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Liudvytska O, Ponczek MB, Krzyżanowska-Kowalczyk J, Kowalczyk M, Balcerczyk A, Kolodziejczyk-Czepas J. Effects of Rheum rhaponticum and Rheum rhabarbarum extracts on haemostatic activity of blood plasma components and endothelial cells in vitro. JOURNAL OF ETHNOPHARMACOLOGY 2023:116562. [PMID: 37201663 DOI: 10.1016/j.jep.2023.116562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/20/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional medicine recommends the use of Rheum rhaponticum L. and R. rhabarbarum L. to treat over thirty complaints, including disorders related to the cardiovascular system such as heartache, pains in the pericardium, epistaxis and other types of haemorrhage, blood purification as well as disorders of venous circulation. AIM OF THE STUDY This work was dedicated to examining for the first time the effects of extracts from petioles and roots of R. rhaponticum and R. rhabarbarum, as well as two stilbene compounds (rhapontigenin and rhaponticin) on the haemostatic activity of endothelial cells and functionality of blood plasma components of the haemostatic system. MATERIALS AND METHODS The study was based on three main experimental modules, including the activity of proteins of the human blood plasma coagulation cascade and the fibrinolytic system as well as analyses of the haemostatic activity of human vascular endothelial cells. Additionally, interactions of the main components of the rhubarb extracts with crucial serine proteases of the coagulation cascade and fibrinolysis (i.e. thrombin, the coagulation factor Xa and plasmin) were analyzed in silico. RESULTS The examined extracts displayed anticoagulant properties and significantly reduced the tissue factor-induced clotting of human blood plasma (by about 40%). Inhibitory effects of the tested extracts on thrombin and the coagulation factor Xa (FXa) were found as well. For the extracts, the IC50 was ranging from 20.26 to 48.11 μg/ml. Modulatory effects on the haemostatic response of endothelial cells, including the release of von Willebrand factor, tissue-type plasminogen activator and the plasminogen activator inhibitor-1, have been also found. CONCLUSIONS Our results indicated for the first time that the examined Rheum extracts influenced the haemostatic properties of blood plasma proteins and endothelial cells, with the prevalence of the anticoagulant action. The anticoagulant effect of the investigated extracts may be partly attributed to the inhibition of the FXa and thrombin activities, the key serine proteases of the blood coagulation cascade.
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Affiliation(s)
- Oleksandra Liudvytska
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
| | - Michał B Ponczek
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
| | - Justyna Krzyżanowska-Kowalczyk
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, 24-100, Puławy, Poland.
| | - Mariusz Kowalczyk
- Department of Biochemistry and Crop Quality, Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, 24-100, Puławy, Poland.
| | - Aneta Balcerczyk
- Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
| | - Joanna Kolodziejczyk-Czepas
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
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Kolodziejczyk-Czepas J, Czepas J. Plant-Derived Compounds and Extracts as Modulators of Plasmin Activity-A Review. Molecules 2023; 28:molecules28041677. [PMID: 36838662 PMCID: PMC9965408 DOI: 10.3390/molecules28041677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Functionality of the fibrinolytic system is based on activity of its central enzyme, plasmin, responsible for the removal of fibrin clots. Besides the hemostasis, fibrinolytic proteins are also involved in many other physiological and pathological processes, including immune response, extracellular matrix degradation, cell migration, and tissue remodeling. Both the impaired and enhanced activity of fibrinolytic proteins may result in serious physiological consequences: prothrombotic state or excessive bleeding, respectively. However, current medicine offers very few options for treating fibrinolytic disorders, particularly in the case of plasmin inhibition. Although numerous attempts have been undertaken to identify natural or to develop engineered fibrinolytic system modulators, structural similarities within serine proteases of the hemostatic system and pleiotropic activity of fibrinolytic proteins constitute a serious problem in discovering anti- or profibrinolytic agents that could precisely affect the target molecules and reduce the risk of side effects. Therefore, this review aims to present a current knowledge of various classes of natural inhibitors and stimulators of the fibrinolytic system being well-defined low-molecular plant secondary metabolites or constituents of plant extracts as well as plant peptides. This work also discusses obstacles caused by low specificity of most of natural compounds and, hence, outlines recent trends in studies aimed at finding more efficient modulators of plasmin activity, including investigation of modifications of natural pharmacophore templates.
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Affiliation(s)
- Joanna Kolodziejczyk-Czepas
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
- Correspondence:
| | - Jan Czepas
- Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
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Qian S, Xie Z, Liu J, Li M, Wang S, Luo N, Wang C. DBU-Promoted Cascade Annulation of Nitroarylcyclopropane-1,1-dicarbonitriles and 3-Aryl-2-cyanoacrylates: An Access to Highly Functionalized Cyclopenta[b]furan Derivatives. J Org Chem 2018; 83:14768-14776. [DOI: 10.1021/acs.joc.8b02325] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Siran Qian
- School of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Street, Yangzhou 225002, P. R. China
| | - Zengyang Xie
- College of Basic Medicine, Jining Medical University, Jining 272067, P. R. China
| | - Jiaming Liu
- School of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Street, Yangzhou 225002, P. R. China
| | - Mingshuang Li
- School of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Street, Yangzhou 225002, P. R. China
| | - Shan Wang
- School of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Street, Yangzhou 225002, P. R. China
| | - Naili Luo
- School of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Street, Yangzhou 225002, P. R. China
| | - Cunde Wang
- School of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Street, Yangzhou 225002, P. R. China
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Wang DY, Abboud MI, Markoulides MS, Brem J, Schofield CJ. The road to avibactam: the first clinically useful non-β-lactam working somewhat like a β-lactam. Future Med Chem 2016; 8:1063-84. [PMID: 27327972 DOI: 10.4155/fmc-2016-0078] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Avibactam, which is the first non-β-lactam β-lactamase inhibitor to be introduced for clinical use, is a broad-spectrum serine β-lactamase inhibitor with activity against class A, class C, and, some, class D β-lactamases. We provide an overview of efforts, which extend to the period soon after the discovery of the penicillins, to develop clinically useful non-β-lactam compounds as antibacterials, and, subsequently, penicillin-binding protein and β-lactamase inhibitors. Like the β-lactam inhibitors, avibactam works via a mechanism involving covalent modification of a catalytically important nucleophilic serine residue. However, unlike the β-lactam inhibitors, avibactam reacts reversibly with its β-lactamase targets. We discuss chemical factors that may account for the apparently special nature of β-lactams and related compounds as antibacterials and β-lactamase inhibitors, including with respect to resistance. Avenues for future research including non-β-lactam antibacterials acting similarly to β-lactams are discussed.
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Affiliation(s)
| | | | | | - Jürgen Brem
- Department of Chemistry, University of Oxford, UK
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5
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Cateni F, Lucchini V, Zacchigna M, Procida G, Doljak B, Anderluh M. New Triterpenes from the Fungus Gloeophyllum odoratum. Chem Nat Compd 2015. [DOI: 10.1007/s10600-015-1207-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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7
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Li X, Liu Z, Li Y, Li J, Li J, Wang R. A Statistical Survey on the Binding Constants of Covalently Bound Protein-Ligand Complexes. Mol Inform 2010; 29:87-96. [DOI: 10.1002/minf.200900003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2009] [Accepted: 12/15/2009] [Indexed: 11/07/2022]
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8
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Sena Filho JG, Nimmo SL, Xavier HS, Barbosa-Filho JM, Cichewicz RH. Phenylethanoid and lignan glycosides from polar extracts of Lantana, a genus of verbenaceous plants widely used in traditional herbal therapies. JOURNAL OF NATURAL PRODUCTS 2009; 72:1344-1347. [PMID: 19485331 DOI: 10.1021/np900086y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Many references to the use of Lantana spp. can be found in the ethnopharmacological literature from locations around the globe. This study was focused on examining constituents from the polar extracts of Lantana radula Sw. and Lantana canescens Kunth, for which no prior chemical investigations had been reported. A new phenylethanoid glycoside, raduloside, and lignan glycoside, radulignan, were identified along with the known compounds alyssonoside, arenarioside, calceolarioside E, isonuomioside, samioside, and verbascoside.
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Affiliation(s)
- José G Sena Filho
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019-3032, USA
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Yunt Z, Reinhardt K, Li A, Engeser M, Dahse HM, Gütschow M, Bruhn T, Bringmann G, Piel J. Cleavage of four carbon-carbon bonds during biosynthesis of the griseorhodin a spiroketal pharmacophore. J Am Chem Soc 2009; 131:2297-305. [PMID: 19175308 DOI: 10.1021/ja807827k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rubromycins, such as gamma-rubromycin, heliquinomycin, and griseorhodin A, are a family of extensively modified aromatic polyketides that inhibit HIV reverse transcriptase and human telomerase. Telomerase inhibition crucially depends on the presence of a spiroketal moiety that is unique among aromatic polyketides. Biosynthetic incorporation of this pharmacophore into the rubromycins results in a dramatic distortion of the overall polyketide structure, but how this process is achieved by the cell has been obscure. To identify the enzymes involved in spiroketal construction, we generated 14 gene-deletion variants of the griseorhodin A biosynthetic gene cluster isolated from the tunicate-associated bacterium Streptomyces sp. JP95. Heterologous expression and metabolic analysis allowed for an assignment of most genes to various stages of griseorhodin tailoring and pharmacophore generation. The isolation of the novel advanced intermediate lenticulone, which exhibits cytotoxic, antibacterial, and elastase-inhibiting activity, provided direct evidence that the spiroketal is formed by cleavage of four carbon-carbon bonds in a pentangular polyketide precursor. This remarkable transformation is followed by an epoxidation catalyzed by an unusual cytochrome P450/NADPH:ubiquinone oxidoreductase pair that utilizes a saturated substrate. In addition, the absolute configuration of griseorhodin A was determined by quantum-chemical circular dichroism (CD) calculations in combination with experimental CD measurements.
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Affiliation(s)
- Zeynep Yunt
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany
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10
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Nair DG, Sunilkumar PN, Sadasivan C. Modeling of Factor XIII Activation Peptide (28–41) V34L Mutant Bound To Thrombin. J Biomol Struct Dyn 2008; 26:387-94. [DOI: 10.1080/07391102.2008.10507253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Huang W, Yamamoto Y, Li Y, Dou D, Alliston KR, Hanzlik RP, Williams TD, Groutas WC. X-ray snapshot of the mechanism of inactivation of human neutrophil elastase by 1,2,5-thiadiazolidin-3-one 1,1-dioxide derivatives. J Med Chem 2008; 51:2003-8. [PMID: 18318470 DOI: 10.1021/jm700966p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of action of a general class of mechanism-based inhibitors of serine proteases, including human neutrophil elastase (HNE), has been elucidated by determining the X-ray crystal structure of an enzyme-inhibitor complex. The captured intermediate indicates that processing of inhibitor by the enzyme generates an N-sulfonyl imine functionality that is tethered to Ser195, in accordance with the postulated mechanism of action of this class of inhibitors. The identity of the HNE-N-sulfonyl imine species was further corroborated using electrospray ionization mass spectrometry.
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Affiliation(s)
- Weijun Huang
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
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12
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Sharma OP, Sharma S, Pattabhi V, Mahato SB, Sharma PD. A review of the hepatotoxic plant Lantana camara. Crit Rev Toxicol 2007; 37:313-52. [PMID: 17453937 DOI: 10.1080/10408440601177863] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Lantana (Lantana camara Linn) is a noxious weed that grows in many tropical and subtropical parts of the world. Ingestion of lantana foliage by grazing animals causes cholestasis and hepatotoxicity. Both ruminants and nonruminant animals such as guinea pigs, rabbits, and female rats are susceptible to the hepatotoxic action of lantana toxins. The hepatotoxins are pentacyclic triterpenoids called lantadenes. Molecular structure of lantadenes has been determined. Green unripe fruits of the plant are toxic to humans. Lantana spp. exert allelopathic action on the neighboring vegetation. The allelochemicals have been identified as phenolics, with umbelliferone, methylcoumarin, and salicylic acid being the most phytotoxic. In addition to phenolics, a recent report indicates lantadene A and B as more potent allelochemicals. Management of lantana toxicosis in animals is achieved by drenching with activated charcoal and supportive therapy. Recent reports on the bilirubin clearance effect of Chinese herbal tea Yin Zhi Huang (decoction of the plant Yin Chin, Artemisia capillaries, and three other herbs) or its active ingredient 6,7-dimethylesculetin, in jaundice are very exciting and warrant investigations on its, possible, ameliorative effects in lantana intoxicated animals. Research is being conducted on new drug discovery based on natural products in different parts of the lantana plant.
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Affiliation(s)
- Om P Sharma
- Biochemistry Laboratory, Indian Veterinary Research Institute, Regional Station. Kangra Valley, Palampur, India.
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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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15
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Abstract
Human cytomegalovirus (HCMV) is an important pathogen for which there is a significant unmet medical need. New HCMV antivirals, active against novel molecular targets, are undoubtedly needed as the currently available drugs ganciclovir, cidofovir, and foscarnet, which are all viral DNA inhibitors, suffer from limited effectiveness, mainly due to the development of drug resistance, poor bioavailability, and toxicity. One of the newer molecular targets that has been exploited in the search for better drug candidates is HCMV protease. Our deltaAla HCMV protease (wild type variant with the internal cleavage site deleted) was cloned and expressed in E. coli. This viral enzyme was used to develop HCMV protease assays to evaluate potential inhibitors. The chirally pure (SRS)-alpha-methyl pyrrolidine-5,5-trans-lactam template was synthesized, which together with the natural substrate requirements of HCMV protease and detailed SAR, was used to design potent and selective mechanism based inhibitors of HCMV protease. The mechanism of action of these inhibitors of HCMV protease was investigated by ESI/MS, and the X-ray crystal structure of the HCMV protease was used to refine our selective viral enzyme inhibitors to obtain plasma stable antivirals. A novel ELISA antiviral assay was developed which, together with a cytotoxicity assay, enabled us to discover anti-HCMV drug candidates equivalent in potency to ganciclovir that had good pharmacokinetics in the dog and good brain and ocular penetration in the guinea pig.
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Affiliation(s)
- Alan D Borthwick
- Department of Medicinal Chemistry CVU UK, GlaxoSmithKline Research and Development, Medicines Research Centre, Gunnels Wood Road, Stevenage, Herts SG1 2NY, United Kingdom.
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Affiliation(s)
- Wendy A Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia.
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Abstract
The majority of pharmaceutically relevant drug targets cluster into densely populated target families, thus offering a novel approach that complements the currently favoured screening paradigm in medicinal chemistry. This approach uses a privileged structure concept whereby molecular masterkeys are developed that account for a target family wide structural or functional commonality. Numerous lead compounds, based on multipurpose privileged structures, can be generated that address a variety of targets from a gene family of interest, irrespective of therapeutic area. Several different interpretations of the privileged structure concept will be highlighted, with a strong emphasis on the most stringent application: the optimization of a molecular masterkey for a distinct target family of interest.
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Affiliation(s)
- Gerhard Müller
- Axxima Pharmaceuticals AG, Max-Lebsche-Platz 32, 81377 Münich, Germany.
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Castro KNC, Carvalho ALO, Almeida AP, Oliveira DB, Borba HR, Costa SS, Zingali RB. Preliminary in vitro studies on the Marsypianthes chamaedrys (boia-caá) extracts at fibrinoclotting induced by snake venoms. Toxicon 2003; 41:929-32. [PMID: 12782094 DOI: 10.1016/s0041-0101(03)00087-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The extract of Marsypianthes chamaedrys, a plant used against snakebites, in the present study was shown to inhibit fibrinoclotting induced by several Brazilian snake venoms or thrombin. These data indicate that this extract affected thrombin-like enzymes. In this first report we determine some features of the components present in the extract regarding the antifibrinoclotting action. Our results show that active components responsible for those effects are thermo-resistant and are concentrated in the methanolic fraction.
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Affiliation(s)
- K N C Castro
- Departamento de Bioquímica Médica, ICB/CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
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Zavodszky MI, Sanschagrin PC, Korde RS, Kuhn LA. Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J Comput Aided Mol Des 2002; 16:883-902. [PMID: 12825621 DOI: 10.1023/a:1023866311551] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
For the successful identification and docking of new ligands to a protein target by virtual screening, the essential features of the protein and ligand surfaces must be captured and distilled in an efficient representation. Since the running time for docking increases exponentially with the number of points representing the protein and each ligand candidate, it is important to place these points where the best interactions can be made between the protein and the ligand. This definition of favorable points of interaction can also guide protein structure-based ligand design, which typically focuses on which chemical groups provide the most energetically favorable contacts. In this paper, we present an alternative method of protein template and ligand interaction point design that identifies the most favorable points for making hydrophobic and hydrogen-bond interactions by using a knowledge base. The knowledge-based protein and ligand representations have been incorporated in version 2.0 of SLIDE and resulted in dockings closer to the crystal structure orientations when screening a set of 57 known thrombin and glutathione S-transferase (GST) ligands against the apo structures of these proteins. There was also improved scoring enrichment of the dockings, meaning better differentiation between the chemically diverse known ligands and a approximately 15,000-molecule dataset of randomly-chosen small organic molecules. This approach for identifying the most important points of interaction between proteins and their ligands can equally well be used in other docking and design techniques. While much recent effort has focused on improving scoring functions for protein-ligand docking, our results indicate that improving the representation of the chemistry of proteins and their ligands is another avenue that can lead to significant improvements in the identification, docking, and scoring of ligands.
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Affiliation(s)
- Maria I Zavodszky
- Protein Structural Analysis and Design Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Kaur K, Lan MJ, Pratt RF. Mechanism of inhibition of the class C beta-lactamase of Enterobacter cloacae P99 by cyclic acyl phosph(on)ates: rescue by return. J Am Chem Soc 2001; 123:10436-43. [PMID: 11673973 DOI: 10.1021/ja011094v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As previously described (Pratt, R. F.; Hammar, N. J. J. Am. Chem. Soc. 1998, 120, 3004.), 1-hydroxy-4,5-benzo-2,6-dioxaphosphorinone(3)-1-oxide (salicyloyl cyclic phosphate) inactivates the class C beta-lactamase of Enterobacter cloacae P99 in a covalent fashion. The inactivated enzyme slowly reverts to the active form. This paper shows that reactivation involves a recyclization reaction that regenerates salicyloyl cyclic phosphate rather than hydrolysis of the covalent intermediate. The inactivation, therefore, is a slowly reversible covalent modification of the active site. The thermodynamic dissociation constant of the inhibitor from the inactivated enzyme is 0.16 microM. Treatment of the inactivated enzyme with alkali does not produce salicylic acid but does, after subsequent acid hydrolysis, yield one molar equivalent of lysinoalanine. This result proves that salicyloyl cyclic phosphate inactivates the enzyme by (slowly reversible) phosphorylation of the active site serine residue. This result contrasts sharply with the behavior of acyclic acyl phosphates which transiently inactivate the P99 beta-lactamase by acylation (Li, N.; Pratt, R. F. J. Am. Chem. Soc. 1998, 120, 4264.). This chemoselectivity difference is explored by means of molecular modeling. Rather counterintuitively, in view of the relative susceptibility of phosphates and phosphonates to nucleophilic attack at phosphorus, 1-hydroxy-4,5-benzo-2-oxaphosphorinanone(3)-1-oxide, the phosphonate analogue of salicyloyl cyclic phosphate, did not appear to inactivate the P99 beta-lactamase in a time-dependent fashion. It was found, however, to act as a fast reversible inhibitor (K(i) = 10 microM). A closer examination of the kinetics of inhibition revealed that both on and off rates (9.8 x 10(3) s(-1) x M(-1) and 0.098 s(-1), respectively) were much slower than expected for noncovalent binding. This result strongly indicates that the inhibition reaction of the phosphonate also involves phosphylation of the active site. Hence, unlike the situation with bacterial DD-peptidases covalently inactivated by beta-lactams, the P99 beta-lactamase inactivated by the above cyclic acyl phosph(on)ates can be rescued by return. Elimination of the recyclization reaction would lead to more effective inhibitors.
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Affiliation(s)
- K Kaur
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
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21
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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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22
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Macdonald SJ, Dowle MD, Harrison LA, Shah P, Johnson MR, Inglis GG, Clarke GD, Smith RA, Humphreys D, Molloy CR, Amour A, Dixon M, Murkitt G, Godward RE, Padfield T, Skarzynski T, Singh OM, Kumar KA, Fleetwood G, Hodgson ST, Hardy GW, Finch H. The discovery of a potent, intracellular, orally bioavailable, long duration inhibitor of human neutrophil elastase--GW311616A a development candidate. Bioorg Med Chem Lett 2001; 11:895-8. [PMID: 11294386 DOI: 10.1016/s0960-894x(01)00078-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The discovery of a potent intracellular inhibitor of human neutrophil elastase which is orally active and has a long duration of action is described. The pharmacodynamic and pharmacokinetic properties of a trans-lactam development candidate, GW311616A, are described.
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Affiliation(s)
- S J Macdonald
- Medicinal Chemistry 2, GlaxoWellcome Medicines Research Centre, Stevenage, UK.
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23
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Doljak B, Stegnar M, Urleb U, Kreft S, Umek A, Ciglaric M, Strukelj B, Popovic T. Screening for selective thrombin inhibitors in mushrooms. Blood Coagul Fibrinolysis 2001; 12:123-8. [PMID: 11302474 DOI: 10.1097/00001721-200103000-00006] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Thrombin is the key serine proteinase of the coagulation cascade and therefore a suitable target for inhibition of blood coagulation. A number of pharmacologically active secondary metabolites from mushrooms have already been isolated, thus providing the rationale for screening for new thrombin inhibitors in mushrooms. In this study, inhibitory activities of mushroom extracts on thrombin and trypsin were measured using the chromogenic substrates H-D-phenylalanine-L-pipecolyl-L-arginine-paranitroaniline dihydrochloride (S-2238) for thrombin and N-benzoyl-D,L-Arg-p-nitroanilide (BAPNA) for trypsin. The inhibitory activities of extracts from 95 Basidiomycete species have been determined. The majority of samples inhibited trypsin and thrombin with various potencies; however, some extracts showed no activity against one or both of the enzymes. An aqueous extract of Gleophyllum odoratum exhibited high inhibitory activity on both thrombin and trypsin (72 and 60%, respectively), while extracts of Clitocybe gibba, Amanita virosa, Cantharellus lutescens, Suillus tridentinus, Hypoloma fasciculare and Lactarius badiosanguineus considerably inhibited thrombin (49, 48, 36, 34, 32 and 31%, respectively) and showed no inhibitory activity on trypsin. The results at this point are promising for further research with the objective of finding an effective and safe thrombin inhibitor.
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Affiliation(s)
- B Doljak
- Department of Phrmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Slovenia.
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24
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Sadasivan C, Yee VC. Interaction of the factor XIII activation peptide with alpha -thrombin. Crystal structure of its enzyme-substrate analog complex. J Biol Chem 2000; 275:36942-8. [PMID: 10956659 DOI: 10.1074/jbc.m006076200] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The serine protease thrombin proteolytically activates blood coagulation factor XIII by cleavage at residue Arg(37); factor XIII in turn cross-links fibrin molecules and gives mechanical stability to the blood clot. The 2.0-A resolution x-ray crystal structure of human alpha-thrombin bound to the factor XIII-(28-37) decapeptide has been determined. This structure reveals the detailed atomic level interactions between the factor XIII activation peptide and thrombin and provides the first high resolution view of this functionally important part of the factor XIII molecule. A comparison of this structure with the crystal structure of fibrinopeptide A complexed with thrombin highlights several important determinants of thrombin substrate interaction. First, the P1 and P2 residues must be compatible with the geometry and chemistry of the S1 and S2 specificity sites in thrombin. Second, a glycine in the P5 position is necessary for the conserved substrate conformation seen in both factor XIII-(28-37) and fibrinopeptide A. Finally, the hydrophobic residues, which occupy the aryl binding site of thrombin determine the substrate conformation further away from the catalytic residues. In the case of factor XIII-(28-37), the aryl binding site is shared by hydrophobic residues P4 (Val(34)) and P9 (Val(29)). A bulkier residue in either of these sites may alter the substrate peptide conformation.
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Affiliation(s)
- C Sadasivan
- Department of Molecular Cardiology and Structural Biology Center, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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25
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Sharma OP, Singh A, Sharma S. Levels of lantadenes, bioactive pentacyclic triterpenoids, in young and mature leaves of Lantana camara var. aculeata. Fitoterapia 2000; 71:487-91. [PMID: 11449494 DOI: 10.1016/s0367-326x(00)00156-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Levels of the lantadene pentacyclic triterpenes were quantified in young and mature leaf samples of Lantana camara var. aculeata, by HPLC. The amount of different lantadenes (mg/100 g dry wt.) in young and mature leaf samples, respectively, was: lantadene A, 491.5 +/- 6.3, 805.9 +/- 52.8; lantadene B, 347.0 +/- 3.0, 522.3 +/- 37.1; lantadene C, 191.3 +/- 10.3, 424.8 +/- 39.1; lantadene D, 49.7 +/- 5.3, 177.4 +/- 19.0; reduced lantadene A, 19.1 +/- 2.3, 28.7 +/- 4.5; reduced lantadene B, 13.0 +/- 1.3, 18.6 +/- 1.2; and 22 beta-hydroxyoleanonic acid, 82.5 +/- 11.4, 167.7 +/- 30.1.
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Affiliation(s)
- O P Sharma
- Biochemistry Laboratory, Indian Veterinary Research Institute, Regional Station, Kangra Valley, Himachal Pradesh, Palampur 176 061, India.
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26
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Abstract
Lantana camara L. is regarded both as a notorious weed and a popular ornamental garden plant and has found various uses in folk medicine in many parts of the world. Some taxa of the widely variable L. camara complex are toxic to small ruminants and this effect has been associated with the types and relative amounts of some triterpene ester metabolites. However, L. camara also produces a number of metabolites in good yields and some have been shown to possess useful biological activities. All these aspects are considered in this review to allow an evaluation of the potential for utilisation of the large biomass of Lantana available. The phytochemistry of other members of the Lantana genus is included.
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Affiliation(s)
- E L Ghisalberti
- Department of Chemistry, University of Western Australia, Nedlands, Western Australia 6907, Australia.
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27
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Pass M, Abu-Rabie S, Baxter A, Conroy R, Coote SJ, Craven AP, Finch H, Hindley S, Kelly HA, Lowdon AW, McDonald E, Mitchell WL, Pegg NA, Procopiou PA, Ramsden NG, Thomas R, Walker DA, Watson NS, Jhoti H, Mooney CJ, Tang CM, Thomas PJ, Parry S, Patel C. Thrombin inhibitors based on [5,5] trans-fused indane lactams. Bioorg Med Chem Lett 1999; 9:1657-62. [PMID: 10397495 DOI: 10.1016/s0960-894x(99)00244-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A series of trans-fused lactams containing the indane nucleus has been prepared. Compound 19 has much enhanced plasma stability compared with its lactone counterpart and shows appreciable in vitro anticoagulant activity.
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Affiliation(s)
- M Pass
- Glaxo Wellcome Research and Development, Stevenage, Herts, United Kingdom.
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28
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Pass M, Bolton RE, Coote SJ, Finch H, Hindley S, Lowdon A, McDonald E, McLaren J, Owen M, Pegg NA, Mooney CJ, Tang CM, Parry S, Patel C. Synthetic [5,5] trans-fused indane lactones as inhibitors of thrombin. Bioorg Med Chem Lett 1999; 9:431-6. [PMID: 10091697 DOI: 10.1016/s0960-894x(99)00002-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Synthesis of trans-fused lactones containing the indane nucleus has resulted in a series of potent acylating inhibitors of thrombin. As an example compound 11e has an apparent second order rate constant of 11 x 10(6) M(-1)sec(-1) for the inhibition of thrombin. The anticoagulant activity of these compounds is discussed.
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Affiliation(s)
- M Pass
- Glaxo Wellcome Research and Development, Stevenage, Herts, United Kingdom.
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29
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Chapter 9. Anticoagulants: Thrombin and Factor Xa Inhibitors. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1999. [DOI: 10.1016/s0065-7743(08)60571-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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30
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Finch H, Pegg NA, McLaren J, Lowdon A, Bolton R, Coote SJ, Dyer U, Montana JG, Owen MR, Dowle M, Buckley D, Ross BC, Campbell C, Dix C, Mooney C, Man-Tang C, Patel C. 5,5-trans lactone-containing inhibitors of serine proteases: identification of a novel, acylating thrombin inhibitor. Bioorg Med Chem Lett 1998; 8:2955-60. [PMID: 9873654 DOI: 10.1016/s0960-894x(98)00531-9] [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: 11/25/2022]
Abstract
Synthesis of a variety of 5,5-trans fused lactones, related to compounds found in extracts of Lantana camara, has provided a series of novel acylating inhibitors of human thrombin, trypsin, chymotrypsin and human leucocyte elastase. The most effective thrombin inhibitor is 7 with an IC50 of 130 nM and a Kobs/[1] of 4,000 M-1 s-1.
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Affiliation(s)
- H Finch
- Department of Medicinal Chemistry, GlaxoWellcome Research and Development, Stevenage, Herts., U.K.
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31
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Synthesis of trans-fused [5,5] bicyclic lactones/lactams as templates for serine protease inhibition. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)01481-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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