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Steinmetzer T, Baum B, Biela A, Klebe G, Nowak G, Bucha E. Beyond Heparinization: Design of Highly Potent Thrombin Inhibitors Suitable for Surface Coupling. ChemMedChem 2012; 7:1965-73. [DOI: 10.1002/cmdc.201200292] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Indexed: 11/10/2022]
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The role of structural information in the discovery of direct thrombin and factor Xa inhibitors. Trends Pharmacol Sci 2012; 33:279-88. [PMID: 22503439 DOI: 10.1016/j.tips.2012.03.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/05/2012] [Accepted: 03/07/2012] [Indexed: 11/21/2022]
Abstract
The quest for novel medications to treat thromboembolic disorders such as venous thrombosis, pulmonary embolism and stroke received a boost when the 3D structures of two major players in the blood coagulation cascade were determined in 1989 and 1993. Structure-guided design of inhibitors of thrombin (factor IIa, fIIa) and factor Xa (fXa) eventually led to the discovery of potent, selective, efficacious, orally active and safe compounds that proved successful in clinical studies. In 2008, the direct thrombin inhibitor dabigatran etexilate developed by Boehringer Ingelheim became the first novel antithrombotic molecular entity to enter the market in 50 years. Additional compounds targeting factor Xa were subsequently granted marketing authorization or are in late-stage clinical studies. In this review, I use selected case studies to describe the discovery of novel fIIa and fXa inhibitors, with a particular emphasis on the pre-eminent role that structural information played in this process.
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Specificity and selectivity profile of EP217609: a new neutralizable dual-action anticoagulant that targets thrombin and factor Xa. Blood 2011; 119:2187-95. [PMID: 22144183 DOI: 10.1182/blood-2011-09-381764] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
EP217609 is a new dual-action parenteral anticoagulant that combines an indirect factor Xa inhibitor (fondaparinux analog) and a direct thrombin inhibitor (α-NAPAP analog) in a single molecule together with a biotin tag to allow avidin neutralization. EP217609 exhibits an unprecedented pharmacologic profile in showing high bioavailability, long plasma half-life, and potent antithrombotic activity in animals without the complications of thrombin rebound. Here we report the exceptional specificity and selectivity profile of EP217609. EP217609 inhibited thrombin with rapid kinetics (k(on) > 10(7)M(-1)s(-1)), a high affinity (K(I) = 30-40pM), and more than 1000-fold selectivity over other coagulation and fibrinolytic protease targets, comparing favorably with the best direct thrombin inhibitors known. EP217609 bound antithrombin with high affinity (K(D) = 30nM) and activated the serpin to rapidly (k(ass) ∼ 10(6)M(-1)s(-1)) and selectively (> 20-fold) inhibit factor Xa. The dual inhibitor moieties of EP217609 acted largely independently with only modest linkage effects of ligand occupancy of one inhibitor moiety on the potency of the other (∼ 5-fold). In contrast, avidin binding effectively neutralized the potency of both inhibitor moieties (20- to 100-fold). These findings demonstrate the superior anticoagulant efficacy and rapid avidin neutralizability of EP217609 compared with anticoagulants that target thrombin or factor Xa alone.
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Brenna E, Gatti FG, Manfredi A, Monti D, Parmeggiani F. Biocatalyzed Enantioselective Reduction of Activated C=C Bonds: Synthesis of Enantiomerically Enriched α-Halo-β-arylpropionic Acids. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100537] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Straub A, Roehrig S, Hillisch A. Oral, Direct Thrombin and Factor Xa Inhibitors: The Replacement for Warfarin, Leeches, and Pig Intestines? Angew Chem Int Ed Engl 2011; 50:4574-90. [DOI: 10.1002/anie.201004575] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Indexed: 01/09/2023]
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6
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Orale, direkte Thrombin- und Faktor-Xa-Hemmer: Kommt die Ablösung für Warfarin, Blutegel und Schweinedärme? Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201004575] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Adang AEP, Hermkens PHH, Linders JTM, Ottenheijm HCJ, van Staveren CJ. Case histories of peptidomimetics: Progression from peptides to drugs. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130202] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
The MEROPS website (http://merops.sanger.ac.uk) includes information on peptidase inhibitors as well as on peptidases and their substrates. Displays have been put in place to link peptidases and inhibitors together. The classification of protein peptidase inhibitors is continually being revised, and currently inhibitors are grouped into 67 families based on comparisons of protein sequences. These families can be further grouped into 38 clans based on comparisons of tertiary structure. Small molecule inhibitors are important reagents for peptidase characterization and, with the increasing importance of peptidases as drug targets, they are also important to the pharmaceutical industry. Small molecule inhibitors are now included in MEROPS and over 160 summaries have been written.
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Affiliation(s)
- Neil D Rawlings
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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Hicks LD, Hyatt JL, Stoddard S, Tsurkan L, Edwards CC, Wadkins RM, Potter PM. Improved, selective, human intestinal carboxylesterase inhibitors designed to modulate 7-ethyl-10-[4-(1-piperidino)-1-piperidino]carbonyloxycamptothecin (Irinotecan; CPT-11) toxicity. J Med Chem 2009; 52:3742-52. [PMID: 19534556 DOI: 10.1021/jm9001296] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CPT-11 is an antitumor prodrug that is hydrolyzed by carboxylesterases (CE) to yield SN-38, a potent topoisomerase I poison. However, the dose limiting toxicity delays diarrhea that is thought to arise, in part, from activation of the prodrug by a human intestinal CE (hiCE). Therefore, we have sought to identify selective inhibitors of hiCE that may have utility in modulating drug toxicity. We have evaluated one such class of molecules (benzene sulfonamides) and developed QSAR models for inhibition of this protein. Using these predictive models, we have synthesized a panel of fluorene analogues that are selective for hiCE, demonstrating no cross reactivity to the human liver CE, hCE1, or toward human cholinesterases, and have K(i) values as low as 14 nM. These compounds prevented hiCE-mediated hydrolysis of the drug and the potency of enzyme inhibition correlated with the clogP of the molecules. These studies will allow the development and application of hiCE-specific inhibitors designed to selectively modulate drug hydrolysis in vivo.
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Affiliation(s)
- Latorya D Hicks
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105-2794, USA
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Frédérick R, Robert S, Charlier C, de Ruyck J, Wouters J, Pirotte B, Masereel B, Pochet L. 3,6-Disubstituted Coumarins as Mechanism-Based Inhibitors of Thrombin and Factor Xa. J Med Chem 2005; 48:7592-603. [PMID: 16302799 DOI: 10.1021/jm050448g] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, coumarins were screened on thrombin (THR) and factor Xa (FXa), two of the most promising targets for the development of anticoagulant drugs. This allowed us to highlight compound 30, characterized by a 2,5-dichlorophenyl ester in the 3-position and a chloromethyl moiety in the 6-position, as a very potent THR inhibitor (ki/KI= 37,000 M(-1) s(-1)). Moreover, this compound exhibits good selectivity over FXa (168-fold) and trypsin (54-fold). The mechanism of inactivation was investigated in this series and significantly differs from that previously observed with alpha-chymotrypsin. Indeed, the addition of hydrazine on the THR-inhibitor complex promotes a partial induced THR reactivation. This reactivation, confirmed by LC/MS, showed the resurgence of the native THR and a new dihydrazide complex. Docking experiments were then efficiently used to explain the trends observed in the enzymatic assays as well as to corroborate the postulated inhibition mechanism. Finally, the cell permeability of our derivatives was estimated using a computational approach.
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Affiliation(s)
- Raphaël Frédérick
- Department of Pharmacy and CBS Laboratory, University of Namur, FUNDP, 61, Rue de Bruxelles, B-5000 Namur, Belgium
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11
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Affiliation(s)
- W Bode
- Proteinase Research Group, Max-Planck-Institute of Biochemistry, Am Klopferspitz, Martinsried, Germany.
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Franke L, Byvatov E, Werz O, Steinhilber D, Schneider P, Schneider G. Extraction and Visualization of Potential Pharmacophore Points Using Support Vector Machines: Application to Ligand-Based Virtual Screening for COX-2 Inhibitors. J Med Chem 2005; 48:6997-7004. [PMID: 16250658 DOI: 10.1021/jm050619h] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Support vector machines (SVM) were trained to predict cyclooxygenase 2 (COX-2) and thrombin inhibitors. The classifiers were obtained using sets of known COX-2 and thrombin inhibitors as "positive examples" and a large collection of screening compounds as "negative examples". Molecules were encoded by topological pharmacophore-point triangles. In retrospective virtual screening, 50-90% of the known active compounds were listed within the first 0.1% of the ranked database. To check the validity of the constructed classifiers, we developed a method for feature extraction and visualization using SVM. As a result, potential pharmacophore points were weighted according to their importance for COX-2 and thrombin inhibition. Known thrombin and COX-2 pharmacophore points were correctly recognized by the machine learning system. In a prospective virtual screening study, several potential COX-2 inhibitors were predicted and tested in a cellular activity assay. A benzimidazole derivative exhibited significant inhibitory activity with an IC(50) of 0.2 microM, which is better than Celecoxib in our assay. It was demonstrated that the SVM machine-learning method can be used in virtual screening and be analyzed in a human-interpretable way that results in a set of rules for designing novel molecules.
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Affiliation(s)
- Lutz Franke
- Institut für Organische Chemie und Chemische Biologie and Institut für Pharmazeutische Chemie, Johann Wolfgang Goethe-Universität, Marie-Curie-Strasse 9, D-60439 Frankfurt, Germany
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13
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Srivastava S, Goswami LN, Dikshit DK. Progress in the design of low molecular weight thrombin inhibitors. Med Res Rev 2005; 25:66-92. [PMID: 15389730 DOI: 10.1002/med.20016] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intravascular thrombosis and its complication, embolism, is a leading cause of morbidity and mortality throughout the world. Past few decades have seen a great deal of progress in the development of antithrombotic agents, though the current treatment options are limited to heparin, LMW heparins, and warfarin. Detailed understanding of the biochemical and biophysical mechanisms of activation and regulation of blood coagulation have helped in developing specific inhibitors of enzymes, especially thrombin, within the coagulation cascade. Thrombin plays a central role in the coagulation cascade and so has become the primary target for the development of antithrombotic drugs. The review covers the main pharmacological aspects of haemostasis and thrombosis and provides an update on low molecular weight thrombin inhibitors along with the limitations of the prevalent antithrombotic agents. Recent developments in small molecule inhibitors of Protease Activated Receptor-1 (PAR-1) which can be helpful for the treatment of thrombotic and vascular proliferative disorders, have also been discussed.
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Affiliation(s)
- Stuti Srivastava
- Medicinal Chemistry Division, Central Drug Research Institute, Lucknow, India
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14
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Ilies MA, Supuran CT, Scozzafava A. Therapeutic applications of serine protease inhibitors. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.12.8.1181] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Markwardt F. Historical perspective of the development of thrombin inhibitors. PATHOPHYSIOLOGY OF HAEMOSTASIS AND THROMBOSIS 2004; 32 Suppl 3:15-22. [PMID: 12811007 DOI: 10.1159/000069104] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Progress in molecular biology has stimulated interest in the structure and function of thrombin. It has improved our understanding of its central role in thrombogenesis and has clarified the molecular events of inhibitor binding. This development has resulted in the production of recombinant hirudins and hirudin analogues. It has also allowed the molecular design of synthetic antithrombins, and encouraged the development of these products for clinical use. All pharmacological aspects speak in favor of the use of direct thrombin inhibitors as antithrombotic agents, especially in the potential indications where thrombin plays a crucial pathogenetic role. If their apparent advantages compared with heparin can be definitely demonstrated, the direct thrombin inhibitors may become the drug of choice for certain indications.
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Affiliation(s)
- Fritz Markwardt
- International Institute of Thrombosis and Vascular Diseases, Erfurt-Frienstedt, Germany.
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Ruppert C, Pucker C, Markart P, Schmidt R, Grimminger F, Seeger W, Stürzebecher J, Günther A. Selective inhibition of large-to-small surfactant aggregate conversion by serine protease inhibitors of the bis-benzamidine type. Am J Respir Cell Mol Biol 2003; 28:95-102. [PMID: 12495937 DOI: 10.1165/rcmb.4591] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Conversion of the biophysically active large surfactant aggregate subtype (LA) of alveolar surfactant into the less surface active small surfactant aggregates (SA) occurs in vivo and is reproduced under conditions of cyclic surface area changes in vitro. A serine-active carboxyl esterase has been suggested as the responsible enzymatic activity, although the exact mechanisms underlying the conversion process are presently unclear. We investigated the influence of exogenous serine proteases and synthetic and natural serine protease inhibitors on the conversion kinetics of natural rabbit surfactant, obtained as bronchoalveolar lavage fluid (BALF). In vitro cycling of BALF was performed for various time periods in the absence or presence of increasing amounts of several serine proteases (trypsin, plasmin, thrombin, tryptase), and one natural (aprotinin) and 25 synthetic serine protease inhibitors (including regular benzamidines [group A], 3-amidinophenylalanine derivatives [group B], bis-benzamidines [group C], and analogs of naphthylsulfonyl-glycyl-4-amidinophenylalanine piperidide [group D]). LA were separated from SA by 48,000 x g centrifugation. Surface activity of the LA fraction was measured by means of the pulsating bubble surfactometer. None of the "classical" serine proteases forwarded any acceleration of the LA-to-SA conversion kinetics. Some of the serine protease inhibitors caused moderate retardation of conversion, but at the same dose range inhibited the surface tension-lowering properties of the LA fraction, which per se explained their inhibitory effect. In contrast, specific dose-dependent inhibition of the LA-to-SA transition was observed for four derivatives of the bis-benzamidine group: full blockage of conversion over 240 min of cycling was noted at doses that did not interfere with the surface activity of the LA fraction. In addition, the prototype of these bis-benzamidines, 1,4-bis-[beta-naphthylsulfonyl-(3-aminophenylalanine)]-piperazide, was found to inhibit the activity of the rabbit liver carboxylesterase ES-2 in two different synthetic substrate assays reflecting the amidase and esterase properties of carboxylesterases. These findings support the hypothesis that the LA-to-SA conversion is an enzymatically-driven process with serine-active carboxyl esterase(s) being centrally involved. Synthetic bis-benzamidine-type serine protease inhibitors may offer specific inhibition of this event.
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Affiliation(s)
- Clemens Ruppert
- Department of Internal Medicine, Justus-Liebig-University Giessen, Germany
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Rauh D, Reyda S, Klebe G, Stubbs MT. Trypsin mutants for structure-based drug design: expression, refolding and crystallisation. Biol Chem 2002; 383:1309-14. [PMID: 12437122 DOI: 10.1515/bc.2002.148] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
New techniques in drug discovery are essential for the fast and efficient development of novel innovative drugs to deal with the challenges of the future. Structure determinations of various members of serine proteinases have provided a basis for computer-based drug design within this class of enzymes. In many proteins of interest, however, this course is blocked through a lack of suitable crystals. As a strategy for circumventing such problems, we have investigated the use of surrogate proteins for studying protein-ligand interactions. To test the feasibility of this approach, we have chosen bovine trypsin as a scaffold to reconstruct the ligand binding site of factor Xa. The simple modular design of trypsin, its readiness to crystallise and straightforward handling lends itself to such drug design by proxy. The expression, folding, purification, crystallographic and kinetic characterisation of bovine trypsin forms with factor Xa phenotype are presented.
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Affiliation(s)
- Daniel Rauh
- Institut für Pharmazeutische Chemie der Philipps-Universität Marburg, Germany
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Hauptmann J, Steinmetzer T, Vieweg H, Wikström P, Stürzebecher J. Influence of structural variations in peptidomimetic 4-amidinophenylalanine-derived thrombin inhibitors on plasma clearance and biliary excretion in rats. Pharm Res 2002; 19:1027-33. [PMID: 12180535 DOI: 10.1023/a:1016426724831] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
PURPOSE Systemic and hepato-biliary clearance of peptidomimetic thrombin inhibitors of the 4-amidinophenylalanine amide-type, derived from NAPAP (Nalpha-[2-naphthylsulfonyl-glycyl]-4-amidinophenylalanine-piperidide) by substituting Gly in P2 for natural and unnatural amino acids or by varying the C- and N-terminal moieties. resp., were investigated. METHODS Concentrations of the compounds administered as intravenous bolus injection at a dose of 1 mg/kg to bile duct-cannulated rats were determined in plasma and bile samples collected over 4 hours using reversed-phase HPLC. RESULTS NAPAP and the derivatives with additional charged groups are comparatively hydrophilic compounds. For NAPAP and most of the derivatives the biliary clearance accounted for a high percentage of the rapid systemic plasma clearance. Derivatives 2a-c with a second basic group in P2 position showed lower systemic and biliary clearance compared to NAPAP, whereas their cumulative biliary excretion after a period of 120 min was less affected. Bis-benzamidine derivatives 4a and 5 with the second amidino group in the N-terminal moiety had the lowest biliary clearance. Additional carboxylic groups reduced the systemic and biliary clearance only as free amidinophenylalanine carboxyl in 3a and 5. No influence compared to NAPAP was observed for 2d with a free carboxyl group in P2 position. CONCLUSIONS The weak correlation of the log P values of the compounds with the clearance parameters indicates the influence of structural variations, especially of charged groups, in this series of compounds rather than overall lipophilicity on hepato-biliary elimination mediated by hepatocellular transporters.
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Affiliation(s)
- Jörg Hauptmann
- Center for Vascular Biology and Medicine, Friedrich Schiller University Jena, Erfurt, Germany
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Cozzini P, Fornabaio M, Marabotti A, Abraham DJ, Kellogg GE, Mozzarelli A. Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water. J Med Chem 2002; 45:2469-83. [PMID: 12036355 DOI: 10.1021/jm0200299] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prediction of the binding affinity between a protein and ligands is one of the most challenging issues for computational biochemistry and drug discovery. While the enthalpic contribution to binding is routinely available with molecular mechanics methods, the entropic contribution is more difficult to estimate. We describe and apply a relatively simple and intuitive calculation procedure for estimating the free energy of binding for 53 protein-ligand complexes formed by 17 proteins of known three-dimensional structure and characterized by different active site polarity. HINT, a software model based on experimental LogP(o/w) values for small organic molecules, was used to evaluate and score all atom-atom hydropathic interactions between the protein and the ligands. These total scores (H(TOTAL)), which have been previously shown to correlate with DeltaG(interaction) for protein-protein interactions, correlate with DeltaG(binding) for protein-ligand complexes in the present study with a standard error of +/-2.6 kcal mol(-1) from the equation DeltaG(binding) = -0.001 95 H(TOTAL) - 5.543. A more sophisticated model, utilizing categorized (by interaction class) HINT scores, produces a superior standard error of +/-1.8 kcal mol(-1). It is shown that within families of ligands for the same protein binding site, better models can be obtained with standard errors approaching +/-1.0 kcal mol(-1). Standardized methods for preparing crystallographic models for hydropathic analysis are also described. Particular attention is paid to the relationship between the ionization state of the ligands and the pH conditions under which the binding measurements are made. Sources and potential remedies of experimental and modeling errors affecting prediction of DeltaG(binding) are discussed.
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Affiliation(s)
- Pietro Cozzini
- Department of General and Inorganic Chemistry, Department of Biochemistry and Molecular Biology, National Institute for the Physics of Matter, University of Parma, 43100 Parma, Italy
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Steinmetzer T, Schweinitz A, Künzel S, Wikström P, Hauptmann J, Stürzebecher J. Structure-activity relationships of new NAPAP-analogs. JOURNAL OF ENZYME INHIBITION 2002; 16:241-9. [PMID: 11697044 DOI: 10.1080/14756360109162372] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Several new analogs of the known thrombin inhibitor NAPAP were synthesized, in which the P2 glycine residue was substituted by natural and unnatural amino acids. The thrombin inhibitory potency was comparable to that of NAPAP. Several of the compounds had inhibition constants lower than 10 nM and a very high selectivity compared to trypsin, factor Xa and plasmin. In addition, analogs were prepared by alkylation of the N alpha-atom of the 4-amidinophenylalanine in P1 position, which showed a more than 10-fold lower thrombin inhibition. Furthermore, azaglycine was introduced instead of P2 glycine. For most of the inhibitors similar fast elimination rates were seen in rats after intravenous dosing, as found previously for NAPAP. Only some compounds, which contained a second basic group showed a slightly decreased cumulative biliary clearance.
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Affiliation(s)
- T Steinmetzer
- Inst. of Biochemistry & Biophysics, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
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22
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Linusson A, Gottfries J, Olsson T, Ornskov E, Folestad S, Nordén B, Wold S. Statistical molecular design, parallel synthesis, and biological evaluation of a library of thrombin inhibitors. J Med Chem 2001; 44:3424-39. [PMID: 11585448 DOI: 10.1021/jm010833f] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A library of thrombin inhibitors has been designed using statistical molecular design. An aromatic scaffold was used, with three varied positions corresponding to three pockets at the active site of thrombin (the S-, P-, and D-pockets). The selection was performed in the building block space, and previously acquired data were included in the design procedure. The design resulted in six, four, and six building blocks for the first (S), second (P), and third (D) pockets, respectively. A second round of selection applied to the combined selected building blocks resulted in a subset of 18 compounds. The selected library was synthesized in parallel and biologically evaluated. The compounds were analyzed with respect to their inhibition (pIC(50)) of thrombin; membrane permeability, estimated by migration behavior in micellar media (CE log k') and pK(a); and specificity with respect to inhibition (K(i)) of trypsin. Multivariate QSAR studies of the responses yielded valuable results and information that could only be found using statistical molecular design in combination with multivariate analysis.
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Affiliation(s)
- A Linusson
- AstraZeneca R&D Mölndal, S-431 83 Mölndal, Sweden.
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Steinmetzer T, Hauptmann J, Sturzebecher J. Advances in the development of thrombin inhibitors. Expert Opin Investig Drugs 2001; 10:845-64. [PMID: 11322862 DOI: 10.1517/13543784.10.5.845] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Thromboembolic diseases are a major cause of morbidity and mortality, particularly in the Western world, which has stimulated enormous research efforts by the pharmaceutical industry to introduce new antithrombotic therapies. One strategy is the development of direct inhibitors of the serine protease thrombin, which holds a central position in the final steps of the blood coagulation cascade and in platelet activation. At present there is only limited clinical use of some parenteral preparations of thrombin inhibitors in acute situations, especially when the common antithrombotic drugs heparin, warfarin and aspirin are ineffective or associated with side effects. However, for use in prophylaxis of thrombotic diseases such inhibitors should be orally available, must be safe to avoid bleeding complications and should have an appropriate half-life, allowing once or twice daily dosing to maintain adequate antithrombotically effective blood levels. Details of several new and potent thrombin inhibitors have been published during the last years. For some of them oral bioavailability is claimed and they are effective in in vitro coagulation assays. However, most of them showed only limited efficacy in animal studies with respect to the doses administered. For that reason, effort is concentrated on the evaluation and optimisation of the overall physicochemical characteristics of the inhibitors in order to improve the pharmacokinetics and, thus, the development of promising drug candidates. Nevertheless, only careful clinical studies can give clear answers about the true therapeutical benefit of new developments in this field. This review summarises the current status of direct thrombin inhibitors which are already in clinical use and clinical development and gives an overview on recently published and promising new compounds.
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Supuran CT, Briganti F, Scozzafava A, Ilies MA. Protease inhibitors: Part 4. Synthesis of weakly basic thrombin inhibitors incorporating pyridinium-sulfanilylaminoguanidine moieties. JOURNAL OF ENZYME INHIBITION 2001; 15:335-56. [PMID: 10995066 DOI: 10.1080/14756360009040692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Three series of derivatives have been prepared by reaction of sulfanilylaminoguanidine with pyrylium salts, with the pyridinium derivatives of glycine and with the pyridinium derivatives of beta-alanine, respectively. The new compounds were assayed as inhibitors of two serine proteases, thrombin and trypsin. The study showed that in contrast to the leads, possessing KI's around 100-300 nM against thrombin, and 450-1420 nM against trypsin, respectively, the new derivatives showed inhibition constants in the range of 15-50 nM against thrombin, whereas their affinity for trypsin remained relatively low. Derivatives of beta-alanine were more active than the corresponding glycine derivatives, which in turn were more inhibitory than the pyridinium derivatives of sulfanilylaminoguanidine possessing the same substitution pattern at the pyridinium ring. Thus, the present study proposes two novel approaches for the preparation of high affinity, specific thrombin inhibitors: a novel S1 anchoring moiety in the already large family of arginine/amidine-based inhibitors, i.e., the SO2NHNHC(=NH)NH2 group, and novel non-peptidomimetic scaffolds obtained by incorporating alkyl-/aryl-substituted-pyridinium moieties in the hydrophobic binding site(s). The first one is important for obtaining bioavailable thrombin inhibitors, devoid of the high basicity of the commonly used arginine/amidine-based inhibitors, whereas the second one may lead to improved water solubility of such compounds.
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Affiliation(s)
- C T Supuran
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Florence, Italy.
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Clare BW, Scozzafava A, Briganti F, Iorga B, Supuran CT. Protease inhibitors. Part 2. Weakly basic thrombin inhibitors incorporating sulfonyl-aminoguanidine moieties as S1 anchoring groups: synthesis and structure-activity correlations. JOURNAL OF ENZYME INHIBITION 2000; 15:235-64. [PMID: 10811030 DOI: 10.3109/14756360009040686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Two series of derivatives have been prepared and assayed as inhibitors of two physiologically relevant serine proteases, human thrombin and human trypsin. The first series includes alkyl-/ aralkyl-/aryl- and hetarylsulfonyl-aminoguanidines. It was thus observed that sulfanilyl-aminoguanidine possesses moderate but intrinsically selective thrombin inhibitory properties, with KI values around 90 and 1400 nM against thrombin and trypsin respectively. Further elaboration of this molecule afforded compounds that inhibited thrombin with KI values in the range 10-50 nM, whereas affinity for trypsin remained relatively low. Such compounds were obtained either by attaching benzyloxycarbonyl- or 4-toluenesulfonylureido-protected amino acids (such as D-Phe, L-Pro) or dipeptides (such as Phe-Pro, Gly His, beta-Ala-His or Pro-Gly) to the N-4 atom of the lead molecule, sulfanilyl-aminoguanidine, or by attaching substituted-pyridinium propylcarboxamido moieties to this lead. Thus, this study brings novel insights regarding a novel non-basic S1 anchoring moiety (i.e., SO2NHNHC(=NH)NH2), and new types of peptidomimetic scaffolds obtained by incorporating tosylureido-amino acids/pyridinium-substituted-GABA moieties in the hydrophobic binding site(s). Structure-activity correlations of the new serine protease inhibitors are also discussed based on a QSAR model described previously for a large series of structurally-related derivatives (Supuran et al. (1999) J. Med. Chem., in press).
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Affiliation(s)
- B W Clare
- Division of Science, Murdoch University, Perth, W.A., Australia.
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26
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Supuran CT, Scozzafava A, Briganti F, Clare BW. Protease inhibitors: synthesis and QSAR study of novel classes of nonbasic thrombin inhibitors incorporating sulfonylguanidine and O-methylsulfonylisourea moieties at P1. J Med Chem 2000; 43:1793-806. [PMID: 10794696 DOI: 10.1021/jm9903693] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using benzamidine as a lead molecule, two series of alkyl/aralkyl/arylsulfonylguanidines/sulfonyl-O-methylisoureas+ ++ have been prepared and assayed as inhibitors of two serine proteases, thrombin and trypsin. The study showed that sulfaguanidine and its corresponding O-methylisourea derivative possess moderate but intrinsically selective thrombin inhibitory properties, with K(I)'s around 100 nM against thrombin and 1350-1500 nM against trypsin. Further elaboration of these two molecules afforded compounds that inhibited thrombin with K(I)'s in the range of 12-50 nM, whereas affinity for trypsin remained relatively low. Such compounds were obtained by attaching benzyloxycarbonyl- or 4-toluenesulfonylureido-protected amino acids (such as L- and D-Phe or L-Pro) or dipeptides (such as Phe-Pro, Gly-His, beta-Ala-His, or Pro-Gly) to the two leads mentioned above, sulfaguanidine and 4-aminobenzenesulfonyl-O-methylisourea. Thus, the present study proposes two novel approaches for the preparation of high-affinity, specific thrombin inhibitors: two novel S1 anchoring moieties in the already large family of arginine/amidine-based inhibitors and novel peptidomimetic scaffolds obtained by incorporating tosylureido amino acids in the hydrophobic binding site(s). The first one is important for obtaining bioavailable thrombin inhibitors, devoid of the high basicity of the commonly used arginine/amidine-based inhibitors, whereas the second one may lead to improved water solubility of such compounds due to facilitated metal (sodium) salts formation (at the relatively acidic SO(2)NHCO protons) as well as increased stability at hydrolysis (in vivo). A QSAR study also explained the activity in terms of global properties of the molecules, electronic properties of the sulfonylguanidine/sulfonylisourea moiety, and novel descriptors, the frontier orbital phase angles (FOPA), that account for the directions of the nodes in the pi orbitals in the aromatic portion of those of the drugs in which the sulfonyl group was bound to a benzene ring. For thrombin inhibition, the size of the molecule was the dominant influence, while for trypsin inhibition the FOPA was the principal determinant of activity. The dependence of activity on the FOPA variables is perhaps the clearest example of a quantum effect in pharmacology and suggests a promising new tool for drug design.
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Affiliation(s)
- C T Supuran
- Laboratorio di Chimica Inorganica e Bioinorganica, Università degli Studi, Via Gino Capponi 7, I-50121 Florence, Italy.
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27
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Wiley MR, Weir LC, Briggs S, Bryan NA, Buben J, Campbell C, Chirgadze NY, Conrad RC, Craft TJ, Ficorilli JV, Franciskovich JB, Froelich LL, Gifford-Moore DS, Goodson T, Herron DK, Klimkowski VJ, Kurz KD, Kyle JA, Masters JJ, Ratz AM, Milot G, Shuman RT, Smith T, Smith GF, Tebbe AL, Tinsley JM. Structure-based design of potent, amidine-derived inhibitors of factor Xa: evaluation of selectivity, anticoagulant activity, and antithrombotic activity. J Med Chem 2000; 43:883-99. [PMID: 10715155 DOI: 10.1021/jm9903287] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To enhance the potency of 1,2-dibenzamidobenzene-derived inhibitors of factor Xa (fXa), an amidine substituent was incorporated on one of the benzoyl side chains to interact with Asp189 in the S1 specificity pocket. Lead molecule 1 was docked into the active site of fXa to facilitate inhibitor design. Subsequently, iterative SAR studies and molecular modeling led to a 1000-fold increase in fXa affinity and a refined model of the new inhibitors in the fXa active site. Strong support for the computational model was achieved through the acquisition of an X-ray crystal structure using thrombin as a surrogate protein. The amidines in this series show high levels of selectivity for the inhibition of fXa relative to other trypsin-like serine proteases. Furthermore, the fXa affinity of compounds in this series (K(ass) = 50-500 x 10(6) L/mol) translates effectively into both anticoagulant activity in vitro and antithrombotic activity in vivo.
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Affiliation(s)
- M R Wiley
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA.
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28
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Brundish D, Bull A, Donovan V, Fullerton JD, Garman SM, Hayler JF, Janus D, Kane PD, McDonnell M, Smith GP, Wakeford R, Walker CV, Howarth G, Hoyle W, Allen MC, Ambler J, Butler K, Talbot MD. Design and synthesis of thrombin inhibitors: analogues of MD-805 with reduced stereogenicity and improved potency. J Med Chem 1999; 42:4584-603. [PMID: 10579821 DOI: 10.1021/jm9811209] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitsubishi's MD-805, a potent and selective inhibitor of thrombin which contains four stereogenic centers, has been the starting point for an optimization program. A systematic synthetic study resulted in thrombin inhibitors achiral at P2 and P3 but with a 10-fold increase in potency over the original lead. A number of 4-substituted piperidines were synthesized and examined as replacements for 2-carboxy-4-methylpiperidine at P2; 4-fluoroethylpiperidine (FEP) among others provided inhibitors (e.g. 45g) of increased potency. An enantioselective route was developed to 3(R)-methyl-1,2,3,4-tetrahydroquinolinesulfonyl chloride. Inhibitors containing this enantiomerically pure P3 (42d) had similar potency to the racemic material and provided support, with modeling studies, for the preparation of the gem 3,3-disubstituted compounds. A series of inhibitors containing the novel 3, 3-dimethyl-1,2,3,4-tetrahydroquinolinesulfonyl (DMTHQS) P3 (Table 5) were synthesized and showed a similar activity profile as the monomethyl series. The combination of P3-DMTHQS, P2-FEP, and P1-arginine (45g) had a K(i) of 6 nM (MD-805 K(i) = 85 nM). In animal models of both venous and arterial thrombosis, one inhibitor (42e) was shown to produce a dose-dependent inhibition of thrombus formation that in some situations was superior to that of MD-805.
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Affiliation(s)
- D Brundish
- Department of Chemistry, Drug Discovery Support, Novartis Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex RH12 5AB, U.K
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29
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Scozzafava A, Briganti F, Supuran CT. Protease inhibitors - Part 3. Synthesis of non-basic thrombin inhibitors incorporating pyridinium-sulfanilylguanidine moieties at the P1 site. Eur J Med Chem 1999; 34:939-952. [PMID: 10889318 DOI: 10.1016/s0223-5234(99)00115-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using benzamidine and sulfaguanidine as lead molecules, three series of derivatives have been prepared by reaction of sulfaguanidine with pyrylium salts, with the pyridinium derivatives of glycine and with the pyridinium derivatives of beta-alanine, respectively. The new compounds were assayed as inhibitors of two serine proteases, thrombin and trypsin. The study showed that in contrast to the leads, possessing K(I)'s around 100-300 nM against thrombin, and 1200-1500 nM against trypsin, respectively, the new derivatives showed inhibition constants in the range of 15-50 nM against thrombin, whereas their affinity for trypsin remained relatively low. Derivatives of beta-alanine were more active than the corresponding Gly derivatives, which in turn were more inhibitory than the pyridinium derivatives of sulfaguanidine possessing the same substitution pattern at the pyridinium ring. Thus, the present study proposes two novel approaches for the preparation of high affinity, specific thrombin inhibitors: a novel S1 anchoring moiety in the already large family of arginine/amidine-based inhibitors, i.e., the SO(2)N=C(NH(2))(2) group, and novel non-peptidomimetic scaffolds obtained by incorporating alkyl-/aryl-substituted-pyridinium moieties in the hydrophobic binding site(s). The first one is important for obtaining bioavailable thrombin inhibitors, devoid of the high basicity of the commonly used arginine/amidine-based inhibitors, whereas the second one may lead to improved water solubility of such compounds due to facilitated salt formation as well as increased stability at hydrolysis (in vivo).
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Affiliation(s)
- A Scozzafava
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Via Gino Capponi 7, I-50121, Florence, Italy
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30
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Hoffmann D, Kramer B, Washio T, Steinmetzer T, Rarey M, Lengauer T. Two-stage method for protein-ligand docking. J Med Chem 1999; 42:4422-33. [PMID: 10543886 DOI: 10.1021/jm991090p] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A two-stage method for the computational prediction of the structure of protein-ligand complexes is proposed. Given an experimentally determined structure of the protein, in the first stage a large number of plausible ligand conformations is generated using the fast docking algorithm FlexX. In the second stage these conformations are minimized and reranked using a method based on a classical force field. The two-stage method is tested for 10 different protein-ligand complexes. For 9 of them experimentally determined structures are known. It turns out that the two-stage method strongly improves the predictive power as compared to that of the fast docking stage alone. The tenth case is a bona fide prediction of a complex of thrombin with a new inhibitor for which no experimentally determined structure is available so far.
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Affiliation(s)
- D Hoffmann
- German National Research Center for Information Technology, Institute for Algorithms and Scientific Computing (GMD-SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany.
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31
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Steinmetzer T, Renatus M, Künzel S, Eichinger A, Bode W, Wikström P, Hauptmann J, Stürzebecher J. Design and evaluation of novel bivalent thrombin inhibitors based on amidinophenylalanines. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 265:598-605. [PMID: 10504391 DOI: 10.1046/j.1432-1327.1999.00742.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two bivalent thrombin inhibitors were synthesized, which consist of a benzamidine-based active-site-blocking segment, a fibrinogen recognition exosite inhibitor and a peptidic linker connecting these fragments. BZA-1 hirulog contains an Nalpha-(2-naphthylsulfonyl)-S-3-amidinophenylalanyl-is onipecotic acid residue connected via the carboxyl group to the linker segment. The active-site-directed moiety of BZA-2 hirulog [Nalpha-(2-naphthylsulfonyl-glutamyl)-R-4-amidinophenylal anyl-piperid ide] was coupled to the linker via the side chain of the glutamic acid. Both BZA-hirulogs contain almost identical linker-exo site inhibitor parts, except for the substitution of a glycine as the first linker residue in BZA-1 hirulog by a gamma-amino butyric acid in BZA-2 hirulog, thus increasing flexibility and linker length by two additional atoms. BZA-1 hirulog showed moderate potency (Ki = 0. 50 +/- 0.14 nM), while BZA-2 hirulog was characterized as a slow, tight binding inhibitor of thrombin (Ki = 0.29 +/- 0.08 pM). The stability in human plasma of both analogs was strongly improved compared with hirulog-1. For BZA-2 hirulog a significantly reduced plasma clearance was observed after intravenous injection in rats compared with BZA-1 hirulog and hirulog-1. The X-ray structure of the BZA-2 hirulog in complex with human alpha-thrombin was solved and confirmed the expected bivalent binding mode.
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Affiliation(s)
- T Steinmetzer
- Friedrich-Schiller-Universität, Institut für Biochemie & Biophysik, Jena, Germany.
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32
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33
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Steinmetzer T, Batdorsdhjin M, Kleinwächter P, Seyfarth L, Greiner G, Reissmann S, Stürzebecher J. New thrombin inhibitors based on D-cha-Pro-derivatives. JOURNAL OF ENZYME INHIBITION 1999; 14:203-16. [PMID: 10445044 DOI: 10.3109/14756369909030317] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A series of new analogs with modifications in the C-terminal residue were prepared based on the known thrombin inhibitor D-Phe-Pro-agmatine. These include several compounds alkylated at the N delta-, N omega- and N omega'-atoms of the guanidino group and a number of inhibitors derived from commercially available diamines. All analogs with alkylation of the guanidino group showed very poor activity. In contrast, the most potent and selective inhibitor with a cyclic and basic residue in the P1-position was found to be Ph-CH2-SO2-D-Cha-Pro-4-(amidomethyl) amidinopiperidine 11 with a Ki of 0.27 nM. In addition, a number of compounds were synthesized, in which the basic amidino group of the P1-residue was replaced by a hydroxyl group. Although the inhibition constants of these phenol derivatives showed still remarkable potency (16, Ki = 130 nM), their activity in clotting assays was strongly reduced.
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Affiliation(s)
- T Steinmetzer
- Inst. of Biochemistry & Biophysics, Friedrich Schiller University, Jena, Germany.
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34
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Li M, Lin Z, Johnson ME. Structure-based design and synthesis of novel thrombin inhibitors based on phosphinic peptide mimetics. Bioorg Med Chem Lett 1999; 9:1957-62. [PMID: 10450962 DOI: 10.1016/s0960-894x(99)00319-4] [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: 10/27/2022]
Abstract
Based on the structure of the thrombin--NAPAP complex, phosphinic dipeptide mimetics were designed as novel thrombin inhibitors. Synthesis and evaluation of these inhibitors revealed a promising lead with an IC50 of 0.6 microM.
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Affiliation(s)
- M Li
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry & Pharmacognosy, University of Illinois at Chicago, 60607-7173, USA
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35
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Buijsman RC, Basten JE, van Dinther TG, van der Marel GA, van Boeckel CA, van Boom JH. Design and synthesis of a novel synthetic NAPAP-penta-saccharide conjugate displaying a dual antithrombotic action. Bioorg Med Chem Lett 1999; 9:2013-8. [PMID: 10450972 DOI: 10.1016/s0960-894x(99)00320-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The synthesis of a novel antithrombotic consisting of a heparin pentasaccharide conjugated to the active site inhibitor N-(2-naphtalenesulfonyl)-glycyl-(D)-4-aminophenyl-alanyl-piperidin e (NAPAP) (i.e. compound I) is reported. This conjugate shows a unique pharmacological profile both in vitro and in vivo having direct anti-thrombin and ATIII-mediated anti-Xa activity. Furthermore, conjugate I has a prolonged in vivo half-life compared to NAPAP (1.5 h vs 9 min.).
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Affiliation(s)
- R C Buijsman
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
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36
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Zhou Y, Johnson ME. Comparative molecular modeling analysis of-5-amidinoindole and benzamidine binding to thrombin and trypsin: specific H-bond formation contributes to high 5-amidinoindole potency and selectivity for thrombin and factor Xa. J Mol Recognit 1999; 12:235-41. [PMID: 10440994 DOI: 10.1002/(sici)1099-1352(199907/08)12:4<235::aid-jmr460>3.0.co;2-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The coagulation cascade enzymes thrombin and factor Xa are known to have specificity pockets very similar to those of trypsin and plasmin. However, comparative molecular modeling analysis of the crystal structures of benzamidine-thrombin and benzamidine-trypsin, in conjunction with a docking analysis of 5-amidinoindole and related inhibitors in both enzymes reveals subtle differences between the specificity sites of the two types of enzymes. Specifically, thrombin and factor Xa, which have an alanine residue at position 190, exhibit increased activities for the rigid and more bulky bicyclic derivatives of benzamidine (e.g. amidinobenzofuran, amidinothiophene and amidinoindole), because of additional hydrophobic and H-bond interactions between the inhibitors and the specificity sites, whereas enzymes with a serine residue at position 190, like trypsin and plasmin, exhibit little difference in activity among the same set of compounds because of the orientational restriction imposed on the inhibitors by Ser190, which forms an additional H-bond with the amidino group of the inhibitors. Enzymes of both groups show similar responses to the flexible aminobenzamidine since the smaller size and the rotatable anilino group of the inhibitor would allow the inhibitor to achieve favorable electrostatic interactions with both groups of enzymes. 5-amidinoindole is the most dramatic example of the rigid bicyclic type inhibitor. Based on our docking analysis, we propose that a selective H-bond with the hydroxyl group of the catalytic Ser195 and the subtle differences in steric fit imposed by Ala/Ser at position 190 explain the high potency and selectivity of 5-amidinoindole for thrombin and factor Xa.
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Affiliation(s)
- Y Zhou
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood St (m/c 874), Chicago, IL 60612-7230, USA
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37
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Rewinkel JB, Lucas H, van Galen PJ, Noach AB, van Dinther TG, Rood AM, Jenneboer AJ, van Boeckel CA. 1-Aminoisoquinoline as benzamidine isoster in the design and synthesis of orally active thrombin inhibitors. Bioorg Med Chem Lett 1999; 9:685-90. [PMID: 10201829 DOI: 10.1016/s0960-894x(99)00069-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Replacement of the highly basic benzamidine moiety of NAPAP by the moderately basic 1-aminoisoquinoline moiety resulted in thrombin inhibitors with improved selectivity towards trypsin and enhanced Caco-2 cell permeability.
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Affiliation(s)
- J B Rewinkel
- NV Organon, Scientific Development Group, Oss, The Netherlands
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38
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Abstract
Thrombin and factor Xa (fXa) are the only serine proteases for which small, potent, selective, noncovalent inhibitors have been developed, which are ultimately intended as drug development candidates (in this case as anticoagulants). Noncovalent inhibitors may be more selective and chemically and metabolically less reactive than covalent inhibitors. In addition, noncovalent inhibitors are more likely to have fast-binding kinetics which is particularly important in the development of thrombin inhibitors. TAME derived noncovalent thrombin inhibitors argatroban, napsagatran, and UK 156,406 have entered clinical trials as anticoagulants, the latter as an orally active agent. Serine trap deletion from substrate-like peptides led to the development of inogatran and melagatran, both of which have entered clinical trials as intravenous agents. The use of 3-aminopyridinone and pyrazinone acetamide peptidomimetic templates has resulted in the development of L-375,378 which has been chosen for clinical development as an orally active anticoagulant. Recently, compounds which do not have the conventional hydrogen bonding capabilities of peptides have begun to appear in the thrombin literature. Publications on noncovalent fXa inhibitors cover this type of peptidomimetic almost exclusively.
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Affiliation(s)
- P E Sanderson
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA
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39
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The development of novel noncovalent thrombin inhibitors. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1874-5113(99)80004-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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40
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Renatus M, Bode W, Huber R, Stürzebecher J, Stubbs MT. Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: implications for the inhibition of factor Xa, tPA, and urokinase. J Med Chem 1998; 41:5445-56. [PMID: 9876114 DOI: 10.1021/jm981068g] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The trypsin-like serine proteinase superfamily contains a number of potential therapeutic targets, many of which are unsuitable for routine X-ray crystallographic studies. We have cocrystallized a selection of benzamidine-based inhibitors with bovine trypsin and solved their structures to a resolution of up to 1.7 A. Despite similar chemical formulas, the inhibitors exhibit a range of diverse binding modes that reflect their inhibitory spectra against the serine proteinases trypsin, thrombin, factor Xa, tissue-type plasminogen activator (tPA) and urokinase (uPA). In contrast to the compact folded conformations of thrombin inhibitors which allow optimal binding in the well-defined hydrophobic S2/S4 pocket of thrombin, those effective against factor Xa exhibit an extended conformation that allows occupation of the S3/S4 region, where hydrophobic and electrostatic interactions can stabilize the conformation. One group of inhibitors containing an N-terminal 2,4, 6-triisopropylphenylsulfonyl (TIPPS) moiety show little or no penetration into the S3/S4 subsites of trypsin. These latter sites are occluded in uPA, explaining why this class of compounds is effective against uPA. Despite presenting an extensive hydrophobic surface toward the solvent, the Ki values for TIPPS-containing compounds against trypsin is in the range 10(-7) to 10(-8) M. Comparison of the binding of a bis-benzamidine inhibitor in trypsin and tPA indicate that a shift in potency can be induced by relatively minor changes in binding mode. Implications for the inhibition of these proteinases are discussed.
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Affiliation(s)
- M Renatus
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany
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41
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Kent DR, Cody WL, Doherty AM. The asymmetric synthesis of arginine mimetics: derivatives of (S)-2-, 3- and 4-amidinophenylalanine suitable for incorporation into enzyme inhibitors and/or peptides. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1998; 52:201-7. [PMID: 9774233 DOI: 10.1111/j.1399-3011.1998.tb01477.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The specific inhibition of trypsin-like serine proteases has become an important therapeutic target. These proteases have been implicated in several physiological and pathophysiological processes, including blood coagulation, digestion, and inflammation. Proteases of this class cleave polypeptide chains C-terminal to a basic residue (arginine or lysine). It has been shown that selectivity for a particular serine protease can be conferred based upon the structural moiety incorporated in the P1 position. In this regard, the three isomers (ortho, meta, and para) of amidinophenylalanine represent modified arginine residues and are important synthetic targets. Herein, a convenient asymmetric synthesis of (S)-Nalpha-(tert-butyloxycarbonyl)-2-, (S)-Nalpha-(tert-butyloxycarbonyl)-3-, and (S)-Nalpha-(tert-butyloxycarbonyl)-4-amidinophenyl-alanine N,O-dimethylamides (Weinreb amides) will be described. These derivatives represent key synthetic intermediates for the synthesis of enzyme inhibitors because the amidine can be readily orthogonally protected, while the Weinreb amide is easily converted to a variety of electrophilic carbonyls via reduction to the corresponding aldehyde or by reaction with various lithiated heterocycles. Likewise, the Weinreb amide can be reduced to the aldehyde and subsequently oxidized to the corresponding carboxylate, which is suitable for solid- or solution-phase peptide synthetic strategies.
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Affiliation(s)
- D R Kent
- Parke-Davis Pharmaceutical Research, Division of Warner-Lambert Company, Ann Arbor, Michigan 48105, USA
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42
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Dumas D, Leclerc G, Baldwin JJ, Lewis SD, Murcko M, Naylor-Olsen AM. Design, syntheses, and activity of new 3-[(sulfonylaryl)-amino]-1,4-benzodiazepin-2-one derivatives as α-thrombin inhibitors. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(98)80048-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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43
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De Simone G, Lombardi A, Galdiero S, Nastri F, Della Morte R, Staiano N, Pedone C, Bolognesi M, Pavone V. Hirunorms are true hirudin mimetics. The crystal structure of human alpha-thrombin-hirunorm V complex. Protein Sci 1998; 7:243-53. [PMID: 9521099 PMCID: PMC2143932 DOI: 10.1002/pro.5560070203] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A novel class of synthetic, multisite-directed thrombin inhibitors, known as hirunorms, has been described recently. These compounds were designed to mimic the binding mode of hirudin, and they have been proven to be very strong and selective thrombin inhibitors. Here we report the crystal structure of the complex formed by human alpha-thrombin and hirunorm V, a 26-residue polypeptide containing non-natural amino acids, determined at 2.1 A resolution and refined to an R-factor of 0.176. The structure reveals that the inhibitor binding mode is distinctive of a true hirudin mimetic, and it highlights the molecular basis of the high inhibitory potency (Ki is in the picomolar range) and the strong selectivity of hirunorm V. Hirunorm V interacts through the N-terminal tetrapeptide with the thrombin active site in a nonsubstrate mode; at the same time, this inhibitor specifically binds through the C-terminal segment to the fibrinogen recognition exosite. The backbone of the N-terminal tetrapeptide Chg1"-Val2"-2-Nal3"-Thr4" (Chg, cyclohexyl-glycine; 2-Nal, beta-(2-naphthyl)-alanine) forms a short beta-strand parallel to thrombin main-chain residues Ser214-Gly219. The Chg1" side chain fills the S2 subsite, Val2" is located at the entrance of S1, whereas 2-Nal3" side chain occupies the aryl-binding site. Such backbone orientation is very close to that observed for the N-terminal residues of hirudin, and it is similar to that of the synthetic retro-binding peptide BMS-183507, but it is opposite to the proposed binding mode of fibrinogen and of small synthetic substrates. Hirunorm V C-terminal segment binds to the fibrinogen recognition exosite, similarly to what observed for hirudin C-termninal tail and related compounds. The linker polypeptide segment connecting hirunorm V N-and C-terminal regions is not observable in the electron density maps. The crystallographic analysis proves the correctness of the design and it provides a compelling proof on the interaction mechanism for this novel class of high potency multisite-directed synthetic thrombin inhibitors.
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Affiliation(s)
- G De Simone
- Centro Interuniversitario di Ricerca su Peptidi Bioattivi, & Centro di Studio di Biocristallografia-CNR, University of Napoli Federico II, Italy
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44
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Stürzebecher J, Prasa D, Hauptmann J, Vieweg H, Wikström P. Synthesis and structure-activity relationships of potent thrombin inhibitors: piperazides of 3-amidinophenylalanine. J Med Chem 1997; 40:3091-9. [PMID: 9301673 DOI: 10.1021/jm960668h] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Thrombin is the key enzyme in the blood coagulation system, and inhibitors of its proteolytic activity are of therapeutic interest since they are potential anticoagulants. The most potent inhibitor of the benzamidine type is N alpha-[(2-naphthylsulfonyl)glycyl]-4-amidinophenylalanylpiperid ide (NAPAP). However, NAPAP and other benzamidine derivatives do not show favorable pharmacological properties; above all, they have very low systemic bioavailability after oral administration. The goal of designing new compounds was to obtain potent inhibitors with improved pharmacokinetic properties. Piperazide derivatives of 3-amidinophenylalanine as the key building block were synthesized. The piperazine moiety opened the possibility to introduce quite different substituents on the second nitrogen using common synthetic procedures. Some of the newly synthesized compounds are potent inhibitors of thrombin and offer an approach to study structure-function relationships for inhibition of thrombin and related enzymes and for the improvement of their pharmacokinetic properties.
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Affiliation(s)
- J Stürzebecher
- Klinikum der Friedrich-Schiller-Universität Jena, Erfurt, Germany
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45
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Babine RE, Bender SL. Molecular Recognition of Proteinminus signLigand Complexes: Applications to Drug Design. Chem Rev 1997; 97:1359-1472. [PMID: 11851455 DOI: 10.1021/cr960370z] [Citation(s) in RCA: 712] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert E. Babine
- Agouron Pharmaceuticals, Inc., 3565 General Atomics Court, San Diego, California 92121-1122
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46
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Wessel HP, Banner D, Gubernator K, Hilpert K, Müller K, Tschopp T. 6-Guanidiniopyranosen — neuartige Peptidmimetika auf Kohlenhydratbasis. Angew Chem Int Ed Engl 1997. [DOI: 10.1002/ange.19971090725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Eckhardt U, Stüber W, Dickneite G, Reers M, Petzinger E. First-pass elimination of a peptidomimetic thrombin inhibitor is due to carrier-mediated uptake by the liver. Interaction with bile acid transport systems. Biochem Pharmacol 1996; 52:85-96. [PMID: 8678912 DOI: 10.1016/0006-2952(96)00141-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
CRC 220 (4-methoxy-2, 3, 6-trimethylphenylsulfonyl-L-aspartyl-D-4-amidinophenylalanyl -piperidide) is a competitive peptide-based trombin inhibitor with high affinity to human alpha-thrombin (Ki 2.5 nM). The amphiphilic compound exhibits virtually no systemic bioavailability despite proteolytic stability and proven enteral absorption. After intravenous application (V. jejunalis) in rats CRC 220 is almost completely excreted into bile. Simultaneous administration of bile acids considerably decreases this first-pass elimination. CRC 220 is extensively taken up in isolated rat hepatocytes by a saturable carrier-mediated transport with Km 23.7 microM and Vmax 775 pmol x mg-1 x min-1. A large part of this transport is energy-dependent. At temperatures above 20 degrees C, the uptake is accelerated exponentially. The activation energy amounts to 82 kj/mol. A minor portion of CRC 220 uptake occurs by physical diffusion with a permeability coefficient of 7.83 x 10(-7) cm/sec at 12 degrees C. Sodium ions energize CRC 220 uptake. Replacement of sodium by choline or lithium decreases the transport rate of 23-40%. In addition, a negative membrane potential facilitates the uptake. CRC 220 transport is only observed in hepatocytes: it is absent in BHK, FAO, HepG2, HPCT 1E3, and HPCT 1E3-TC cells. In the presence of 4-amidinophenylalanine derivatives, CRC 220 uptake is considerably decreased. Inhibition also occurs with bile acids and bromosulfophthalein, but less with bumetanide. Because CRC 220 inhibits bile acid uptake into hepatocytes and vice versa, the results suggest that the first-pass elimination of this amphiphilic thrombin inhibitor is due to an active carrier-mediated transport process in the basolateral plasma membrane of rat hepatocytes, and that this transport occurs via a bile acid transport system.
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Affiliation(s)
- U Eckhardt
- Institute of Pharmacology and Toxicology, Justus-Liebig-University, Giessen, Germany
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48
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Jetten M, Peters CA, Visser A, Grootenhuis PD, van Nispen JW, Ottenheijm HC. Peptide-derived transition state analogue inhibitors of thrombin; synthesis, activity and selectivity. Bioorg Med Chem 1995; 3:1099-114. [PMID: 7582983 DOI: 10.1016/0968-0896(95)00102-m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In a study to combine the transition state analogue concept with the principle of catalytic site spanning, a series of peptide-derived transition state analogue (TSA) inhibitors of thrombin has been synthesized and tested. In the sequence H-D-Phe-Pro-Arg-Gly-OH (2) the Arg-Gly amide bond has been replaced by three classes of transition state analogues, being the ketomethylene, the hydroxyethylene and the hydroxymethylene amide bond replacements. Compound 12a, in which the amide bond has been replaced by the ketomethylene group, was found to be the most potent thrombin inhibitor of the series studied. Subsequently, penta- and hexapeptide sequences with good affinity for thrombin were developed, i.e. H-D-Phe-Pro-Arg-Gly-Phe-OH (16) and H-D-Phe-Pro-Arg-Gly-Phe-Lys-OH (26). In these sequences the Arg-Gly amide bond was then replaced by the ketomethylene group. The resulting compounds 43a and 47a, respectively, were evaluated in vitro as inhibitors of thrombin and factor Xa. Compound 47a was found to be the most potent thrombin inhibitor of the series studied (Ki = 29 nM). The combination of the transition state analogue concept and the principle of peptide elongation (tetrapeptide-->hexapeptide) yields thrombin inhibitors of high potency and selectivity. The effects of these two alterations reinforce each other indicating a synergistic effect. This might be rationalized by entropy factors.
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Affiliation(s)
- M Jetten
- N.V. Organon, Oss, The Netherlands
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49
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Rupin A, Mennecier P, de Nanteuil G, Laubie M, Verbeuren TJ. A screening procedure to evaluate the anticoagulant activity and the kinetic behaviour of direct thrombin inhibitors. Thromb Res 1995; 78:217-25. [PMID: 7631302 DOI: 10.1016/0049-3848(95)00051-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of a fibrin clot microassay to define both the kinetic behaviour and the anticoagulant activity of direct thrombin inhibitors targeting various domains of thrombin (catalytic site, anion binding exosite or both) is described. Since classical kinetics studies are difficult to perform in a fibrin-clot assay, methodological conditions were selected in order to obtain a linear relationship between fibrin formation and the thrombin concentration i.e. 0.67 nM thrombin, 6 microM fibrinogen, 5 minutes reaction. Under those conditions, the concentration of the complex thrombin-inhibitor can easily be calculated from a standard curve performed with increasing concentrations of thrombin and fitted versus the total inhibitor concentration using adapted equations. To detect the slow establishment of the thrombin inhibition, results obtained with a protocol in which the inhibitor is pre-incubated with thrombin before the addition of fibrinogen is compared to a protocol in which the inhibitor is pre-incubated with fibrinogen before thrombin is added. Our assay which is validated using different types of thrombin inhibitors (classical competitive: NAPAP and hirudin 55-65; tight binding: r-hirudin; slow tight binding: DUP-714), provides a rapid screening protocol allowing to evaluate the biochemical and anticoagulant properties of any direct thrombin inhibitor.
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Affiliation(s)
- A Rupin
- Servier Research Institute, Division of Angiology, Suresnes, France
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50
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Abstract
This review covers the recent advances in the development of highly potent inhibitors of platelet aggregation as potential therapeutic drugs for thrombosis related to cardiovascular and cerebrovascular diseases. The discovery of RGD sequence-directed cell surface receptors (the integrins) has led to extensive research in the development of small RGD containing peptides and their mimetics as antithrombotic agents. These agents work by inhibiting platelet aggregation through competitive blocking of fibrinogen to the platelet surface receptor, GPIIb/IIIa. The pharmacophoric nature of the aspartic acid and arginine side chains of the RGD unit has allowed the development of strategies for rational design, largely based on assumed bioactive RGD conformations and lead optimization. Applications of such strategies, from RGD peptides to peptide hybrids and then to non-peptide mimetics, are described. Also discussed is the important issue of specificity toward GPIIb/IIIa, keeping in view that the RGD unit is a key recognition signal for a variety of cell surface receptors.
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Affiliation(s)
- I Ojima
- Department of Chemistry, State University of New York at Stony Brook 11794-3400, USA
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