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Liu J, Zhang M, Huang Z, Fang J, Wang Z, Zhou C, Qiu X. Diversity, Biosynthesis and Bioactivity of Aeruginosins, a Family of Cyanobacteria-Derived Nonribosomal Linear Tetrapeptides. Mar Drugs 2023; 21:md21040217. [PMID: 37103356 PMCID: PMC10143770 DOI: 10.3390/md21040217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Aeruginosins, a family of nonribosomal linear tetrapeptides discovered from cyanobacteria and sponges, exhibit in vitro inhibitory activity on various types of serine proteases. This family is characterized by the existence of the 2-carboxy-6-hydroxy-octahydroindole (Choi) moiety occupied at the central position of the tetrapeptide. Aeruginosins have attracted much attention due to their special structures and unique bioactivities. Although many studies on aeruginosins have been published, there has not yet been a comprehensive review that summarizes the diverse research ranging from biogenesis, structural characterization and biosynthesis to bioactivity. In this review, we provide an overview of the source, chemical structure as well as spectrum of bioactivities of aeruginosins. Furthermore, possible opportunities for future research and development of aeruginosins were discussed.
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Affiliation(s)
- Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Chengxu Zhou
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
- Correspondence:
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2
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Identification of new pyrazolyl piperidine molecules as factor Xa inhibitors: Design, synthesis, in silico, and biological evaluation. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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3
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Wilson AJ, Zhou Q, Vargas I, Palekar R, Grabau R, Pan H, Wickline SA. Formulation and Characterization of Antithrombin Perfluorocarbon Nanoparticles. Methods Mol Biol 2020; 2118:111-120. [PMID: 32152974 DOI: 10.1007/978-1-0716-0319-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thrombin, a major protein involved in the clotting cascade by the conversion of inactive fibrinogen to fibrin, plays a crucial role in the development of thrombosis. Antithrombin nanoparticles enable site-specific anticoagulation without increasing bleeding risk. Here we outline the process of making and the characterization of bivalirudin and D-phenylalanyl-L-prolyl-L-arginyl-chloromethyl ketone (PPACK) nanoparticles. Additionally, the characterization of these nanoparticles, including particle size, zeta potential, and quantification of PPACK/bivalirudin loading, is also described.
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Affiliation(s)
- Alexander J Wilson
- The USF Health Heart Institute, University of South Florida, Tampa, FL, USA
| | - Qingyu Zhou
- College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Ian Vargas
- The USF Health Heart Institute, University of South Florida, Tampa, FL, USA
| | - Rohun Palekar
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan Grabau
- The USF Health Heart Institute, University of South Florida, Tampa, FL, USA
| | - Hua Pan
- The USF Health Heart Institute, University of South Florida, Tampa, FL, USA
| | - Samuel A Wickline
- The USF Health Heart Institute, University of South Florida, Tampa, FL, USA.
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Jaiswal PK, Sharma V, Kumar S, Mathur M, Swami AK, Yadav DK, Chaudhary S. Non-peptide-based new class of platelet aggregation inhibitors: Design, synthesis, bioevaluation, SAR, andin silicostudies. Arch Pharm (Weinheim) 2018. [DOI: 10.1002/ardp.201700349] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Pradeep K. Jaiswal
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry; Malaviya National Institute of Technology; Jaipur India
| | - Vashundhra Sharma
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry; Malaviya National Institute of Technology; Jaipur India
| | - Surendra Kumar
- College of Pharmacy; Gachon University of Medicine and Science; Incheon City Korea
| | - Manas Mathur
- Department of Advance Molecular Microbiology; Seminal Applied Sciences Pvt. Ltd.; Jaipur India
| | - Ajit K. Swami
- Department of Advance Molecular Microbiology; Seminal Applied Sciences Pvt. Ltd.; Jaipur India
| | - Dharmendra K. Yadav
- College of Pharmacy; Gachon University of Medicine and Science; Incheon City Korea
- Department of Biochemistry; All India Institute of Medical Sciences (AIIMS); Jodhpur Rajasthan India
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry; Malaviya National Institute of Technology; Jaipur India
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Xing J, Yang L, Yang Y, Zhao L, Wei Q, Zhang J, Zhou J, Zhang H. Design, synthesis and biological evaluation of novel 2,3-dihydroquinazolin- 4(1H)-one derivatives as potential fXa inhibitors. Eur J Med Chem 2016; 125:411-422. [PMID: 27689724 DOI: 10.1016/j.ejmech.2016.09.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 09/16/2016] [Accepted: 09/18/2016] [Indexed: 12/31/2022]
Abstract
Coagulation factor Xa (fXa) is a particularly attractive target for the development of effective and safe anticoagulants. In this study, novel 2,3-dihydroquinazolin-4(1H)-one derivatives were designed as potential fXa inhibitors based on anthranilamide structure which has been reported in our previous research. The experimental data showed that most of the designed compounds exhibited significant in vitro potency against fXa. Among them, compound 8e displayed the strongest potency against fXa with the IC50 value of 21 nM and highly selectivity versus thrombin (IC50 = 67 μM) and excellent in vitro antithrombotic activity with its 2 × PT value of 1.2 μM and 2 × aPTT value of 0.6 μM. In addition, 8e also displayed excellent in vivo antithrombotic activity in the rat arteriovenous shunt (AV-SHUNT) model. The bleeding risk evaluation showed that 8e had a similar safety profile as that of betrixaban. All results demonstrated that compound 8e could be considered as a potential fXa inhibitor for the prevention and treatment of thromboembolic diseases.
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Affiliation(s)
- Junhao Xing
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, 210009 Nanjing, PR China.
| | - Lingyun Yang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, 210009 Nanjing, PR China
| | - Yifei Yang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, 210009 Nanjing, PR China
| | - Leilei Zhao
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, 210009 Nanjing, PR China
| | - Qiangqiang Wei
- Department of Medicinal Chemistry, China Pharmaceutical University, TongjiaXiang 24, 210009 Nanjing, PR China
| | - Jian Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, 210009 Nanjing, PR China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, TongjiaXiang 24, 210009 Nanjing, PR China
| | - Huibin Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, 210009 Nanjing, PR China; Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing 210009, PR China.
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New Approaches to the Role of Thrombin in Acute Coronary Syndromes: Quo Vadis Bivalirudin, a Direct Thrombin Inhibitor? Molecules 2016; 21:284. [PMID: 26927051 PMCID: PMC6273416 DOI: 10.3390/molecules21030284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 12/12/2022] Open
Abstract
The pathophysiology of acute coronary syndrome (ACS) involves platelet activation and thrombus formation after the rupture of atherosclerotic plaques. Thrombin is generated at the blood-plaque interface in association with cellular membranes on cells and platelets. Thrombin also amplifies the response to the tissue injury, coagulation and platelet response, so the treatment of ACS is based on the combined use of both antiplatelet (such as aspirin, clopidogrel, prasugrel and ticagrelor) and antithrombotic drugs (unfractionated heparin, enoxaparin, fondaparinux and bivalirudin). Bivalirudin competitively inhibits thrombin with high affinity, a predictable response from its linear pharmacokinetics and short action. However, a present remarkable controversy exists between the latest main Guidelines in Clinical Practice and the key trials evaluating the use of bivalirudin in ACS. The aim of this review is to update the development of bivalirudin, including pharmacological properties, obtained information from clinical trials evaluating efficacy and safety of bivalirudin in ACS; as well as the recommendations of clinical Guidelines.
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Kopylovich MN, Haukka M, Mahmudov KT. Co(II)-mediated synthesis of 2-carbamimidoylbenzoates and isoindole-1,3-diaminates. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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He LW, Dai WC, Li NG. Development of Orally Active Thrombin Inhibitors for the Treatment of Thrombotic Disorder Diseases. Molecules 2015; 20:11046-62. [PMID: 26083038 PMCID: PMC6272601 DOI: 10.3390/molecules200611046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022] Open
Abstract
Thrombotic disorders represent the major share of the various cardiovascular diseases, and significant progress has been made in the development of synthetic thrombin inhibitors as new anticoagulants. In addition to the development of highly potent and selective inhibitors with improved safety and suitable half-life, several allosteric inhibitors have been designed and synthesized, that did not fully nullify the procoagulant signal and thus could result in reduced bleeding complications. Furthermore, natural products with thrombin inhibitory activity have been isolated, and some natural products have been modified in order to improve their inhibitory activity and metabolic stability. This review summarizes the development of orally active thrombin inhibitors for the treatment of thrombotic disorder diseases, which could serve as a reference for the interested researchers.
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Affiliation(s)
- Li-Wei He
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Wei-Chen Dai
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Nian-Guang Li
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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Shi ZH, Li NG, Tang YP, Duan JA. Prolinamide derivatives as thrombin inhibitors for the treatment of thrombin-mediated diseases: a patent evaluation of US2013296245. Expert Opin Ther Pat 2014; 24:1139-48. [PMID: 25231888 DOI: 10.1517/13543776.2014.959493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Thrombotic disorders can lead to deep vein thrombosis, myocardial infarction and stroke. Thrombin plays a vital role in cascade reaction of blood coagulation, inhibition of the activity of thrombin can block the formation of thrombus and direct thrombin inhibitor has a prospect to overcome the limitations in application of the traditional anticoagulant drugs. AREAS COVERED The current patent US2013296245 describes a series of prolinamide derivatives with formula (I) as thrombin inhibitors. These new compounds are defined to be pharmaceutically acceptable salts derived from pharmaceutically acceptable inorganic acid and organic acid, and pharmaceutically acceptable prodrug where N-alkoxycarbonyl is protected or carboxylic acid is protected by ester. EXPERT OPINION The patent used formamidine and its N-alkoxycarbonyl-protected derivatives as the P1 group; these groups were less basic compared with the traditional guanidine group, so their lipophilicity could be optimized to achieve oral absorption. Furthermore, these pharmaceutically acceptable prodrugs where N-alkoxycarbonyl is protected or carboxylic acid is protected by ester could achieve prolonged half-life for a convenient once- or twice-daily oral dosing. These efforts gave a new hope and confidence to treat thrombotic disorders with selective and orally active thrombin inhibitors.
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Affiliation(s)
- Zhi-Hao Shi
- Nanjing University of Chinese Medicine, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine , 138 Xianlin Road, Nanjing 210023, Jiangsu , PR China +86 25 85811916 ; +86 25 85811916 ; ,
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10
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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11
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Liu C, Tan JL, Xiao SY, Liao JF, Zou GR, Ai XX, Chen JB, Xiang Y, Yang Q, Zuo H. 1,4-Benzoxazine-3(4 H)-ones as Potent Inhibitors of Platelet Aggregation: Design, Synthesis and Structure–Activity Relations. Chem Pharm Bull (Tokyo) 2014; 62:915-20. [DOI: 10.1248/cpb.c14-00330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Chang Liu
- College of Pharmaceutical Sciences, Southwest University
| | - Jia-Lian Tan
- College of Pharmaceutical Sciences, Southwest University
| | - Si-Yu Xiao
- College of Pharmaceutical Sciences, Southwest University
| | - Jie-Feng Liao
- College of Pharmaceutical Sciences, Southwest University
| | - Guang-Rong Zou
- College of Pharmaceutical Sciences, Southwest University
| | - Xi-Xi Ai
- College of Pharmaceutical Sciences, Southwest University
| | - Jian-Bin Chen
- College of Pharmaceutical Sciences, Southwest University
| | - Yi Xiang
- Fourth People’s Hospital of Sichuan Province
| | - Quan Yang
- Fourth People’s Hospital of Sichuan Province
| | - Hua Zuo
- College of Pharmaceutical Sciences, Southwest University
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Figueiredo AC, Clement CC, Zakia S, Gingold J, Philipp M, Pereira PJB. Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors. PLoS One 2012; 7:e34354. [PMID: 22457833 PMCID: PMC3311629 DOI: 10.1371/journal.pone.0034354] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 02/28/2012] [Indexed: 11/30/2022] Open
Abstract
The tremendous social and economic impact of thrombotic disorders, together with the considerable risks associated to the currently available therapies, prompt for the development of more efficient and safer anticoagulants. Novel peptide-based thrombin inhibitors were identified using in silico structure-based design and further validated in vitro. The best candidate compounds contained both l- and d-amino acids, with the general sequence d-Phe(P3)-Pro(P2)-d-Arg(P1)-P1′-CONH2. The P1′ position was scanned with l- and d-isomers of natural or unnatural amino acids, covering the major chemical classes. The most potent non-covalent and proteolysis-resistant inhibitors contain small hydrophobic or polar amino acids (Gly, Ala, Ser, Cys, Thr) at the P1′ position. The lead tetrapeptide, d-Phe-Pro-d-Arg-d-Thr-CONH2, competitively inhibits α-thrombin's cleavage of the S2238 chromogenic substrate with a Ki of 0.92 µM. In order to understand the molecular details of their inhibitory action, the three-dimensional structure of three peptides (with P1′ l-isoleucine (fPrI), l-cysteine (fPrC) or d-threonine (fPrt)) in complex with human α-thrombin were determined by X-ray crystallography. All the inhibitors bind in a substrate-like orientation to the active site of the enzyme. The contacts established between the d-Arg residue in position P1 and thrombin are similar to those observed for the l-isomer in other substrates and inhibitors. However, fPrC and fPrt disrupt the active site His57-Ser195 hydrogen bond, while the combination of a P1 d-Arg and a bulkier P1′ residue in fPrI induce an unfavorable geometry for the nucleophilic attack of the scissile bond by the catalytic serine. The experimental models explain the observed relative potency of the inhibitors, as well as their stability to proteolysis. Moreover, the newly identified direct thrombin inhibitors provide a novel pharmacophore platform for developing antithrombotic agents by exploring the conformational constrains imposed by the d-stereochemistry of the residues at positions P1 and P1′.
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Affiliation(s)
- Ana C. Figueiredo
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Cristina C. Clement
- Department of Chemistry, Lehman College & Biochemistry Program, CUNY Graduate School, New York, New York, United States of America
- * E-mail: (CC); (MP); (PP)
| | - Sheuli Zakia
- Department of Chemistry, Lehman College & Biochemistry Program, CUNY Graduate School, New York, New York, United States of America
| | - Julian Gingold
- MD Program at Mount Sinai School of Medicine, New York, New York, United States of America
| | - Manfred Philipp
- Department of Chemistry, Lehman College & Biochemistry Program, CUNY Graduate School, New York, New York, United States of America
- * E-mail: (CC); (MP); (PP)
| | - Pedro J. B. Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- * E-mail: (CC); (MP); (PP)
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Siles R, Kawasaki Y, Ross P, Freire E. Synthesis and biochemical evaluation of triazole/tetrazole-containing sulfonamides against thrombin and related serine proteases. Bioorg Med Chem Lett 2011; 21:5305-9. [PMID: 21807511 PMCID: PMC3159800 DOI: 10.1016/j.bmcl.2011.07.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Revised: 06/30/2011] [Accepted: 07/06/2011] [Indexed: 11/25/2022]
Abstract
A small library of 25 triazole/tetrazole-based sulfonamides have been synthesized and further evaluated for their inhibitory activity against thrombin, trypsin, tryptase and chymase. In general, the triazole-based sulfonamides inhibited thrombin more efficiently than the tetrazole counterparts. Particularly, compound 26 showed strong thrombin inhibition (K(i)=880 nM) and significant selectivity against other human related serine proteases like trypsin (K(i)=729 μM). Thrombin binding affinity of the same compound was determined by ITC and demonstrated that the binding of this new triazole-based scaffold is enthalpically driven, making it a good candidate for further development.
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Affiliation(s)
- Rogelio Siles
- Department of Biology, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Yuko Kawasaki
- Department of Biology, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Patrick Ross
- Department of Biology, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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Silva VDA, Cargnelutti MT, Giesel GM, Palmieri LC, Monteiro RQ, Verli H, Lima LMTR. Structure and behavior of human α-thrombin upon ligand recognition: thermodynamic and molecular dynamics studies. PLoS One 2011; 6:e24735. [PMID: 21935446 PMCID: PMC3173475 DOI: 10.1371/journal.pone.0024735] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 08/16/2011] [Indexed: 11/19/2022] Open
Abstract
Thrombin is a serine proteinase that plays a fundamental role in coagulation. In this study, we address the effects of ligand site recognition by alpha-thrombin on conformation and energetics in solution. Active site occupation induces large changes in secondary structure content in thrombin as shown by circular dichroism. Thrombin-D-Phe-Pro-Arg-chloromethyl ketone (PPACK) exhibits enhanced equilibrium and kinetic stability compared to free thrombin, whose difference is rooted in the unfolding step. Small-angle X-ray scattering (SAXS) measurements in solution reveal an overall similarity in the molecular envelope of thrombin and thrombin-PPACK, which differs from the crystal structure of thrombin. Molecular dynamics simulations performed with thrombin lead to different conformations than the one observed in the crystal structure. These data shed light on the diversity of thrombin conformers not previously observed in crystal structures with distinguished catalytic and conformational behaviors, which might have direct implications on novel strategies to design direct thrombin inhibitors.
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Affiliation(s)
- Vivian de Almeira Silva
- School of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Federal Institute of Rio de Janeiro for Science and Technology Education, Rio de Janeiro, Brazil
- Medical Biochemistry Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Maria Thereza Cargnelutti
- School of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Medical Biochemistry Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Guilherme M. Giesel
- School of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Center for Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Leonardo C. Palmieri
- School of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Robson Q. Monteiro
- Medical Biochemistry Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Hugo Verli
- School of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Center for Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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Desai BJ, Boothello RS, Mehta AY, Scarsdale JN, Wright HT, Desai UR. Interaction of thrombin with sucrose octasulfate. Biochemistry 2011; 50:6973-82. [PMID: 21736375 DOI: 10.1021/bi2004526] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The serine protease thrombin plays multiple roles in many important physiological processes, especially coagulation, where it functions as both a pro- and anticoagulant. The polyanionic glycosaminoglycan heparin modulates thrombin's activity through binding at exosite II. Sucrose octasulfate (SOS) is often used as a surrogate for heparin, but it is not known whether it is an effective heparin mimic in its interaction with thrombin. We have characterized the interaction of SOS with thrombin in solution and determined a crystal structure of their complex. SOS binds thrombin with a K(d) of ~1.4 μM, comparable to that of the much larger polymeric heparin measured under the same conditions. Nonionic (hydrogen bonding) interactions make a larger contribution to thrombin binding of SOS than to heparin. SOS binding to exosite II inhibits thrombin's catalytic activity with high potency but with low efficacy. Analytical ultracentrifugation shows that bovine and human thrombins are monomers in solution in the presence of SOS, in contrast to their complexes with heparin, which are dimers. In the X-ray crystal structure, two molecules of SOS are bound nonequivalently to exosite II portions of a thrombin dimer, in contrast to the 1:2 stoichiometry of the heparin-thrombin complex, which has a different monomer association mode in the dimer. SOS and heparin binding to exosite II of thrombin differ on both chemical and structural levels and, perhaps most significantly, in thrombin inhibition. These differences may offer paths to the design of more potent exosite II binding, allosteric small molecules as modulators of thrombin function.
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Affiliation(s)
- Bijoy J Desai
- Departments of Medicinal Chemistry and Biochemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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Myerson J, He L, Lanza G, Tollefsen D, Wickline S. Thrombin-inhibiting perfluorocarbon nanoparticles provide a novel strategy for the treatment and magnetic resonance imaging of acute thrombosis. J Thromb Haemost 2011; 9:1292-300. [PMID: 21605330 PMCID: PMC3686484 DOI: 10.1111/j.1538-7836.2011.04339.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND As a regulator of the penultimate step in the coagulation cascade, thrombin represents a principal target of direct and specific anticoagulants. OBJECTIVE A potent thrombin inhibitor complexed with a colloidal nanoparticle was devised as a first-in-class anticoagulant with prolonged and highly localized therapeutic impact conferred by its multivalent thrombin-absorbing particle surface. METHODS PPACK (Phe[D]-Pro-Arg-Chloromethylketone) was secured covalently to the surface of perfluorocarbon-core nanoparticle structures. PPACK and PPACK nanoparticle inhibition of thrombin were assessed in vitro via thrombin activity against a chromogenic substrate. In vivo antithrombotic activity of PPACK, heparin, non-functionalized nanoparticles and PPACK nanoparticles was assessed through intravenous (i.v.) administration prior to acute photochemical injury of the common carotid artery. Perfluorocarbon particle retention in extracted carotid arteries from injured mice was assessed via (19) F magnetic resonance spectroscopy (MRS) and imaging (MRI) at 11.7 T. Activated partial thromboplastin time (APTT) measurements determined the systemic effects of the PPACK nanoparticles at various times after injection. RESULTS An optical assay verified that PPACK nanoparticles exceeded PPACK's intrinsic activity against thrombin. Application of an in vivo acute arterial thrombosis model demonstrated that PPACK nanoparticles outperformed both heparin (P=0.001) and uncomplexed PPACK (P = 0.0006) in inhibiting thrombosis. (19) F MRS confirmed that PPACK nanoparticles specifically bound to sites of acute thrombotic injury. APTT normalized within 20 min of PPACK nanoparticles injection. CONCLUSIONS PPACK nanoparticles present thrombin-inhibiting surfaces at sites of acutely forming thrombi that continue to manifest local clot inhibition even as systemic effects rapidly diminish and thus represent a new platform for localized control of acute thrombosis.
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Affiliation(s)
- J Myerson
- Washington University, Saint Louis, MO, USA
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17
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Rupin A, Marx I, Vallez MO, Mennecier P, Gloanec P, De Nanteuil G, Verbeuren TJ. S35972, a direct-acting thrombin inhibitor with high oral bioavailability and antithrombotic efficacy. J Thromb Haemost 2011; 9:1375-82. [PMID: 21481181 DOI: 10.1111/j.1538-7836.2011.04286.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Dabigatran etexilate is the first oral thrombin inhibitor to demonstrate superior efficacy to warfarin for stroke prevention in patients with atrial fibrillation. This study describes the in vitro, ex vivo anticoagulant and in vivo antithrombotic effects of an oral thrombin inhibitor, S35972, in comparison with dabigatran etexilate. METHODS Enzyme assays with thrombin and related serine proteases were performed. Clotting times, including activated partial thromboplastin time (APTT) and thrombin time (TT), were measured in vitro in different species and ex vivo in dogs and rats to determine pharmacologic bioavailabilities. The formation of occlusive venous and arterial thrombi in the rat vena cava and aorta was induced with stasis plus thromboplastin or ferrous chloride, respectively. RESULTS S35972 inhibited human thrombin with an IC(50) of 3.7 nm, and did not inhibit other serine proteases. The anticoagulant activities of S35972 in vitro were comparable in dog and human plasmas, and the sensitivity of the clotting times to S35972 was TT > APTT > prothrombin time. In the fasted dog, oral administration of 3 mg kg(-1) S35972 increased TT rapidly and for at least 8 h, and its pharmacologic bioavailability was 75.4% ± 0.1%. In the rat venous thrombosis model, 3 mg kg(-1) oral S35972 or dabigatran etexilate significantly decreased the thrombus weight. In the rat aortic thrombosis model, oral S35972 at 10mg kg(-1) significantly decreased thrombus weight, by approximately 50%, whereas, at this dose, no effect was obtained with dabigatran etexilate. CONCLUSIONS S35972 is a non-prodrug thrombin inhibitor with high selectivity, oral bioavailability, and antithrombotic efficacy.
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Affiliation(s)
- A Rupin
- Divisions of Angiology and Medicinal Chemistry, Institut de Recherches Servier, rue des Moulineaux, Suresnes, France
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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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Lee YK, Player MR. Developments in factor Xa inhibitors for the treatment of thromboembolic disorders. Med Res Rev 2011; 31:202-83. [DOI: 10.1002/med.20183] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Hanessian S, Larsson A, Fex T, Knecht W, Blomberg N. Design and synthesis of macrocyclic indoles targeting blood coagulation cascade Factor XIa. Bioorg Med Chem Lett 2010; 20:6925-8. [DOI: 10.1016/j.bmcl.2010.09.141] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 09/27/2010] [Accepted: 09/28/2010] [Indexed: 11/27/2022]
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21
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Synthesis of a versatile 2 (1H)-pyrazinone core for the preparation of Tissue Factor-Factor VIIa inhibitors. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.02.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Hanessian S, Therrien E, Zhang J, Otterlo WV, Xue Y, Gustafsson D, Nilsson I, Fjellström O. From natural products to achiral drug prototypes: potent thrombin inhibitors based on P2/P3 dihydropyrid-2-one core motifs. Bioorg Med Chem Lett 2009; 19:5429-32. [PMID: 19674897 DOI: 10.1016/j.bmcl.2009.07.107] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 07/21/2009] [Accepted: 07/22/2009] [Indexed: 11/16/2022]
Abstract
A series of dihydropyrid-2-ones was synthesized and tested for inhibitory activity against serine protease enzymes. Moderate to low nanomolar inhibitory activities were obtained against thrombin and excellent selectivity against trypsin was observed.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C. P. 6128, Succ. Centre-Ville, Montréal, P. Q., Canada H3C 3J7.
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23
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Wang G, Goyal N, Hopkinson B. Preparation of l-proline based aeruginosin 298-A analogs: Optimization of the P1-moiety. Bioorg Med Chem Lett 2009; 19:3798-803. [DOI: 10.1016/j.bmcl.2009.04.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 04/08/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
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24
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Nisius B, Rester U. Fragment Shuffling: An Automated Workflow for Three-Dimensional Fragment-Based Ligand Design. J Chem Inf Model 2009; 49:1211-22. [DOI: 10.1021/ci8004572] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Britta Nisius
- Bayer HealthCare AG, Global Drug Discovery, Lead Generation and Optimization, Aprather Weg 18a, D-42096 Elberfeld, Germany
| | - Ulrich Rester
- Bayer HealthCare AG, Global Drug Discovery, Lead Generation and Optimization, Aprather Weg 18a, D-42096 Elberfeld, Germany
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25
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Lima LMTR, Becker CF, Giesel GM, Marques AF, Cargnelutti MT, de Oliveira Neto M, Monteiro RQ, Verli H, Polikarpov I. Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:873-81. [PMID: 19332154 DOI: 10.1016/j.bbapap.2009.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2008] [Revised: 02/24/2009] [Accepted: 03/09/2009] [Indexed: 11/15/2022]
Abstract
Suramin is a hexasulfonated naphthylurea which has been recently characterized as a non-competitive inhibitor of human alpha-thrombin activity over fibrinogen, although its binding site and mode of interaction with the enzyme remain elusive. Here, we determined two X-ray structure of the thrombin:suramin complex, refined at 2.4 A resolution. While a single thrombin:suramin complex was found in the asymmetric unit cell of the crystal, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. Molecular dynamics simulations with the 1:1 complex demonstrate a large rearrangement of suramin in the complex, but with the protein scaffold and the more extensive protein-ligand regions keep unchanged. Small-angle X-ray scattering measurements at high micromolar concentration demonstrate a suramin-induced dimerization of the enzyme. These data indicating a dissimilar binding mode in the monomeric and oligomeric states, with a monomeric, 1:1 complex to be more likely to exist at the thrombin physiological, nanomolar concentration range. Collectively, close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin.
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Affiliation(s)
- Luis Maurício T R Lima
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-590, Rio de Janeiro, RJ, Brazil.
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26
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Ilaš J, Jakopin Ž, Borštnar T, Stegnar M, Kikelj D. 3,4-Dihydro-2H-1,4-benzoxazine Derivatives Combining Thrombin Inhibitory and Glycoprotein IIb/IIIa Receptor Antagonistic Activity as a Novel Class of Antithrombotic Compounds with Dual Function. J Med Chem 2008; 51:5617-29. [DOI: 10.1021/jm8003448] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia, and Department of Vascular Diseases, University Medical Centre Ljubljana, Zaloška 7, SI-1525 Ljubljana, Slovenia
| | - Žiga Jakopin
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia, and Department of Vascular Diseases, University Medical Centre Ljubljana, Zaloška 7, SI-1525 Ljubljana, Slovenia
| | - Tina Borštnar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia, and Department of Vascular Diseases, University Medical Centre Ljubljana, Zaloška 7, SI-1525 Ljubljana, Slovenia
| | - Mojca Stegnar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia, and Department of Vascular Diseases, University Medical Centre Ljubljana, Zaloška 7, SI-1525 Ljubljana, Slovenia
| | - Danijel Kikelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia, and Department of Vascular Diseases, University Medical Centre Ljubljana, Zaloška 7, SI-1525 Ljubljana, Slovenia
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27
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Synthesis of octahydropyrano[3,2-b]pyrrole-2-carboxylic acid derivatives from d-mannose. Carbohydr Res 2008; 343:1743-53. [DOI: 10.1016/j.carres.2008.03.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2007] [Revised: 03/06/2008] [Accepted: 03/10/2008] [Indexed: 11/20/2022]
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28
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Total synthesis of aeruginosin 298-A analogs containing ring oxygenated variants of 2-carboxy-6-hydroxyoctahydroindole. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.03.107] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Zürcher M, Diederich F. Structure-Based Drug Design: Exploring the Proper Filling of Apolar Pockets at Enzyme Active Sites. J Org Chem 2008; 73:4345-61. [DOI: 10.1021/jo800527n] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Zürcher
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
| | - François Diederich
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
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30
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Hanessian S, Simard D, Bayrakdarian M, Therrien E, Nilsson I, Fjellström O. Design, synthesis, and thrombin-inhibitory activity of pyridin-2-ones as P2/P3 core motifs. Bioorg Med Chem Lett 2008; 18:1972-6. [DOI: 10.1016/j.bmcl.2008.01.122] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 01/30/2008] [Accepted: 01/30/2008] [Indexed: 11/25/2022]
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31
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Ersmark K, Del Valle J, Hanessian S. Aeruginosine: Chemie und Biologie der Serinprotease-Inhibitoren. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200605219] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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Ersmark K, Del Valle J, Hanessian S. Chemistry and Biology of the Aeruginosin Family of Serine Protease Inhibitors. Angew Chem Int Ed Engl 2008; 47:1202-23. [DOI: 10.1002/anie.200605219] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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33
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Li W, Blankman JL, Cravatt BF. A Functional Proteomic Strategy to Discover Inhibitors for Uncharacterized Hydrolases. J Am Chem Soc 2007; 129:9594-5. [PMID: 17629278 DOI: 10.1021/ja073650c] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Weiwei Li
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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34
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Hanessian S, Ersmark K, Wang X, Del Valle JR, Blomberg N, Xue Y, Fjellström O. Structure-based organic synthesis of unnatural aeruginosin hybrids as potent inhibitors of thrombin. Bioorg Med Chem Lett 2007; 17:3480-5. [PMID: 17428662 DOI: 10.1016/j.bmcl.2007.03.075] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Revised: 03/21/2007] [Accepted: 03/23/2007] [Indexed: 11/21/2022]
Abstract
Based on X-ray crystallographic data of complexes of chlorodysinosin A with the enzyme thrombin, a series of analogs were synthesized varying the nature of the P(1), P(2), and P(3) pharmacophoric sites and the central octahydroindole carboxyamide core. In general, introduction of a hydrophobic substituent on the d-leucine amide residue dramatically improved the inhibition of the enzyme. This is rationalized based on a better fit of the P(3) subunit in the hydrophobic S(3) enzyme site. Single digit nanomolar inhibition expressed as IC(50) was observed for several analogs.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, PO Box 6128, Station, Centre-Ville, Montréal, QC, Canada H3C 3J7.
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35
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Blomberg D, Fex T, Xue Y, Brickmann K, Kihlberg J. Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold. Org Biomol Chem 2007; 5:2599-605. [DOI: 10.1039/b705344d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Winum JY, Scozzafava A, Montero JL, Supuran CT. Therapeutic potential of sulfamides as enzyme inhibitors. Med Res Rev 2006; 26:767-92. [PMID: 16710859 DOI: 10.1002/med.20068] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sulfamide, a quite simple molecule incorporating the sulfonamide functionality, widely used by medicinal chemists for the design of a host of biologically active derivatives with pharmacological applications, may give rise to at least five types of derivatives, by substituting one to four hydrogen atoms present in it, which show specific biological activities. Recently, some of these compounds started to be exploited for the design of many types of therapeutic agents. Among the enzymes for which sulfamide-based inhibitors were designed, are the carbonic anhydrases (CAs), a large number of proteases belonging to the aspartic protease (HIV-1 protease, gamma-secretase), serine protease (elastase, chymase, tryptase, and thrombin among others), and metalloprotease (carboxypeptidase A (CPA) and matrix metalloproteinases (MMP)) families. Some steroid sulfatase (STS) and protein tyrosine phosphatase inhibitors belonging to the sulfamide class of derivatives have also been reported. In all these compounds, many of which show low nanomolar affinity for the target enzymes for which they have been designed, the free or substituted sulfamide moiety plays important roles for the binding of the inhibitor to the active site cavity, either by directly coordinating to a metal ion found in some metalloenzymes (CAs, CPA, STS), usually by means of one of the nitrogen atoms present in the sulfamide motif, or as in the case of the cyclic sulfamides acting as HIV protease inhibitors, interacting with the catalytically critical aspartic acid residues of the active site by means of an oxygen atom belonging to the HN-SO2-NH motif, which substitutes a catalytically essential water molecule. In other cases, the sulfamide moiety is important for inducing desired physico-chemical properties to the drug-like compounds incorporating it, such as enhanced water solubility, better bioavailability, etc., because of the intrinsic properties of this highly polarized moiety when attached to an organic scaffold. This interesting motif is thus of great value for the design of pharmacological agents with a lot of applications.
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Affiliation(s)
- Jean-Yves Winum
- Université Montpellier II, Laboratoire de Chimie Biomoléculaire, UMR 5032, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex, France.
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Nie X, Wang G. Synthesis of a ring-oxygenated variant of the 2-carboxy-6-hydroxyoctahydroindole core of aeruginosin 298-A from glucose. J Org Chem 2006; 70:8687-92. [PMID: 16238296 DOI: 10.1021/jo0507901] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] The design and synthesis of a new core structure, a ring-oxygenated variant of 2-carboxy-6-hydroxyoctahydroindole (Choi) from D-glucose, is reported. Choi, a rigid bicyclic unnatural amino acid, is the core structure of about 15 aeruginosins natural compounds. These compounds are thrombin, trypsin, and factor VIIa inhibitors and Choi is important for their biological activity. The ring-oxygenated variant of 2-carboxy-6-hydroxyoctahydroindole can potentially be used as a surrogate of Choi in the design and synthesis of aeruginosin-based thrombin inhibitors.
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Affiliation(s)
- Xiaoping Nie
- Department of Chemistry, University of New Orleans, Louisiana 70148, USA
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38
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Hanessian S, Therrien E, van Otterlo WAL, Bayrakdarian M, Nilsson I, Fjellström O, Xue Y. Phenolic P2/P3 core motif as thrombin inhibitors—Design, synthesis, and X-ray co-crystal structure. Bioorg Med Chem Lett 2006; 16:1032-6. [PMID: 16290930 DOI: 10.1016/j.bmcl.2005.10.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 10/14/2005] [Accepted: 10/24/2005] [Indexed: 10/25/2022]
Abstract
Prototypical thrombin inhibitors were synthesized based on a trisubstituted phenol as a core motif. A naphthylsulfonamide analogue showed excellent antithrombin activity. An X-ray co-crystal structure showed the expected interactions.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, PQ, Canada H3C 3J7.
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Kohrt JT, Filipski KJ, Cody WL, Cai C, Dudley DA, Van Huis CA, Willardsen JA, Narasimhan LS, Zhang E, Rapundalo ST, Saiya-Cork K, Leadley RJ, Edmunds JJ. The discovery of fluoropyridine-based inhibitors of the factor VIIa/TF complex—Part 2. Bioorg Med Chem Lett 2006; 16:1060-4. [PMID: 16289811 DOI: 10.1016/j.bmcl.2005.10.076] [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] [Received: 09/06/2005] [Revised: 10/21/2005] [Accepted: 10/21/2005] [Indexed: 10/25/2022]
Abstract
The activated factor VII/tissue factor complex (FVIIa/TF) is known to play a key role in the formation of blood clots. Inhibition of this complex may lead to new antithrombotic drugs. A fluoropyridine-based series of FVIIa/TF inhibitors was discovered which utilized a diisopropylamino group for binding in the S2 and S3 binding pockets of the active site of the enzyme complex. In this series, an enhancement in binding affinity was observed by substitution at the 5-position of the hydroxybenzoic acid sidechain. An X-ray crystal structure indicates that amides at this position may increase inhibitor binding affinity through interactions with the S1'/S2' pocket.
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Affiliation(s)
- Jeffrey T Kohrt
- Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.
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Schweizer E, Hoffmann-Röder A, Olsen JA, Seiler P, Obst-Sander U, Wagner B, Kansy M, Banner DW, Diederich F. Multipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors. Org Biomol Chem 2006; 4:2364-75. [PMID: 16763681 DOI: 10.1039/b602585d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two series of tricyclic inhibitors of the serine protease thrombin, imides (+/-)-1-(+/-)-8 and lactams (+/-)-9-(+/-)-13, were analysed to evaluate contributions of orthogonal multipolar interactions with the backbone C=O moiety of Asn98 to the free enthalpy of protein-ligand complexation. The lactam derivatives are much more potent and more selective inhibitors (K(i) values between 0.065 and 0.005 microM, selectivity for thrombin over trypsin between 361- and 1609-fold) than the imide compounds (Ki values between 0.057 and 23.7 microM, selectivity for thrombin over trypsin between 3- and 67-fold). The increase in potency and selectivity is explained by the favorable occupancy of the P-pocket of thrombin by the additional isopropyl substituent in the lactam derivatives. The nature of the substituent on the benzyl ring filling the D pocket strongly influences binding potency in the imide series, with Ki values increasing in the sequence: F < OCH2O < Cl < H < OMe < OH < N(pyr)<< Br. This sequence can be explained by both steric fit and the occurrence of orthogonal multipolar interactions with the backbone C[double bond, length as m-dash]O moiety of Asn98. In contrast, the substituent on the benzyl ring hardly affects the ligand potency in the lactam series. This discrepancy was clarified by the comparison of X-ray structures solved for co-crystals of thrombin with imide and lactam ligands. Whereas the benzyl substituents in the imide inhibitors are sufficiently close (< or =3.5 Angstroms) to the C=O group of Asn98 to allow for attractive orthogonal multipolar interactions, the distances in the lactam series are too large (> or =4 Angstroms) for attractive dipolar contacts to be effective.
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Affiliation(s)
- Eliane Schweizer
- Laboratorium für Organische Chemie, ETH-Zürich, Hönggerberg HCI, Switzerland
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41
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Winum JY, Scozzafava A, Montero JL, Supuran CT. The sulfamide motif in the design of enzyme inhibitors. Expert Opin Ther Pat 2005; 16:27-47. [DOI: 10.1517/13543776.16.1.27] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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