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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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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Dirofilaria immitis possesses molecules with anticoagulant properties in its excretory/secretory antigens. Parasitology 2020; 147:559-565. [DOI: 10.1017/s0031182020000104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractDirofilaria immitis is a parasitic nematode that survives in the circulatory system of suitable hosts for many years, causing the most severe thromboembolisms when simultaneous death of adult worms occurs. The two main mechanisms responsible for thrombus formation in mammals are the activation and aggregation of platelets and the generation of fibrin through the coagulation cascade. The aim of this work was to study the anticoagulant potential of excretory/secretory antigens from D. immitis adult worms (DiES) on the coagulation cascade of the host. Anticoagulant and inhibition assays respectively showed that DiES partially alter the coagulation cascade of the host and reduce the activity of the coagulation factor Xa, a key enzyme in the coagulation process. In addition, a D. immitis protein was identified by its similarity to the homologous serpin 6 from Brugia malayi as a possible candidate to form an inhibitory complex with FXa by sodium dodecyl sulfate polyacrylamide gel electrophoresis and mass spectrometry. These results indicate that D. immitis could use the anticoagulant properties of its excretory/secretory antigens to control the formation of blood clots in its immediate intravascular habitat as a survival mechanism.
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Sun ZG, Yang-Liu, Zhang JM, Cui SC, Zhang ZG, Zhu HL. The Research Progress of Direct Thrombin Inhibitors. Mini Rev Med Chem 2019; 20:1574-1585. [PMID: 31644402 DOI: 10.2174/1389557519666191015201125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 03/18/2019] [Accepted: 05/19/2019] [Indexed: 11/22/2022]
Abstract
Blood coagulation is the process of changing the blood from the flowing state to the gel state. It is an important part of the hemostatic function. Coagulation is a process by which a series of coagulation factors are sequentially activated, and finally thrombin is formed to form fibrin clot. Direct thrombin inhibitors are important anticoagulant drug. These drugs can selectively bind to the active site of thrombin, inhibit thrombin activity, have strong action and high specificity, and have important significance in the clinical treatment of thrombus diseases. Some of them come from natural products of animals or plants, and many of them have been applied in the clinic. The other part is derived from the design, synthesis and activity studies of small molecule inhibitors. This review discusses the progress of direct thrombin inhibitors in recent years.
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Affiliation(s)
- Zhi-Gang Sun
- Central Laboratory, Linyi Central Hospital, No.17 Jiankang Road, Linyi 276400, China,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, No.163 Xianlin Road, Nanjing 210023, China
| | - Yang-Liu
- Central Laboratory, Linyi Central Hospital, No.17 Jiankang Road, Linyi 276400, China
| | - Jin-Mai Zhang
- Room 205, BIO-X white house, Shanghai Jiao Tong University, No.1954 Huashan Road, Shanghai 200030,China
| | - Shi-Chang Cui
- Central Laboratory, Linyi Central Hospital, No.17 Jiankang Road, Linyi 276400, China
| | - Zhi-Gang Zhang
- Department of Cardiovascular Medicine, Linyi Central Hospital, No.17 Jiankang Road, Linyi 276400, China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, No.163 Xianlin Road, Nanjing 210023, 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: 25] [Impact Index Per Article: 5.0] [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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14
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How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals. Structure 2018; 27:211-217. [PMID: 30595456 DOI: 10.1016/j.str.2018.11.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 01/01/2023]
Abstract
Discovery and development of 210 new molecular entities (NMEs; new drugs) approved by the US Food and Drug Administration 2010-2016 was facilitated by 3D structural information generated by structural biologists worldwide and distributed on an open-access basis by the PDB. The molecular targets for 94% of these NMEs are known. The PDB archive contains 5,914 structures containing one of the known targets and/or a new drug, providing structural coverage for 88% of the recently approved NMEs across all therapeutic areas. More than half of the 5,914 structures were published and made available by the PDB at no charge, with no restrictions on usage >10 years before drug approval. Citation analyses revealed that these 5,914 PDB structures significantly affected the very large body of publicly funded research reported in publications on the NME targets that motivated biopharmaceutical company investment in discovery and development programs that produced the NMEs.
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Ben-Shalom IY, Pfeiffer-Marek S, Baringhaus KH, Gohlke H. Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations. J Chem Inf Model 2017; 57:170-189. [DOI: 10.1021/acs.jcim.6b00373] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ido Y. Ben-Shalom
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Stefania Pfeiffer-Marek
- LGCR/Pharmaceutical
Sciences Operations, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Karl-Heinz Baringhaus
- R&D Resources/Site Direction, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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16
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Abstract
Thrombosis is a complex process involving multiple pathways. Currently, therapy relies on the combination of two or more antithrombotic drugs, showing that inhibiting more than one target provides benefits in the prevention and treatment of thrombosis. This review focuses on structure-activity relationship studies of molecules possessing multiple actions against thrombosis, namely, dual inhibitors of coagulation, dual inhibitors of coagulation and platelet aggregation, and also dual inhibitors of platelet aggregation. EP217609 has just entered clinical trials, which raise the expectations on the multitarget strategy to prevent or treat thrombosis.
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17
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Theoretical Study of Molecular Structure and Physicochemical Properties of Novel Factor Xa Inhibitors and Dual Factor Xa and Factor IIa Inhibitors. Molecules 2016; 21:molecules21020185. [PMID: 26861270 PMCID: PMC6273828 DOI: 10.3390/molecules21020185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 01/27/2016] [Accepted: 01/27/2016] [Indexed: 12/13/2022] Open
Abstract
The geometries and energies of factor Xa inhibitors edoxaban, eribaxaban, fidexaban, darexaban, letaxaban, and the dual factor Xa and thrombin inhibitors tanogitran and SAR107375 in both the gas-phase and aqueous solution were studied using the Becke3LYP/6-31++G(d,p) or Grimme’s B97D/6-31++G(d,p) method. The fully optimized conformers of these anticoagulants show a characteristic l-shape structure, and the water had a remarkable effect on the equilibrium geometry. According to the calculated pKa values eribaxaban and letaxaban are in neutral undissociated form at pH 7.4, while fidexaban and tanogitran exist as zwitterionic structures. The lipophilicity of the inhibitors studied lies within a large range of log P between 1 and 4. The dual inhibitor SAR107375 represents an improvement in structural, physicochemical and pharmacokinetic characteristics over tanogitran. At blood pH, SAR107375 predominantly exists in neutral form. In contrast with tanogitran, it is better absorbed and more lipophilic and active after oral application.
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18
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Prathipati P, Mizuguchi K. Integration of Ligand and Structure Based Approaches for CSAR-2014. J Chem Inf Model 2015; 56:974-87. [PMID: 26492437 DOI: 10.1021/acs.jcim.5b00477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The prediction of binding poses and affinities is an area of active interest in computer-aided drug design (CADD). Given the documented limitations with either ligand or structure based approaches, we employed an integrated approach and developed a rapid protocol for binding mode and affinity predictions. This workflow was applied to the three protein targets of Community Structure-Activity Resource-2014 (CSAR-2014) exercise: Factor Xa (FXa), Spleen Tyrosine Kinase (SYK), and tRNA (guanine-N(1))-methyltransferase (TrmD). Our docking and scoring workflow incorporates compound clustering and ligand and protein structure based pharmacophore modeling, followed by local docking, minimization, and scoring. While the former part of the protocol ensures high-quality ligand alignments and mapping, the subsequent minimization and scoring provides the predicted binding modes and affinities. We made blind predictions of docking pose for 1, 5, and 14 ligands docked into 1, 2, and 12 crystal structures of FXa, SYK, and TrmD, respectively. The resulting 174 poses were compared with cocrystallized structures (1, 5, and 14 complexes) made available at the end of CSAR. Our predicted poses were related to the experimentally determined structures with a mean root-mean-square deviation value of 3.4 Å. Further, we were able to classify high and low affinity ligands with the area under the curve values of 0.47, 0.60, and 0.69 for FXa, SYK, and TrmD, respectively, indicating the validity of our approach in at least two of the three systems. Detailed critical analysis of the results and CSAR methodology ranking procedures suggested that a straightforward application of our workflow has limitations, as some of the performance measures do not reflect the actual utility of pose and affinity predictions in the biological context of individual systems.
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Affiliation(s)
- Philip Prathipati
- National Institutes of Biomedical Innovation, Health and Nutrition , 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition , 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
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19
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Martiny VY, Martz F, Selwa E, Iorga BI. Blind Pose Prediction, Scoring, and Affinity Ranking of the CSAR 2014 Dataset. J Chem Inf Model 2015; 56:996-1003. [DOI: 10.1021/acs.jcim.5b00337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Virginie Y. Martiny
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT, 91198 Gif-sur-Yvette, France
- Department
of Nephrology and Dialysis, AP-HP, Tenon Hospital, INSERM UMR_S 1155, 75020 Paris, France
| | - François Martz
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT, 91198 Gif-sur-Yvette, France
| | - Edithe Selwa
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT, 91198 Gif-sur-Yvette, France
| | - Bogdan I. Iorga
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT, 91198 Gif-sur-Yvette, France
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20
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Arepally GM, Ortel TL. Changing practice of anticoagulation: will target-specific anticoagulants replace warfarin? Annu Rev Med 2015; 66:241-53. [PMID: 25587651 DOI: 10.1146/annurev-med-051113-024633] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The target-specific oral anticoagulants are a class of agents that inhibit factor Xa or thrombin. They are effective and safe compared to warfarin for the prevention of stroke and systemic embolism in patients with atrial fibrillation and for the treatment of venous thromboembolism, and they are comparable to low-molecular-weight heparin for thromboprophylaxis after hip or knee arthroplasty. For other indications, however, such as the prevention of stroke in patients with mechanical heart valves, initial studies have been unfavorable for the newer agents, leaving warfarin the anticoagulant of choice. Further studies are needed before the target-specific anticoagulants can be recommended for patients with cancer-associated thrombosis or heparin-induced thrombocytopenia. Concerns also persist about difficulties with the laboratory assessment of anticoagulant effect and the lack of a specific reversal agent. For these reasons, we anticipate that the vitamin K antagonists will continue to be important anticoagulants for years to come.
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21
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Kudryavtsev KV, Shulga DA, Chupakhin VI, Sinauridze EI, Ataullakhanov FI, Vatsadze SZ. Synthesis of novel bridged dinitrogen heterocycles and their evaluation as potential fragments for the design of biologically active compounds. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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The characteristics of thrombin in osteoarthritic pathogenesis and treatment. BIOMED RESEARCH INTERNATIONAL 2014; 2014:407518. [PMID: 25313362 PMCID: PMC4182002 DOI: 10.1155/2014/407518] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/01/2014] [Indexed: 01/08/2023]
Abstract
Osteoarthritis (OA) is a mechanical abnormality associated with degradation of joints. It is characterized by chronic, progressive degeneration of articular cartilage, abnormalities of bone, and synovial change. The most common symptom of OA is local inflammation resulting from exogenous stress or endogenous abnormal cytokines. Additionally, OA is associated with local and/or systemic activation of coagulation and anticoagulation pathways. Thrombin plays an important role in the stimulation of fibrin deposition and the proinflammatory processes in OA. Thrombin mediates hemostatic and inflammatory responses and guides the immune response to tissue damage. Thrombin activates intracellular signaling pathways by interacting with transmembrane domain G protein coupled receptors (GPCRs), known as protease-activated receptors (PARs). In pathogenic mechanisms, PARs have been implicated in the development of acute and chronic inflammatory responses in OA. Therefore, discovery of thrombin signaling pathways would help us to understand the mechanism of OA pathogenesis and lead us to develop therapeutic drugs in the future.
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23
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Xue T, Ding S, Guo B, Zhou Y, Sun P, Wang H, Chu W, Gong G, Wang Y, Chen X, Yang Y. Design, Synthesis, and Structure–Activity and Structure–Pharmacokinetic Relationship Studies of Novel [6,6,5] Tricyclic Fused Oxazolidinones Leading to the Discovery of a Potent, Selective, and Orally Bioavailable FXa Inhibitor. J Med Chem 2014; 57:7770-91. [DOI: 10.1021/jm501045e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Xue
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shi Ding
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bin Guo
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yuren Zhou
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Peng Sun
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Heyao Wang
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjing Chu
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guoqing Gong
- Department
of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu Province 210009, China
| | - Yinye Wang
- Department
of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaoyan Chen
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yushe Yang
- State
Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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24
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Effect of Toona microcarpa Harms leaf extract on the coagulation system. BIOMED RESEARCH INTERNATIONAL 2014; 2014:615363. [PMID: 24818147 PMCID: PMC4003838 DOI: 10.1155/2014/615363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 11/18/2022]
Abstract
Toona microcarpa Harms is a tonic, antiperiodic, antirheumatic, and antithrombotic agent in China and India and an astringent and tonic for treating diarrhea, dysentery, and other intestinal infections in Indonesia. In this study, we prepared ethyl-acetate extract from the air-dried leaves of Toona microcarpa Harms and investigated the anticoagulant activities in vitro by performing activated partial thromboplastin time (APTT), prothrombin time (PT), and thrombin time (TT) assays. Antiplatelet aggregation activity of the extract was examined using adenosine diphosphate (ADP), collagen, and thrombin as agonists, and the inhibitions of factor Xa and thrombin were also investigated. Bleeding and clotting times in mice were used to determine its anticoagulant activities in vivo. It is found that Toona microcarpa Harms leaf extract (TMHE) prolonged APTT, PT, and TT clotting times in a dose-dependent manner and significantly inhibited platelet aggregation induced by thrombin, but not ADP or collagen. Clotting time and bleeding time assays showed that TMHE significantly prolonged clotting and bleeding times in vivo. In addition, at the concentration of 1 mg/mL, TMHE inhibited human thrombin activity by 73.98 ± 2.78%. This is the first report to demonstrate that THME exhibits potent anticoagulant effects, possibly via inhibition of thrombin activity.
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25
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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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26
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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27
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Bijak M, Ponczek MB, Nowak P. Polyphenol compounds belonging to flavonoids inhibit activity of coagulation factor X. Int J Biol Macromol 2014; 65:129-35. [PMID: 24444877 DOI: 10.1016/j.ijbiomac.2014.01.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 12/26/2013] [Accepted: 01/09/2014] [Indexed: 11/29/2022]
Abstract
Blood coagulation consists of series of zymogens which can be converted by limited proteolysis to active enzymes leading to the generation of thrombin and conversion of fibrinogen into fibrin by this enzyme. The activated factor X (FXa) forms prothrombinase complex on phosphatidylserine containing surface which is responsible for conversion of prothrombin to thrombin. One molecule of FXa generates more than 1000 thrombin molecules. Therefore FXa is a novel target for modern anticoagulant therapy. The aim of our present study is to examine the effects of the well-known plant polyphenolic compounds on factor Xa amidolytic activity and characterization of these interactions using bioinformatic ligand docking method. We observed that only four polyphenols belonging to flavonoids group: procyanidin B2, cyanidin, quercetin and silybin, had inhibitory effect on FXa activity. Bioinformatic analyses revealed that procyanidin B2, cyanidin, quercetin and silybin bound in the S1-S4 pockets located in vicinity of the FXa active site and blocked access of substrates to Ser195. The results presented here showed that flavonoids might be potential structural bases for design of new nature-based, safe, orally bioavailable direct FXa inhibitors.
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Affiliation(s)
- Michal Bijak
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
| | - Michal Blazej Ponczek
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Pawel Nowak
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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28
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So YH, Chang HT, Chiu WJ, Huang CC. Graphene oxide modified with aptamer-conjugated gold nanoparticles and heparin: a potent targeted anticoagulant. Biomater Sci 2014; 2:1332-1337. [DOI: 10.1039/c4bm00156g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis of a nanocomposite of aptamer-conjugated gold nanoparticles and heparin co-immobilized graphene oxide that acts as a highly effective anticoagulant by controlling the thrombin activity towards fibrinogen.
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Affiliation(s)
- Yi-Heng So
- Institute of Bioscience and Biotechnology
- National Taiwan Ocean University
- Keelung, Taiwan
| | | | - Wei-Jane Chiu
- Institute of Bioscience and Biotechnology
- National Taiwan Ocean University
- Keelung, Taiwan
| | - Chih-Ching Huang
- Institute of Bioscience and Biotechnology
- National Taiwan Ocean University
- Keelung, Taiwan
- Center of Excellence for the Oceans
- National Taiwan Ocean University
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29
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Sidhu PS, Abdel Aziz MH, Sarkar A, Mehta AY, Zhou Q, Desai UR. Designing allosteric regulators of thrombin. Exosite 2 features multiple subsites that can be targeted by sulfated small molecules for inducing inhibition. J Med Chem 2013; 56:5059-70. [PMID: 23718540 DOI: 10.1021/jm400369q] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We recently designed a group of novel exosite-2-directed sulfated, small, allosteric inhibitors of thrombin. To develop more potent inhibitors, monosulfated benzofuran tri- and tetrameric homologues of the parent designed dimers were synthesized in seven to eight steps and found to exhibit a wide range of potencies. Among these, trimer 9a was found to be nearly 10-fold more potent than the first generation molecules. Michaelis-Menten studies indicated an allosteric mechanism of inhibition. Competitive studies using a hirudin peptide (exosite 1 ligand) and unfractionated heparin, heparin octasaccharide, and γ'-fibrinogen peptide (exosite 2 ligands) demonstrated exosite 2 recognition in a manner different from that of the parent dimers. Alanine scanning mutagenesis of 12 Arg/Lys residues of exosite 2 revealed a defect in 9a potency for Arg233Ala thrombin only confirming the major difference in site of recognition between the two structurally related sulfated benzofurans. The results suggest that multiple avenues are available within exosite 2 for inducing thrombin inhibition.
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Affiliation(s)
- Preetpal Singh Sidhu
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23219, USA
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30
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Abstract
Orally active small molecules that selectively and specifically inhibit coagulation serine proteases have been developed for clinical use. Dabigatran etexilate, rivaroxaban and apixaban are given at fixed doses and do not require monitoring. In most circumstances, these drugs have predictable bioavailability, pharmacokinetic effects, and pharmacodynamic effects. However, there will be clinical circumstances when assessment of the anticoagulant effect of these drugs will be required. The effect of these drugs on laboratory tests has been determined in vitro by spiking normal samples with a known concentration of active compound, or ex vivo by using plasma samples from volunteers and patients. Data on the sensitivity of different reagents are now available, and so guidance as to the effect and interpretation of a test result is now possible. Laboratories should be aware of the sensitivity of their own assays to each drug. This may be achieved by using appropriate calibrated plasma samples.
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Affiliation(s)
- T Baglin
- Department of Haematology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Trust, Cambridge, UK.
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31
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Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG. Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J Am Chem Soc 2013; 135:2879-82. [PMID: 23398247 DOI: 10.1021/ja3108214] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Arginine methylation has emerged as a widespread post-translational modification with influence over myriad cellular processes. However, the molecular mechanisms underlying such methylarginine-dependent phenomena remain unclear. To aid in this research, a facile method was developed to install methylarginine analogues on recombinant protein for use in biochemical, biophysical, and structural studies. Through chemical conjugation of novel α,β-unsaturated amidine precursors with proteins, methylarginine mimics can be displayed with control of methylation site, extent, and regiospecificity. Analogue installation into histones using this strategy produced modified proteins that were recognized by antibodies specific to endogenous methylarginine, and these histones retained the capacity to form mononucleosomes. Moreover, a native methylarginine-specific binding domain was shown to interact with methylarginine analogue-modified substrates. This chemical conjugation method for installing methylarginine analogues provides an efficient route to produce homogeneous modified proteins for subsequent investigations of methylarginine-dependent processes.
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Affiliation(s)
- Daniel D Le
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, 600 16th Street, MC2280, San Francisco, California 94158, USA
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32
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Zhorov BS, Tikhonov DB. Ligand action on sodium, potassium, and calcium channels: role of permeant ions. Trends Pharmacol Sci 2013; 34:154-61. [PMID: 23375737 DOI: 10.1016/j.tips.2013.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/04/2013] [Accepted: 01/07/2013] [Indexed: 12/22/2022]
Abstract
Ion channels are targets for many naturally occurring toxins and small-molecule drugs. Despite great progress in the X-ray crystallography of ion channels, we still do not have a complete understanding of the atomistic mechanisms of channel modulation by ligands. In particular, the importance of the simultaneous interaction of permeant ions with the ligand and the channel protein has not been the focus of much attention. Considering these interactions often allows one to rationalize the highly diverse experimental data within the framework of relatively simple structural models. This has been illustrated in earlier studies on the action of local anesthetics, sodium channel activators, as well as blockers of potassium and calcium channels. Here, we discuss the available data with a view to understanding the use-, voltage-, and current carrying cation-dependence of the ligand action, paradoxes in structure--activity relationships, and effects of mutations in these ion channels.
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Affiliation(s)
- Boris S Zhorov
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
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