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Gogoi D, Chattopadhyay P, Dolui SK, Khan MR, Mukherjee AK. Studies on in vivo antithrombotic activity of quercetin, a natural flavonoid isolated from a traditional medicinal plant, African eggplant (Solanum indicum). JOURNAL OF ETHNOPHARMACOLOGY 2024; 335:118686. [PMID: 39127114 DOI: 10.1016/j.jep.2024.118686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 07/30/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Every year, cardiovascular diseases (CVDs) account for about 17.9 million deaths, making them the primary cause of both morbidity and mortality. Conventional drugs, which are often prescribed to treat cardiovascular diseases, are costly and have adverse effects. Consequently, dietary modifications and other medications are needed. Traditional use of Solanum indicum as cardiotonic to treat hypertension and anticoagulant potency has been reported but poorly evaluated scientifically. AIM OF THE STUDY This study investigated the in vivo anticoagulant activity and mechanism of anticoagulation of quercetin (QC), a bioactive compound isolated from S. indicum (SI) hydroethanolic fruit extract. MATERIALS AND METHODS Bioassay-guided fractionation (anticoagulant activity) extracted QC from hydroethanolic SI extract. QC was extensively characterized biochemically and pharmacologically. The interaction between QC and thrombin was investigated using spectrofluorometric and isothermal calorimetric methods. Cytotoxicity, antiplatelet, and thrombolytic studies were carried out in vitro. The Swiss albino mice were used to assess the in vivo, anticoagulant, and antithrombotic activities of QC. RESULTS QC exhibits anticoagulant activity via (i) uncompetitive inhibition of thrombin but not FXa with a Ki value of 33.11 ± 4.2 μM and (ii) a partial inhibition of thrombin-catalyzed platelet aggregation with an IC50 value of 13.2 ± 1.2 μM. The experimental validation of the in silico study's prediction of QC's binding to thrombin was confirmed by spectrofluorometric and isothermal calorimetric analyses. QC was nontoxic to mammalian, non-hemolytic cells and demonstrated thrombolytic activity by activating plasminogen. QC demonstrated in vivo anticoagulant efficacy, preventing k-carrageen-induced thrombus formation in mice's tails. In the acute circulatory stasis paradigm in mice, QC reduces thromboxane B2 (TXB2) and endothelin-1 (ET-1) while increasing nitric oxide synthase (eNOS) and 6-keto prostaglandin F1α (6-keto-PGF1 α). CONCLUSION Effective in vivo anticoagulant and antithrombotic properties of S. indicum's bioactive component QC point to the plant's potential use as a herbal anticoagulant medication for preventing and treating cardiovascular diseases linked to thrombosis.
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Affiliation(s)
- Debananda Gogoi
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, School of Sciences, Tezpur University, Tezpur, 784028, Assam, India
| | | | - Swapan K Dolui
- Department of Chemical Sciences, Tezpur University, Tezpur, Assam, India
| | - Mujibur R Khan
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, 781035, Assam, India
| | - Ashis K Mukherjee
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, School of Sciences, Tezpur University, Tezpur, 784028, Assam, India; Division of Life Sciences, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, 781035, Assam, India.
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Hubálek F, Cramer CN, Helleberg H, Johansson E, Nishimura E, Schluckebier G, Steensgaard DB, Sturis J, Kjeldsen TB. Enhanced disulphide bond stability contributes to the once-weekly profile of insulin icodec. Nat Commun 2024; 15:6124. [PMID: 39033137 PMCID: PMC11271312 DOI: 10.1038/s41467-024-50477-9] [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] [Received: 01/31/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024] Open
Abstract
Insulin icodec is a once-weekly insulin analogue that has a long half-life of approximately 7 days, making it suitable for once weekly dosing. The Insulin icodec molecule was developed based on the hypothesis that lowering insulin receptor affinity and introducing a strong albumin-binding moiety would result in a long insulin half-life, provided that non-receptor-mediated clearance is diminished. Here, we report an insulin clearance mechanism, resulting in the splitting of insulin molecules into its A-chain and B-chain by a thiol-disulphide exchange reaction. Even though the substitutions in insulin icodec significantly stabilise insulin against such degradation, some free B-chain is observed in plasma samples from minipigs and people with type 2 diabetes. In summary, we identify thiol-disulphide exchange reactions to be an important insulin clearance mechanism and find that stabilising insulin icodec towards this reaction significantly contributes to its long pharmacokinetic/pharmacodynamic profile.
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Saladini LY, Magalhães-Junior MJ, da Silva CCF, Oliveira PGC, Kodama RT, Gomes L, Nishiyama-Jr MY, Spencer PJ, da Silva WD, Portaro FCV. Evaluation of the Inhibitory Potential of Synthetic Peptides Homologous to CDR3 Regions of a Monoclonal Antibody against Bothropic Venom Serine Proteases. Int J Mol Sci 2024; 25:5181. [PMID: 38791221 PMCID: PMC11121450 DOI: 10.3390/ijms25105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024] Open
Abstract
Snakebite accidents, neglected tropical diseases per the WHO, pose a significant public health threat due to their severity and frequency. Envenomation by Bothrops genus snakes leads to severe manifestations due to proteolytic enzymes. While the antibothropic serum produced by the Butantan Institute saves lives, its efficacy is limited as it fails to neutralize certain serine proteases. Hence, developing new-generation antivenoms, like monoclonal antibodies, is crucial. This study aimed to explore the inhibitory potential of synthetic peptides homologous to the CDR3 regions of a monoclonal antibody targeting a snake venom thrombin-like enzyme (SVTLE) from B. atrox venom. Five synthetic peptides were studied, all stable against hydrolysis by venoms and serine proteases. Impressively, four peptides demonstrated uncompetitive SVTLE inhibition, with Ki values ranging from 10-6 to 10-7 M. These findings underscore the potential of short peptides homologous to CDR3 regions in blocking snake venom toxins, suggesting their promise as the basis for new-generation antivenoms. Thus, this study offers potential advancements in combatting snakebites, addressing a critical public health challenge in tropical and subtropical regions.
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Affiliation(s)
- Lucas Yuri Saladini
- Laboratory of Structure and Function of Biomolecules, Butantan Institute, São Paulo 05503-900, Brazil (C.C.F.d.S.); (P.G.C.O.); (R.T.K.); (L.G.)
| | | | | | - Priscila Gonçalves Coutinho Oliveira
- Laboratory of Structure and Function of Biomolecules, Butantan Institute, São Paulo 05503-900, Brazil (C.C.F.d.S.); (P.G.C.O.); (R.T.K.); (L.G.)
| | - Roberto Tadashi Kodama
- Laboratory of Structure and Function of Biomolecules, Butantan Institute, São Paulo 05503-900, Brazil (C.C.F.d.S.); (P.G.C.O.); (R.T.K.); (L.G.)
| | - Lais Gomes
- Laboratory of Structure and Function of Biomolecules, Butantan Institute, São Paulo 05503-900, Brazil (C.C.F.d.S.); (P.G.C.O.); (R.T.K.); (L.G.)
| | - Milton Yutaka Nishiyama-Jr
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil;
| | - Patrick Jack Spencer
- Biotechnology Center, Nuclear and Energy Research Institute (IPEN/CNEN/SP), São Paulo 05503-900, Brazil;
| | | | - Fernanda Calheta Vieira Portaro
- Laboratory of Structure and Function of Biomolecules, Butantan Institute, São Paulo 05503-900, Brazil (C.C.F.d.S.); (P.G.C.O.); (R.T.K.); (L.G.)
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Stojanovski BM, Pelc LA, Di Cera E. Thrombin has dual trypsin-like and chymotrypsin-like specificity. J Thromb Haemost 2024; 22:1009-1015. [PMID: 38160728 PMCID: PMC10960677 DOI: 10.1016/j.jtha.2023.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The residue at the site of activation of protein C is Arg in all species except the ray-finned fish, where it is Trp. This feature raises the question of whether thrombin is the physiological activator of protein C across vertebrates. OBJECTIVES To establish if thrombin can cleave at Trp residues. METHODS The activity of wild-type thrombin and mutant D189S was tested with a library of chromogenic substrates and toward wild-type protein C and mutants carrying substitutions at the site of cleavage. RESULTS Thrombin has trypsin-like and chymotrypsin-like specificity and cleaves substrates at Arg or Trp residues. Cleavage at Arg is preferred, but cleavage at Trp is significant and comparable with that of chymotrypsin. The D189S mutant of thrombin has broad specificity and cleaves at basic and aromatic residues without significant preference. Thrombin also cleaves natural substrates at Arg or Trp residues, showing activity toward protein C across vertebrates, including the ray-finned fish. The rate of activation of protein C in the ray-finned fish is affected by the sequence preceding Trp at the scissile bond. CONCLUSION The results provide a possible solution for the paradoxical presence of a Trp residue at the site of cleavage of protein C in ray-finned fish and support thrombin as the physiological activator of protein C in all vertebrates. The dual trypsin-like and chymotrypsin-like specificity of thrombin suggests that the spectrum of physiological substrates of this enzyme is broader currently assumed.
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Affiliation(s)
- Bosko M Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
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Stojanovski BM, Mohammed BM, Di Cera E. The Prothrombin-Prothrombinase Interaction. Subcell Biochem 2024; 104:409-423. [PMID: 38963494 DOI: 10.1007/978-3-031-58843-3_15] [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: 07/05/2024]
Abstract
The hemostatic response to vascular injury entails a sequence of proteolytic events where several inactive zymogens of the trypsin family are converted to active proteases. The cascade starts with exposure of tissue factor from the damaged endothelium and culminates with conversion of prothrombin to thrombin in a reaction catalyzed by the prothrombinase complex composed of the enzyme factor Xa, cofactor Va, Ca2+, and phospholipids. This cofactor-dependent activation is paradigmatic of analogous reactions of the blood coagulation and complement cascades, which makes elucidation of its molecular mechanism of broad significance to the large class of trypsin-like zymogens to which prothrombin belongs. Because of its relevance as the most important reaction in the physiological response to vascular injury, as well as the main trigger of pathological thrombotic complications, the mechanism of prothrombin activation has been studied extensively. However, a molecular interpretation of this mechanism has become available only recently from important developments in structural biology. Here we review current knowledge on the prothrombin-prothrombinase interaction and outline future directions for the study of this key reaction of the coagulation cascade.
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Affiliation(s)
- Bosko M Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Bassem M Mohammed
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.
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Xie ZS, Han XY, Zhou ZY, Li SY, Zhu JY, Zhang L, Xue ST. Design and synthesis of dabigatran etexilate derivatives with inhibiting thrombin activity for hepatocellular carcinoma treatment. Biomed Pharmacother 2024; 170:116018. [PMID: 38113628 DOI: 10.1016/j.biopha.2023.116018] [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] [Received: 10/16/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most fatal solid malignancies worldwide. Evidence suggests that thrombin stimulates tumor progression via fibrin formation and platelet activation. Meanwhile, we also found a correlation between thrombin and HCC through bioinformatics analysis. Dabigatran is a selective, direct thrombin inhibitor that reversibly binds to thrombin. Dabigatran was used as the lead agent in this study, and 19 dabigatran derivatives were designed and synthesized based on docking mode. The thrombin-inhibitory activity of the derivative AX-2 was slightly better than that of dabigatran. BX-2, a prodrug of AX-2, showed a fairly strong inhibitory effect on thrombin-induced platelet aggregation, and effectively antagonized proliferation of HCC tumor cells induced by thrombin at the cellular level. Furthermore, BX-2 reduced tumor volume, weight, lung metastasis, and secondary tumor occurrence in nude mouse models. BX-2 combined with sorafenib increased sorafenib efficacy. This study lays the foundation for discovering new anti-HCC mechanism based on thrombin. BX-2 can be used as an anti-HCC drug lead for further research.
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Affiliation(s)
- Zhuo-Song Xie
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiao-Yang Han
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zi-Ying Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Si-Yan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiang-Yi Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lei Zhang
- School of Biological & Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, China.
| | - Si-Tu Xue
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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García-Faustino LL, Morris SM, Elston SJ, Montelongo Y. Detection of Biomarkers through Functionalized Polymers. SMALL METHODS 2024; 8:e2301025. [PMID: 37814377 DOI: 10.1002/smtd.202301025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Indexed: 10/11/2023]
Abstract
Over the past decade, there has been a rising interest in utilizing functionalized porous polymers for sensor applications. By incorporating functional groups into nanostructured materials like hydrogels, nanosheets, and nanopores, exciting new opportunities have emerged for biomarker detection. The ability of functionalized polymers to undergo physical changes and deformations makes them perfect for modulating optical signals. This chemical mechanism enables the creation of biocompatible sensors for in situ biomarker measurement. Here a comprehensive overview of the current publication trends is provided in functionalized polymers, encompassing functional groups that can induce measurable physical deformations. It explores various materials categorized based on their detection targets, which include proteins, carbohydrates, ions, and deoxyribonucleic acid. As such, this work serves as a valuable reference for the development of functionalized polymer-based sensors.
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Affiliation(s)
- Litzy L García-Faustino
- School of Engineering and Sciences, Tecnológico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, NL, 64849, Mexico
| | - Stephen M Morris
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Steve J Elston
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Yunuen Montelongo
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
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Acquasaliente L, Pierangelini A, Pagotto A, Pozzi N, De Filippis V. From haemadin to haemanorm: Synthesis and characterization of full-length haemadin from the leech Haemadipsa sylvestris and of a novel bivalent, highly potent thrombin inhibitor (haemanorm). Protein Sci 2023; 32:e4825. [PMID: 37924304 PMCID: PMC10683372 DOI: 10.1002/pro.4825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Hirudin from Hirudo medicinalis is a bivalent α-Thrombin (αT) inhibitor, targeting the enzyme active site and exosite-I, and is currently used in anticoagulant therapy along with its simplified analogue hirulog. Haemadin, a small protein (57 amino acids) isolated from the land-living leech Haemadipsa sylvestris, selectively inhibits αT with a potency identical to that of recombinant hirudin (KI = 0.2 pM), with which it shares a common disulfide topology and overall fold. At variance with hirudin, haemadin targets exosite-II and therefore (besides the free protease) it also blocks thrombomodulin-bound αT without inhibiting the active intermediate meizothrombin, thus offering potential advantages over hirudin. Here, we produced in reasonably high yields and pharmaceutical purity (>98%) wild-type haemadin and the oxidation resistant Met5 → nor-Leucine analogue, both inhibiting αT with a KI of 0.2 pM. Thereafter, we used site-directed mutagenesis, spectroscopic, ligand-displacement, and Hydrogen/Deuterium Exchange-Mass Spectrometry techniques to map the αT regions relevant for the interaction with full-length haemadin and with the synthetic N- and C-terminal peptides Haem(1-10) and Haem(45-57). Haem(1-10) competitively binds to/inhibits αT active site (KI = 1.9 μM) and its potency was enhanced by 10-fold after Phe3 → β-Naphthylalanine exchange. Conversely to full-length haemadin, haem(45-57) displays intrinsic affinity for exosite-I (KD = 1.6 μM). Hence, we synthesized a peptide in which the sequences 1-9 and 45-57 were joined together through a 3-Glycine spacer to yield haemanorm, a highly potent (KI = 0.8 nM) inhibitor targeting αT active site and exosite-I. Haemanorm can be regarded as a novel class of hirulog-like αT inhibitors with potential pharmacological applications.
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Affiliation(s)
- Laura Acquasaliente
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Andrea Pierangelini
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Anna Pagotto
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Nicola Pozzi
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research CenterSaint Louis UniversitySt. LouisMissouriUSA
| | - Vincenzo De Filippis
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
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Troisi R, Napolitano V, Rossitto E, Osman W, Nagano M, Wakui K, Popowicz G, Yoshimoto K, Sica F. Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide. Nucleic Acids Res 2023; 51:8880-8890. [PMID: 37503836 PMCID: PMC10484730 DOI: 10.1093/nar/gkad634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Ligand/protein molecular recognition involves a dynamic process, whereby both partners require a degree of structural plasticity to regulate the binding/unbinding event. Here, we present the characterization of the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. M08s-1 is the most active anticoagulant aptamer selected thus far. Circular dichroism and gel electrophoresis analyses indicate that both intramolecular and intermolecular G-quadruplex structures are populated in solution. The presence of thrombin stabilises the antiparallel intramolecular chair-like G-quadruplex conformation, that provides by far the main contribution to the biological activity of the aptamer. The crystal structure of the thrombin-oligonucleotide complex reveals that M08s-1 adopts a kinked structural organization formed by a G-quadruplex domain and a long duplex module, linked by a stretch of five purine bases. The quadruplex motif hooks the exosite I region of thrombin and the duplex region is folded towards the surface of the protein. This structural feature, which has never been observed in other anti-exosite I aptamers with a shorter duplex motif, hinders the approach of a protein substrate to the active site region and may well explain the significant increase in the anticoagulant activity of M08s-1 compared to the other anti-exosite I aptamers.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Valeria Napolitano
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Emanuele Rossitto
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Waleed Osman
- Research and Development Division, LinkBIO Co., Ltd., The ICI Center, 5270 Terada, Toride-shi, Ibaraki 302-0021, Japan
| | - Masanobu Nagano
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Keitaro Yoshimoto
- Research and Development Division, LinkBIO Co., Ltd., The ICI Center, 5270 Terada, Toride-shi, Ibaraki 302-0021, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
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Crossen J, Shankar KN, Diamond SL. Investigating thrombin-loaded fibrin in whole blood clot microfluidic assay via fluorogenic peptide. Biophys J 2023; 122:697-712. [PMID: 36635963 PMCID: PMC9989883 DOI: 10.1016/j.bpj.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/19/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
During clotting under flow, thrombin rapidly generates fibrin, whereas fibrin potently sequesters thrombin. This co-regulation was studied using microfluidic whole blood clotting on collagen/tissue factor, followed by buffer wash, and a start/stop cycling flow assay using the thrombin fluorogenic substrate, Boc-Val-Pro-Arg-AMC. After 3 min of clotting (100 s-1) and 5 min of buffer wash, non-elutable thrombin activity was easily detected during cycles of flow cessation. Non-elutable thrombin was similarly detected in plasma clots or arterial whole blood clots (1000 s-1). This thrombin activity was ablated by Phe-Pro-Arg-chloromethylketone (PPACK), apixaban, or Gly-Pro-Arg-Pro to inhibit fibrin. Reaction-diffusion simulations predicted 108 nM thrombin within the clot. Heparin addition to the start/stop assay had little effect on fibrin-bound thrombin, whereas addition of heparin-antithrombin (AT) required over 6 min to inhibit the thrombin, indicating a substantial diffusion limitation. In contrast, heparin-AT rapidly inhibited thrombin within microfluidic plasma clots, indicating marked differences in fibrin structure and functionality between plasma clots and whole blood clots. Addition of GPVI-Fab to blood before venous or arterial clotting (200 or 1000 s-1) markedly reduced fibrin-bound thrombin, whereas GPVI-Fab addition after 90 s of clotting had no effect. Perfusion of AF647-fibrinogen over washed fluorescein isothiocyanate (FITC)-fibrin clots resulted in an intense red layer around, but not within, the original FITC-fibrin. Similarly, introduction of plasma/AF647-fibrinogen generated substantial red fibrin masses that did not penetrate the original green clots, demonstrating that fibrin cannot be re-clotted with fibrinogen. Overall, thrombin within fibrin is non-elutable, easily accessed by peptides, slowly accessed by average-sized proteins (heparin/AT), and not accessible to fresh fibrinogen.
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Affiliation(s)
- Jennifer Crossen
- Institute for Medicine and Engineering, Department of Chemical and Biomolecular Engineering, 1024 Vagelos Research Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Kaushik N Shankar
- Institute for Medicine and Engineering, Department of Chemical and Biomolecular Engineering, 1024 Vagelos Research Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Scott L Diamond
- Institute for Medicine and Engineering, Department of Chemical and Biomolecular Engineering, 1024 Vagelos Research Laboratory, University of Pennsylvania, Philadelphia, PA 19104.
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Ibrahim MA, Masoud HMM. Purification and characterization of thrombin from camel plasma: interaction with camel tick salivary gland thrombin inhibitor. J Genet Eng Biotechnol 2023; 21:7. [PMID: 36689046 PMCID: PMC9871101 DOI: 10.1186/s43141-023-00464-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/11/2023] [Indexed: 01/24/2023]
Abstract
BACKGROUND Thrombin is the most important enzyme in the hemostatic process by permitting rapid and localized coagulation in case of tissue damage. Camel thrombin is the natural and proper target enzyme for the previously purified camel tick salivary gland thrombin inhibitor. RESULTS In this study, the camel thrombin was purified homogenously in a single affinity chromatographic step on the heparin-agarose affinity column with a specific activity of 3242 NIH units/mg proteins. On SDS-PAGE, the purified camel thrombin contained two forms, 37 kDa α-thrombin and 28 kDa β-thrombin, and the camel prothrombin was visualized as 72 kDa. The camel thrombin Km value was found out as 60 µM of N-(p-Tosyl)-Gly-Pro-Arg-p-nitroanilide acetate and displayed its optimum activity at pH 8.3. The PMSF was the most potent inhibitor of camel thrombin. Camel tick salivary gland thrombin inhibitor has two binding sites on camel thrombin and inhibited it competitively with Ki value of 0.45 µM. CONCLUSIONS The purified camel thrombin was found to be more susceptible toward the camel tick salivary gland thrombin inhibitor than bovine thrombin.
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Affiliation(s)
- Mahmoud A. Ibrahim
- grid.419725.c0000 0001 2151 8157Molecular Biology Department, National Research Centre, Dokki, Giza, Egypt ,grid.419725.c0000 0001 2151 8157Proteome Research Laboratory, Central Laboratories Network and Centers of Excellence, National Research Centre, El-Tahrir St, Dokki, Giza, Egypt
| | - Hassan M. M. Masoud
- grid.419725.c0000 0001 2151 8157Molecular Biology Department, National Research Centre, Dokki, Giza, Egypt ,grid.419725.c0000 0001 2151 8157Proteome Research Laboratory, Central Laboratories Network and Centers of Excellence, National Research Centre, El-Tahrir St, Dokki, Giza, Egypt
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Jiang S, Zhang X, Li DL, Wang TT, Ma F, Zhang CY. Construction of a gold nanoparticle-based single-molecule biosensor for simple and sensitive detection of Argonaute 2 activity. J Mater Chem B 2022; 10:5594-5601. [PMID: 35796467 DOI: 10.1039/d2tb00802e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Argonaute 2 (Ago2) is an essential component of the RNA-induced silencing complex (RISC) and it participates in diverse physiological processes, while dysregulation of Ago2 activity is closely linked to a variety of human diseases including cancers. The reported Ago2 assays often suffer from laborious procedures, complicated reaction schemes, and unsatisfactory sensitivity. Herein, we develop a new gold nanoparticle (AuNP)-based single-molecule biosensor for simple and sensitive detection of Ago2 activity. The Ago2-responsive AuNP nanoprobe is constructed through the self-assembly of multiple Cy5-labeled signal probes onto the AuNP, in which the Cy5 fluorescence is efficiently quenched by the AuNP. Target Ago2 can bind with guide RNA to form an active RISC, inducing the cyclic cleavage of the signal probes and the release of Cy5 moieties from the AuNP nanoprobe. The released Cy5 molecules can be simply quantified by single-molecule counting. This single-molecule biosensor enables detection of Ago2 activity with the involvement of only a single AuNP nanoprobe, eliminating the use of any extra antibodies and protein enzymes. This single-molecule biosensor achieves good specificity and high sensitivity with a detection limit of 9.1 pM, and it can be exploited for the screening of Ago2 inhibitors, Ago2 kinetic analysis, and the imaging of intracellular Ago2 activity in live cells, holding great promise in Ago2-related biomedical research and clinical diagnosis.
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Affiliation(s)
- Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Xinyi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan 528458, China
| | - Dong-Ling Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Ting-Ting Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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13
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Ruben EA, Summers B, Rau MJ, Fitzpatrick JAJ, Di Cera E. Cryo-EM structure of the prothrombin-prothrombinase complex. Blood 2022; 139:3463-3473. [PMID: 35427420 PMCID: PMC9203702 DOI: 10.1182/blood.2022015807] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/30/2022] [Indexed: 11/23/2022] Open
Abstract
The intrinsic and extrinsic pathways of the coagulation cascade converge to a common step where the prothrombinase complex, comprising the enzyme factor Xa (fXa), the cofactor fVa, Ca2+ and phospholipids, activates the zymogen prothrombin to the protease thrombin. The reaction entails cleavage at 2 sites, R271 and R320, generating the intermediates prethrombin 2 and meizothrombin, respectively. The molecular basis of these interactions that are central to hemostasis remains elusive. We solved 2 cryogenic electron microscopy (cryo-EM) structures of the fVa-fXa complex, 1 free on nanodiscs at 5.3-Å resolution and the other bound to prothrombin at near atomic 4.1-Å resolution. In the prothrombin-fVa-fXa complex, the Gla domains of fXa and prothrombin align on a plane with the C1 and C2 domains of fVa for interaction with membranes. Prothrombin and fXa emerge from this plane in curved conformations that bring their protease domains in contact with each other against the A2 domain of fVa. The 672ESTVMATRKMHDRLEPEDEE691 segment of the A2 domain closes on the protease domain of fXa like a lid to fix orientation of the active site. The 696YDYQNRL702 segment binds to prothrombin and establishes the pathway of activation by sequestering R271 against D697 and directing R320 toward the active site of fXa. The cryo-EM structure provides a molecular view of prothrombin activation along the meizothrombin pathway and suggests a mechanism for cleavage at the alternative R271 site. The findings advance our basic knowledge of a key step of coagulation and bear broad relevance to other interactions in the blood.
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Affiliation(s)
- Eliza A Ruben
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | | | | | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging
- Department of Cell Biology and Physiology, and
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO; and
- Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
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14
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Acquasaliente L, Pontarollo G, Radu CM, Peterle D, Artusi I, Pagotto A, Uliana F, Negro A, Simioni P, De Filippis V. Exogenous human α-Synuclein acts in vitro as a mild platelet antiaggregant inhibiting α-thrombin-induced platelet activation. Sci Rep 2022; 12:9880. [PMID: 35701444 PMCID: PMC9198058 DOI: 10.1038/s41598-022-12886-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/18/2022] [Indexed: 11/29/2022] Open
Abstract
α-Synuclein (αSyn) is a small disordered protein, highly conserved in vertebrates and involved in the pathogenesis of Parkinson’s disease (PD). Indeed, αSyn amyloid aggregates are present in the brain of patients with PD. Although the pathogenic role of αSyn is widely accepted, the physiological function of this protein remains elusive. Beyond the central nervous system, αSyn is expressed in hematopoietic tissue and blood, where platelets are a major cellular host of αSyn. Platelets play a key role in hemostasis and are potently activated by thrombin (αT) through the cleavage of protease-activated receptors. Furthermore, both αT and αSyn could be found in the same spatial environment, i.e. the platelet membrane, as αT binds to and activates platelets that can release αSyn from α-granules and microvesicles. Here, we investigated the possibility that exogenous αSyn could interfere with platelet activation induced by different agonists in vitro. Data obtained from distinct experimental techniques (i.e. multiple electrode aggregometry, rotational thromboelastometry, immunofluorescence microscopy, surface plasmon resonance, and steady-state fluorescence spectroscopy) on whole blood and platelet-rich plasma indicate that exogenous αSyn has mild platelet antiaggregating properties in vitro, acting as a negative regulator of αT-mediated platelet activation by preferentially inhibiting P-selectin expression on platelet surface. We have also shown that both exogenous and endogenous (i.e. cytoplasmic) αSyn preferentially bind to the outer surface of activated platelets. Starting from these findings, a coherent model of the antiplatelet function of αSyn is proposed.
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Affiliation(s)
- Laura Acquasaliente
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy.,Center for Thrombosis and Hemostasis (CTH) University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Claudia Maria Radu
- Department of Women's & Children's Health, University of Padua, Padua, Italy.,Thrombotic and Hemorrhagic Diseases Unit, Department of Medicine, University of Padua, via Giustiniani, 2, 35128, Padua, Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy.,Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave. 02115, Boston, MA, USA
| | - Ilaria Artusi
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy
| | - Anna Pagotto
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy
| | - Federico Uliana
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy.,Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Alessandro Negro
- Department of Biomedical Sciences, University of Padua, viale G. Colombo 3, 35100, Padua, Italy.
| | - Paolo Simioni
- Thrombotic and Hemorrhagic Diseases Unit, Department of Medicine, University of Padua, via Giustiniani, 2, 35128, Padua, Italy.
| | - Vincenzo De Filippis
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy. .,Biotechnology Center, CRIBI, University of Padua, Padua, Italy.
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15
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Simulations suggest double sodium binding induces unexpected conformational changes in thrombin. J Mol Model 2022; 28:120. [PMID: 35419655 PMCID: PMC9186379 DOI: 10.1007/s00894-022-05076-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
Abstract
Thrombin is a Na[Formula: see text]-activated serine protease existing in two forms targeted to procoagulant and anticoagulant activities, respectively. There is one Na[Formula: see text]-binding site that has been the focus of the study of the thrombin. However, molecular dynamics (MD) simulations suggest that there might be actually two Na[Formula: see text]-binding sites in thrombin and that Na[Formula: see text] ions can even bind to two sites simultaneously. In this study, we performed 12 independent 2-µs all-atom MD simulations for the wild-type (WT) thrombin and we studied the effects of the different Na[Formula: see text] binding modes on thrombin. From the root-mean-square fluctuations (RMSF) for the [Formula: see text]-carbons, we see that the atomic fluctuations mainly change in the 60s, 170s, and 220s loops, and the connection (residue 167 to 170). The correlation matrices for different binding modes suggest regions that may play an important role in thrombin's allosteric response and provide us a possible allosteric pathway for the sodium binding. Amorim-Hennig (AH) clustering tells us how the structure of the regions of interest changes on sodium binding. Principal component analysis (PCA) shows us how the different regions of thrombin change conformation together with sodium binding. Solvent-accessible surface area (SASA) exposes the conformational change in exosite I and catalytic triad. Finally, we argue that the double binding mode might be an inactive mode and that the kinetic scheme for the Na[Formula: see text] binding to thrombin might be a multiple-step mechanism rather than a 2-step mechanism.
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16
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Abstract
Thrombin is a multifunctional serine protease generated in injured cells. The generation of thrombin in coagulation plays a central role in the functioning of haemostasis. The last enzyme in the coagulation cascade is thrombin, with the function of cleaving fibrinogen to fibrin, which forms the fibrin clot of a haemostatic plug. Although thrombin primarily converts fibrinogen to fibrin, it also has many other positive regulatory effects on coagulation. Thrombin has procoagulant, inflammatory, cellular proliferation and anticoagulant effects. In coagulation system, thrombin has two very distinct roles. Firstly, it acts as a procoagulant when it converts fibrinogen into an insoluble fibrin clot, activates factor (F) XIII, activates thrombin activatable fibrinolysis inhibitor (TAFI) and activates FV, FVIII and FXI. Thrombin also enhances platelet adhesion by inactivating a disintegrin and metalloprotease with thrombospondin type1 motif (ADAMTS13). However, when thrombin activates protein C, it acts as an anticoagulant. A natural anticoagulant pathway that supplies regulation of the blood coagulation system contains protein C, which is the key component. This is accomplished by the specific proteolytic inactivation of FV and FVIII. In this review, the multiple roles of thrombin in the haemostatic response to injury are studied in addition to the cofactors that determine thrombin activity and how thrombin activity is thought to be coordinated.
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17
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Kosinski R, Perez JM, Schöneweiß EC, Ruiz-Blanco YB, Ponzo I, Bravo-Rodriguez K, Erkelenz M, Schlücker S, Uhlenbrock G, Sanchez-Garcia E, Saccà B. The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease. SCIENCE ADVANCES 2022; 8:eabk0425. [PMID: 34985948 PMCID: PMC8730604 DOI: 10.1126/sciadv.abk0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/10/2021] [Indexed: 06/04/2023]
Abstract
DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.
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Affiliation(s)
- Richard Kosinski
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joel Mieres Perez
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elisa-C. Schöneweiß
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Irene Ponzo
- Dynamic Biosensors GmbH, 82152 Martinsried, Germany
| | | | - Michael Erkelenz
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Elsa Sanchez-Garcia
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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18
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Pelc LA, Koester SK, Kukla CR, Chen Z, Di Cera E. The active site region plays a critical role in Na + binding to thrombin. J Biol Chem 2022; 298:101458. [PMID: 34861239 PMCID: PMC8695361 DOI: 10.1016/j.jbc.2021.101458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
The catalytic activity of thrombin and other enzymes of the blood coagulation and complement cascades is enhanced significantly by binding of Na+ to a site >15 Å away from the catalytic residue S195, buried within the 180 and 220 loops that also contribute to the primary specificity of the enzyme. Rapid kinetics support a binding mechanism of conformational selection where the Na+-binding site is in equilibrium between open (N) and closed (N∗) forms and the cation binds selectively to the N form. Allosteric transduction of this binding step produces enhanced catalytic activity. Molecular details on how Na+ gains access to this site and communicates allosterically with the active site remain poorly defined. In this study, we show that the rate of the N∗→N transition is strongly correlated with the analogous E∗→E transition that governs the interaction of synthetic and physiologic substrates with the active site. This correlation supports the active site as the likely point of entry for Na+ to its binding site. Mutagenesis and structural data rule out an alternative path through the pore defined by the 180 and 220 loops. We suggest that the active site communicates allosterically with the Na+ site through a network of H-bonded water molecules that embeds the primary specificity pocket. Perturbation of the mobility of S195 and its H-bonding capabilities alters interaction with this network and influences the kinetics of Na+ binding and allosteric transduction. These findings have general mechanistic relevance for Na+-activated proteases and allosteric enzymes.
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Affiliation(s)
- Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Sarah K Koester
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Cassandra R Kukla
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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19
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Yu H, Zhao Z, Xiao B, Deng M, Wang Z, Li Z, Zhang H, Zhang L, Qian J, Li J. Aptamer-Based Solution-Gated Graphene Transistors for Highly Sensitive and Real-Time Detection of Thrombin Molecules. Anal Chem 2021; 93:13673-13679. [PMID: 34597019 DOI: 10.1021/acs.analchem.1c03129] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombin is an important biomarker for various diseases and biochemical reactions. Rapid and real-time detection of thrombin that quickly neutralizes in early coagulation in the body has gained significant attention for its practical applications. Solution-gated graphene transistors (SGGTs) have been widely studied due to their higher sensitivity and low-cost fabrication for chemical and biological sensing applications. In this paper, the ssDNA aptamer with 29 bases was immobilized on the surface of the gate electrode to specifically recognize thrombin. The SGGT sensor achieved high sensitivity with a limit of detection (LOD) up to fM. The LOD was attributed to the amplification function of SGGTs and the suitable aptamer choice. The ssDNA configuration folding induced by thrombin molecules and the electropositivity of thrombin molecules could arouse the same electrical response of SGGTs, helping the device obtain a high sensitivity. The channel current variation of sensors had a good linear relationship with the logarithm of thrombin concentration in the range of 1 fM to 10 nM. The fabricated device also demonstrated a short response time to thrombin molecules, and the response time to the 1 fM thrombin molecules was about 150 s. In summary, the sensing strategy of aptamer-based SGGTs with high sensitivity and high selectivity has a good prospect in medical diagnosis.
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Affiliation(s)
- Haiyang Yu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China.,Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Zheng Zhao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Bichen Xiao
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Minghua Deng
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Zhaoliang Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Ziqin Li
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Huibin Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Lei Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Jingwen Qian
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
| | - Jinhua Li
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the Green Preparation and Application of Functional Materials, Ministry of Education, Hubei Key Laboratory of Polymer Materials, School of Materials Science and Engineering, Hubei University, Wuhan 430062, China
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20
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Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
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21
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Lee MH, Lee DR, Chon JW, Chung DJ. Hemostatic Patches Based on Crosslinked Chitosan Films Applied in Interventional Procedures. Polymers (Basel) 2021; 13:2402. [PMID: 34372004 PMCID: PMC8348421 DOI: 10.3390/polym13152402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 11/17/2022] Open
Abstract
In this study, we manufactured biocompatible hemostatic crosslinked chitosan (CS) patches and analyzed their physicochemical and biological properties for femoral arterial puncture applications. CS is a representative hemostatic material but has some drawbacks, such as swelling, shrinkage, and brittleness. Thus, it was crosslinked via a 1-ethyl-3-(3-dimethyl aminopropyl) carbodiimide (EDC)/N-hydroxysuccinimide (NHS) coupling reaction and a nucleophilic addition reaction with citric acid (CA), glutaraldehyde (GTA), and genipin (GP) to remedy its shortcomings. The CSCA (crosslinked CS with CA/EDC), CSGTA (crosslinked CS with GTA), and CSG (crosslinked CS with GP) films showed low swelling degrees and good mechanical properties (excluding CSCA) compared with those of neat CS films. Additionally, every crosslinked CS film coated with thrombin (TB-CS) showed enhanced hemostatic ability in the whole blood clotting and activated partial thromboplastin time tests. Furthermore, the CSCA, CSGTA, and CSGP were nontoxic in an in vitro cell cytotoxicity test (3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide assay) using L-929 mouse fibroblasts cells.
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Affiliation(s)
| | | | | | - Dong June Chung
- Department of Polymer Science and Engineering, Sungkyunkwan University, Suwon 16419, Korea; (M.H.L.); (D.R.L.); (J.W.C.)
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22
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Wu Y, Vazquez-Prada KX, Liu Y, Whittaker AK, Zhang R, Ta HT. Recent Advances in the Development of Theranostic Nanoparticles for Cardiovascular Diseases. Nanotheranostics 2021; 5:499-514. [PMID: 34367883 PMCID: PMC8342263 DOI: 10.7150/ntno.62730] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide. CVD includes a group of disorders of the heart and blood vessels such as myocardial infarction, ischemic heart, ischemic injury, injured arteries, thrombosis and atherosclerosis. Amongst these, atherosclerosis is the dominant cause of CVD and is an inflammatory disease of the blood vessel wall. Diagnosis and treatment of CVD remain the main challenge due to the complexity of their pathophysiology. To overcome the limitations of current treatment and diagnostic techniques, theranostic nanomaterials have emerged. The term "theranostic nanomaterials" refers to a multifunctional agent with both therapeutic and diagnostic abilities. Theranostic nanoparticles can provide imaging contrast for a diversity of techniques such as magnetic resonance imaging (MRI), positron emission tomography (PET) and computed tomography (CT). In addition, they can treat CVD using photothermal ablation and/or medication by the drugs in nanoparticles. This review discusses the latest advances in theranostic nanomaterials for the diagnosis and treatment of CVDs according to the order of disease development. MRI, CT, near-infrared spectroscopy (NIR), and fluorescence are the most widely used strategies on theranostics for CVDs detection. Different treatment methods for CVDs based on theranostic nanoparticles have also been discussed. Moreover, current problems of theranostic nanoparticles for CVDs detection and treatment and future research directions are proposed.
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Affiliation(s)
- Yuao Wu
- Queensland Micro- and Nanotechnology, Griffith University, Brisbane, Queensland 4111, Australia
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, Queensland 4072, Australia
| | - Karla X. Vazquez-Prada
- Queensland Micro- and Nanotechnology, Griffith University, Brisbane, Queensland 4111, Australia
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yajun Liu
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew K. Whittaker
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, Queensland 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, the University of Queensland, QLD 4072, Australia
| | - Run Zhang
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hang T. Ta
- Queensland Micro- and Nanotechnology, Griffith University, Brisbane, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Brisbane, Queensland 4111, Australia
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, Queensland 4072, Australia
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23
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Kovach IM. Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System. Life (Basel) 2021; 11:396. [PMID: 33925363 PMCID: PMC8146069 DOI: 10.3390/life11050396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Inquiries into the participation of short hydrogen bonds in stabilizing transition states and intermediate states in the thrombin, factor Xa, plasmin and activated protein C-catalyzed reactions revealed that specific binding of effectors at Sn, n = 1-4 and S'n, n = 1-3 and at remote exosites elicit complex patterns of hydrogen bonding and involve water networks. The methods employed that yielded these discoveries include; (1) kinetics, especially partial or full kinetic deuterium solvent isotope effects with short cognate substrates and also with the natural substrates, (2) kinetic and structural probes, particularly low-field high-resolution nuclear magnetic resonance (1H NMR), of mechanism-based inhibitors and substrate-mimic peptide inhibitors. Short hydrogen bonds form at the transition states of the catalytic reactions at the active site of the enzymes as they do with mechanism-based covalent inhibitors of thrombin. The emergence of short hydrogen bonds at the binding interface of effectors and thrombin at remote exosites has recently gained recognition. Herein, I describe our contribution, a confirmation of this discovery, by low-field 1H NMR. The principal conclusion of this review is that proton sharing at distances below the sum of van der Waals radii of the hydrogen and both donor and acceptor atoms contribute to the remarkable catalytic prowess of serine proteases of the blood clotting system and other enzymes that employ acid-base catalysis. Proton bridges also play a role in tight binding in proteins and at exosites, i.e., allosteric sites, of enzymes.
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Affiliation(s)
- Ildiko M Kovach
- Department of Chemistry, The Catholic University of America, Washington, DC 20064, USA
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Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin. Int J Biol Macromol 2021; 181:858-867. [PMID: 33864869 DOI: 10.1016/j.ijbiomac.2021.04.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022]
Abstract
The long-range communication between the two exosites of human α-thrombin (thrombin) tightly modulates the protein-effector interactions. Duplex/quadruplex aptamers represent an emerging class of very effective binders of thrombin. Among them, NU172 and HD22 aptamers are at the forefront of exosite I and II recognition, respectively. The present study investigates the simultaneous binding of these two aptamers by combining a structural and dynamics approach. The crystal structure of the ternary complex formed by the thrombin with NU172 and HD22_27mer provides a detailed view of the simultaneous binding of these aptamers to the protein, inspiring the design of novel bivalent thrombin inhibitors. The crystal structure represents the starting model for molecular dynamics studies, which point out the cooperation between the binding at the two exosites. In particular, the binding of an aptamer to its exosite reduces the intrinsic flexibility of the other exosite, that preferentially assumes conformations similar to those observed in the bound state, suggesting a predisposition to interact with the other aptamer. This behaviour is reflected in a significant increase of the anticoagulant activity of NU172 when the inactive HD22_27mer is bound to exosite II, providing a clear evidence of the synergic action of the two aptamers.
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Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021; 12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Proteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays. Characterizing proteases in their native environment is still challenging. Here, the authors develop a proteomics workflow for analyzing protease-specific peptides from cell lysates in 96-well format, providing mechanistic insights into blood proteases and enabling the prediction of protease substrates.
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Crossen J, Diamond SL. Thermal shift assay to probe melting of thrombin, fibrinogen, fibrin monomer, and fibrin: Gly-Pro-Arg-Pro induces a fibrin monomer-like state in fibrinogen. Biochim Biophys Acta Gen Subj 2021; 1865:129805. [PMID: 33276061 PMCID: PMC7752828 DOI: 10.1016/j.bbagen.2020.129805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/30/2020] [Accepted: 11/24/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Thrombin activates fibrinogen and binds the fibrin E-domain (Kd ~ 2.8 μM) and the splice variant γ'-domain (Kd ~ 0.1 μM). We investigated if the loading of D-Phe-Pro-Arg-chloromethylketone inhibited thrombin (PPACK-thrombin) onto fibrin could enhance fibrin stability. METHODS A 384-well plate thermal shift assay (TSA) with SYPRO-orange provided melting temperatures (Tm) of thrombin, PPACK-thrombin, fibrinogen, fibrin monomer, and fibrin. RESULTS Large increases in Tm indicated that calcium led to protein stabilization (0 vs. 2 mM Ca2+) for fibrinogen (54.0 vs. 62.3 °C) and fibrin (62.3 vs. 72.2 °C). Additionally, active site inhibition with PPACK dramatically increased the Tm of thrombin (58.3 vs. 78.3 °C). Treatment of fibrinogen with fibrin polymerization inhibitor GPRP increased fibrinogen stability by ΔTm = 9.3 °C, similar to the ΔTm when fibrinogen was converted to fibrin monomer (ΔTm = 8.8 °C) or to fibrin (ΔTm = 10.4 °C). Addition of PPACK-thrombin at high 5:1 M ratio to fibrin(ogen) had little effect on fibrin(ogen) Tm values, indicating that thrombin binding does not detectably stabilize fibrin via a putative bivalent E-domain to γ'-domain interaction. CONCLUSIONS TSA was a sensitive assay of protein stability and detected: (1) the effects of calcium-stabilization, (2) thrombin active site labeling, (3) fibrinogen conversion to fibrin, and (4) GPRP induced changes in fibrinogen stability being essentially equivalent to that of fibrin monomer or polymerized fibrin. SIGNIFICANCE The low volume, high throughput assay has potential for use in understanding interactions with rare or mutant fibrin(ogen) variants.
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Affiliation(s)
- J Crossen
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States..
| | - S L Diamond
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States..
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Smirnov I, Kolganova N, Troisi R, Sica F, Timofeev E. Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:863-871. [PMID: 33614235 PMCID: PMC7868722 DOI: 10.1016/j.omtn.2021.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/08/2021] [Indexed: 01/11/2023]
Abstract
Post-SELEX modification of DNA aptamers is an established strategy to improve their affinity or inhibitory characteristics. In this study, we examined the possibility of increasing the recognition interface between the thrombin-binding aptamer HD1 (TBA) and thrombin by adding a chemically modified side chain to selected nucleotide residues. A panel of 22 TBA variants with N3-modified residues T3 and T12 was prepared by a two-step modification procedure. Aptamers were characterized by a combination of biophysical and biochemical methods. We identified mutants with enhanced affinity and improved anticoagulant activity. The crystal structures of thrombin complexes with three selected modified variants revealed that the modified pyrimidine base invariably allocates in proximity to thrombin residues Tyr76 and Ile82 due to the directing role of the unmodified TT loop. The modifications induced an increase in the contact areas between thrombin and the modified TBAs. Comparative analysis of the structural, biochemical, and biophysical data suggests that the non-equivalent binding modes of the mutants with thrombin in the T3- and T12-modified series account for the observed systematic differences in their affinity characteristics. In this study, we show that extending the recognition surface between the protein and modified aptamers is a promising approach that may improve characteristics of aptamer ligands.
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Affiliation(s)
- Igor Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Natalia Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Edward Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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28
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Introduction of a thrombin sensor based on its interaction with dabigatran as an oral direct thrombin inhibitor. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 119:111417. [PMID: 33321578 DOI: 10.1016/j.msec.2020.111417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/31/2020] [Accepted: 08/15/2020] [Indexed: 01/03/2023]
Abstract
Dabigatran (DAB) is a direct thrombin inhibitor used for preventing blood clots and emboli after orthopedic surgery. The DAB - thrombin interaction was followed by fluorescence and UV-Vis spectroscopic methods. The binding of DAB to thrombin was also modeled by the molecular docking method. The obtained experimental results were consistent with theoretical results. The voltammetric method was also tested for DAB - thrombin interaction. Based on voltammetric findings, carbon paste electrode containing graphite powder, paraffin oil, MWCNTs, and DAB was constructed and used for thrombin monitoring after investigation of the DAB oxidation mechanism for the first time. The decrease in the linear sweep voltammetric (LSV) peak current of DAB in the presence of thrombin was utilized for the thrombin analysis. The calibration plot was linear in the concentration range of 1 to 70 nM (R2 = 0.9992) by LSV technique with a detection limit of 0.3 nM. The applicability of the proposed sensor was evaluated by the determination of thrombin in human serum as a real sample.
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29
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Jackson CM, Esnouf P, Duewer DL. Thrombin: An Approach to Developing a Higher-Order Reference Material and Reference Measurement Procedure for Substance Identity, Amount, and Biological Activities. JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY 2020; 125:125021. [PMID: 39035347 PMCID: PMC10871826 DOI: 10.6028/jres.125.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 07/23/2024]
Abstract
Thrombin, the proteolytic enzyme that catalyzes the transformation of soluble fibrinogen to the polymerized fibrin clot, participates in multiple reactions in blood coagulation in addition to the clotting reaction. Although reference materials have existed for many years, structural characterization and measurement of biological activity have never been sufficient to permit claims of clear metrological traceability for the thrombin preparations. Our current state-of-the-art methods for protein characterization and determination of the catalytic properties of thrombin now make it practical to develop and characterize a metrologically acceptable reference material and reference measurement procedure for thrombin. Specifically, α-thrombin, the biologically produced protease formed during prothrombin activation, is readily available and has been extensively characterized. Dependences of thrombin proteolytic and peptide hydrolytic activities on a variety of substrates, pH, specific ions, and temperature are established, although variability remains for the kinetic parameters that describe thrombin enzymatic action. The roles of specific areas on the surface of the thrombin molecule (exosites) in substrate recognition and catalytic efficiency are described and characterized. It is opportune to develop reference materials of high metrological order and technical feasibility. In this article, we review the properties of α-thrombin important for its preparation and suggest an approach suitable for producing a reference material and a reference measurement procedure that is sensitive to thrombin’s catalytic competency on a variety of substrates.
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Affiliation(s)
| | | | - David L. Duewer
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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30
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Al-Awadhi FH, Luesch H. Targeting eukaryotic proteases for natural products-based drug development. Nat Prod Rep 2020; 37:827-860. [PMID: 32519686 PMCID: PMC7406119 DOI: 10.1039/c9np00060g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to April 2020 Proteases are involved in the regulation of many physiological processes. Their overexpression and dysregulated activity are linked to diseases such as hypertension, diabetes, viral infections, blood clotting disorders, respiratory diseases, and cancer. Therefore, they represent an important class of therapeutic targets. Several protease inhibitors have reached the market and >60% of them are directly related to natural products, even when excluding synthetic natural product mimics. Historically, natural products have been a valuable and validated source of therapeutic agents, as over half of the marketed drugs across targets and diseases are inspired by natural product structures. In the past two decades the number of new protease inhibitors discovered from nature has sharply increased. Additionally, the availability of 3D structural information for proteases has permitted structure-based design and accelerated the synthesis of optimized lead structures with improved potency and selectivity profiles, resulting in some of the most-potent-in-class inhibitors. These discoveries were oftentimes maximized by in-depth biological assessments of lead inhibitors, linking them to a relevant disease state. This review will discuss some of the current and emerging drug targets and their involvement in various disease processes, highlighting selected success stories behind several FDA-approved protease inhibitors that have natural products scaffolds as well as recent selected pharmacologically well-characterized inhibitors derived from marine or terrestrial sources.
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Affiliation(s)
- Fatma H Al-Awadhi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait.
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, USA.
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31
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Ruben EA, Gandhi PS, Chen Z, Koester SK, DeKoster GT, Frieden C, Di Cera E. 19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2. J Biol Chem 2020; 295:8227-8235. [PMID: 32358061 PMCID: PMC7294081 DOI: 10.1074/jbc.ra120.013419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/28/2020] [Indexed: 11/06/2022] Open
Abstract
The conformational properties of trypsin-like proteases and their zymogen forms remain controversial because of a lack of sufficient information on their free forms. Specifically, it is unclear whether the free protease is zymogen-like and shifts to its mature form upon a ligand-induced fit or exists in multiple conformations in equilibrium from which the ligand selects the optimal fit via conformational selection. Here we report the results of 19F NMR measurements that reveal the conformational properties of a protease and its zymogen precursor in the free form. Using the trypsin-like, clotting protease thrombin as a relevant model system, we show that its conformation is quite different from that of its direct zymogen precursor prethrombin-2 and more similar to that of its fully active Na+-bound form. The results cast doubts on recent hypotheses that free thrombin is zymogen-like and transitions to protease-like forms upon ligand binding. Rather, they validate the scenario emerged from previous findings of X-ray crystallography and rapid kinetics supporting a pre-existing equilibrium between open (E) and closed (E*) forms of the active site. In this scenario, prethrombin-2 is more dynamic and exists predominantly in the E* form, whereas thrombin is more rigid and exists predominantly in the E form. Ligand binding to thrombin takes place exclusively in the E form without significant changes in the overall conformation. In summary, these results disclose the structural architecture of the free forms of thrombin and prethrombin-2, consistent with an E*-E equilibrium and providing no evidence that free thrombin is zymogen-like.
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Affiliation(s)
- Eliza A Ruben
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | | | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Sarah K Koester
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Gregory T DeKoster
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
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32
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Troisi R, Balasco N, Vitagliano L, Sica F. Molecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites. J Biomol Struct Dyn 2020; 39:2199-2209. [PMID: 32202471 DOI: 10.1080/07391102.2020.1746693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Human α-thrombin (thrombin) is a multifunctional enzyme that plays a pivotal role in the coagulation pathway. Thrombin activity can be effectively modulated by G-quadruplex-based oligonucleotide aptamers that specifically interact with the two positively charged regions (exosites I and II) on the protein surface. Although insightful atomic-level snapshots of the recognition between thrombin and aptamers have been recently achieved through crystallographic analyses, some dynamic aspects of this interaction have not been fully characterized. We here report molecular dynamics simulations of thrombin in different association states: ligand-free and binary/ternary complexes with the aptamers TBA (at exosite I) and HD22_27mer (at exosite II). The simulations carried out on the binary and ternary complexes formed by thrombin with these aptamers provide a dynamic view of the interactions that stabilize them in a crystal-free environment. Interestingly, the analysis of the dynamics of the exosites in different thrombin binding states clearly indicates that the HD22_27mer binding at the exosite II favours conformations of exosite I that are prone to the TBA binding. Similar effects are observed upon the binding of TBA to the exosite I. These observations provide an atomic-level picture of the exosite inter-communication in thrombin and explain the experimentally detected cooperativity of the TBA/HD22_27mer binding.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
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Role of the I16-D194 ionic interaction in the trypsin fold. Sci Rep 2019; 9:18035. [PMID: 31792294 PMCID: PMC6889508 DOI: 10.1038/s41598-019-54564-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022] Open
Abstract
Activity in trypsin-like proteases is the result of proteolytic cleavage at R15 followed by an ionic interaction that ensues between the new N terminus of I16 and the side chain of the highly conserved D194. This mechanism of activation, first proposed by Huber and Bode, organizes the oxyanion hole and primary specificity pocket for substrate binding and catalysis. Using the clotting protease thrombin as a relevant model, we unravel contributions of the I16-D194 ionic interaction to Na+ binding, stability of the transition state and the allosteric E*-E equilibrium of the trypsin fold. The I16T mutation abolishes the I16-D194 interaction and compromises the architecture of the oxyanion hole. The D194A mutation also abrogates the I16-D194 interaction but, surprisingly, has no effect on the architecture of the oxyanion hole that remains intact through a new H-bond established between G43 and G193. In both mutants, loss of the I16-D194 ionic interaction compromises Na+ binding, reduces stability of the transition state, collapses the 215–217 segment into the primary specific pocket and abrogates the allosteric E*-E equilibrium in favor of a rigid conformation that binds ligand at the active site according to a simple lock-and-key mechanism. These findings refine the structural role of the I16-D194 ionic interaction in the Huber-Bode mechanism of activation and reveal a functional linkage with the allosteric properties of the trypsin fold like Na+ binding and the E*-E equilibrium.
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Chen F, Huang G. Mechanism and inhibition kinetics of peptide P13 as thrombin inhibitor. Int J Biol Macromol 2019; 150:1046-1052. [PMID: 31743711 DOI: 10.1016/j.ijbiomac.2019.10.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/22/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022]
Abstract
Excessive coagulation can easily lead to arterial and venous thrombosis, which is the main reason for the evolution of myocardial infarction and cerebrovascular accidents. As a key coagulation factor for the coagulation pathway, thrombin has become a remarkable target for the control of thrombosis. The synthesized peptide P13 with amino acid sequence of N-RGDAGFAGDDAPR was expected to be an inhibitor with higher antithrombotic activity. The results showed that the IC50 (50% inhibition of thrombin activity) of the peptide P13 was determined by colorimetric method to be 115 µM. And enzyme kinetic experiments showed that P13 was a competitive inhibitor of thrombin with Ki = 106 µM. Fluorescence spectra and three-dimensional fluorescence showed that P13 could alter the secondary structure of thrombin and the microenvironment of certain chromogenic amino acids. P13 can spontaneously bind with thrombin exosite 1 in the form of 1:1 mainly through hydrogen bonding and van der Waals force. And the optimal docking mode of P13 and thrombin was revealed by molecular docking with "-CDOCKER_Energy" of 178.679 kcal mol-1. This study revealed P13 may become a potential anticoagulant drug widely used after further studies in preclinical and clinical trials.
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Affiliation(s)
- Fangyuan Chen
- Key Lab of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Guangrong Huang
- Key Lab of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China.
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Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Sci Rep 2019; 9:12304. [PMID: 31444378 PMCID: PMC6707225 DOI: 10.1038/s41598-019-48839-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/13/2019] [Indexed: 01/07/2023] Open
Abstract
A pre-existing, allosteric equilibrium between closed (E*) and open (E) conformations of the active site influences the level of activity in the trypsin fold and defines ligand binding according to the mechanism of conformational selection. Using the clotting protease thrombin as a model system, we investigate the molecular determinants of the E*-E equilibrium through rapid kinetics and X-ray structural biology. The equilibrium is controlled by three residues positioned around the active site. W215 on the 215-217 segment defining the west wall of the active site controls the rate of transition from E to E* through hydrophobic interaction with F227. E192 on the opposite 190-193 segment defining the east wall of the active site controls the rate of transition from E* to E through electrostatic repulsion of E217. The side chain of E217 acts as a lever that moves the entire 215-217 segment in the E*-E equilibrium. Removal of this side chain converts binding to the active site to a simple lock-and-key mechanism and freezes the conformation in a state intermediate between E* and E. These findings reveal a simple framework to understand the molecular basis of a key allosteric property of the trypsin fold.
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36
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Troisi R, Napolitano V, Spiridonova V, Russo Krauss I, Sica F. Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer. Nucleic Acids Res 2019; 46:12177-12185. [PMID: 30357392 PMCID: PMC6294562 DOI: 10.1093/nar/gky990] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
Despite aptamers are very promising alternative to antibodies, very few of them are under clinical trials or are used as drugs. Among them, NU172 is currently in Phase II as anticoagulant in heart disease treatments. It inhibits thrombin activity much more effectively than TBA, the best-known thrombin binding aptamer. The crystal structure of thrombin-NU172 complex reveals a bimodular duplex/quadruplex architecture for the aptamer, which binds thrombin exosite I through a highly complementary surface involving all three loops of the G-quadruplex module. Although the duplex domain does not interact directly with thrombin, the features of the duplex/quadruplex junction and the solution data on two newly designed NU172 mutants indicate that the duplex moiety is important for the optimization of the protein-ligand interaction and for the inhibition of the enzyme activity. Our work discloses the structural features determining the inhibition of thrombin by NU172 and put the basis for the design of mutants with improved properties.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
| | - Valeria Napolitano
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
| | - Vera Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy.,CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Sesto Fiorentino, FI 50019, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
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37
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Chen F, Jiang H, Chen W, Huang G. Interaction of the synthetic antithrombotic peptide P10 with thrombin: a spectroscopy study. RSC Adv 2019; 9:18498-18505. [PMID: 35515240 PMCID: PMC9064813 DOI: 10.1039/c9ra02994j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/29/2019] [Indexed: 11/21/2022] Open
Abstract
Thrombin is a critical serine protease in the coagulation system and is widely used as a target protein for antithrombotics. Spectroscopic analysis is a simple and effective method that is used to study the interaction between small molecules and proteins. In this study, the interactions of a potential antithrombotic peptide AGFAGDDAPR (P10) with thrombin were investigated by fluorescence spectroscopy, UV-vis spectroscopy, circular dichroism, Fourier-transform infrared spectroscopy and Raman spectroscopy, respectively. The results showed that the peptide P10 bonded to thrombin via hydrogen bonding and van der Waals forces, resulting in fluorescence quenching. And, the secondary structure of thrombin changed, the β-sheet decreased, and the random coil increased. The peptide P10 bonded to proline and lysine, and changed the space structure of thrombin, resulting in inhibition of thrombin activity. The results contributed to exploration of the mechanism of this potential antithrombotic drug interaction with thrombin in order to provide a preliminary understanding of the pharmacodynamic properties of P10.
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Affiliation(s)
- Fangyuan Chen
- Key Lab of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University Hangzhou China +86 571 8687 5628
| | - Han Jiang
- Key Lab of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University Hangzhou China +86 571 8687 5628
| | - Wenwei Chen
- Key Lab of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University Hangzhou China +86 571 8687 5628
| | - Guangrong Huang
- Key Lab of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University Hangzhou China +86 571 8687 5628
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38
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Affiliation(s)
- Hye-Seon Choi
- Department of Microbiology, University of Ulsan, Ulsan 680-749, Korea
| | - Yu-Seon Sa
- Department of Microbiology, University of Ulsan, Ulsan 680-749, Korea
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39
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Salifu EY, Agoni C, Olotu FA, Dokurugu YM, Soliman MES. Deciphering the canonical blockade of activated Hageman factor (FXIIa) by benzamidine in the coagulation cascade: A thorough dynamical perspective. Chem Biol Drug Des 2019; 94:1905-1918. [PMID: 31148409 DOI: 10.1111/cbdd.13573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/09/2019] [Accepted: 05/15/2019] [Indexed: 12/11/2022]
Abstract
The experimental inhibitory potency of benzamidine (BEN) paved way for further design and development of inhibitors that target β-FXIIa. Structural dynamics of the loops and catalytic residues that encompass the binding pocket of β-FXIIa and all serine proteases are crucial to their overall activity. Employing molecular dynamics and post-MD analysis, this study sorts to unravel the structural and molecular events that accompany the inhibitory activity of BEN on human β-FXIIa upon selective non-covalent binding. Analysis of conformational dynamics of crucial loops revealed prominent alterations of the original conformational posture of FXIIa, evidenced by increased flexibility, decreased compactness, and an increased exposure to solvent upon binding of BEN, which could have in turn interfered with the essential roles of these loops in enhancing their procoagulation interactions with biological substrates and cofactors, altogether resulting in the consequential inactivation of FXIIa. A sustained interaction of the catalytic triad residues and key residues of the autolysis loop impeded their roles in catalysis which equally enhanced the inhibitory potency of BEN toward β-FXIIa evidenced by a favorable binding. Findings provide essential structural and molecular insights that could facilitate the structure-based design of novel antithrombotic compounds with enhanced inhibitory activities and low therapeutic risk.
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Affiliation(s)
- Elliasu Y Salifu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yussif M Dokurugu
- College of Pharmacy and Pharmaceutical Sciences, Florida Agricultural and Mechanical University, FAMU, Tallahassee, FL, USA
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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40
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Cheng S, Tu M, Chen H, Xu Z, Wang Z, Liu H, Zhao G, Zhu B, Du M. Identification and inhibitory activity against α-thrombin of a novel anticoagulant peptide derived from oyster (Crassostrea gigas) protein. Food Funct 2019; 9:6391-6400. [PMID: 30457135 DOI: 10.1039/c8fo01635f] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A newly discovered anticoagulant peptide was isolated, purified and identified from the pepsin hydrolysate of oyster (Crassostrea gigas) which could potently prolong the activated partial thromboplastin time and the thrombin time. The anticoagulant peptide with a 1264.36 Da molecular mass was similar to the amino acid sequence of the C-terminal segment (DFEEIPEEYLQ) of hirudin (a potent thrombin inhibitor). The peptide specifically inhibited a vital blood coagulation factor: thrombin. The molecular docking energy scores of the anticoagulant peptide with the active site, exosite-I and exosite-II of thrombin were 132.355 kcal mol-1, 151.266 kcal mol-1 and 147.317 kcal mol-1, respectively. The anticoagulant peptide interacted with thrombin by competing with fibrinogen for an anion-binding exosite I. In the anticoagulant peptide-thrombin complex, there are seven hydrogen bonds and reciprocity exists between hydrogen atoms and oxygen atoms, and electrostatic and hydrophobic interactions are also involved. Such abundant interactions may be accountable for the high affinity and specificity of the anticoagulant peptide.
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Affiliation(s)
- Shuzhen Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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41
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Xiao J, Melvin RL, Salsbury FR. Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning. J Biomol Struct Dyn 2019; 37:982-999. [PMID: 29471734 PMCID: PMC6207482 DOI: 10.1080/07391102.2018.1445032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/17/2018] [Indexed: 12/13/2022]
Abstract
Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associated single deletion of LYS9 in the light chain. By combining supervised and unsupervised machine learning methodologies and more traditional structural analyses on data from 10 μs molecular dynamics simulations, we show that the conformational ensemble of the ΔK9 mutant is significantly perturbed. Our analyses consistently indicate that LYS9 deletion destabilizes both the catalytic cleft and regulatory functional regions and result in some conformational changes that occur in tens to hundreds of nanosecond scaled motions. We also reveal that the two forms of thrombin each prefer a distinct binding mode of a Na+ ion. We expand our understanding of previous experimental observations and shed light on the mechanisms of the LYS9 deletion associated bleeding disorder by providing consistent but more quantitative and detailed structural analyses than early studies in literature. With a novel application of supervised learning, i.e. the decision tree learning on the hydrogen bonding features in the wild-type and ΔK9 mutant forms of thrombin, we predict that seven pairs of critical hydrogen bonding interactions are significant for establishing distinct behaviors of wild-type thrombin and its ΔK9 mutant form. Our calculations indicate the LYS9 in the light chain has both localized and long-range allosteric effects on thrombin, supporting the opinion that light chain has an important role as an allosteric effector.
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Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, USA
- Department of Computer Science, Wake Forest University, Winston Salem, USA
| | - Ryan L. Melvin
- Department of Physics, Wake Forest University, Winston-Salem, USA
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem,USA
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42
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Billur R, Sabo TM, Maurer MC. Thrombin Exosite Maturation and Ligand Binding at ABE II Help Stabilize PAR-Binding Competent Conformation at ABE I. Biochemistry 2019; 58:1048-1060. [PMID: 30672691 DOI: 10.1021/acs.biochem.8b00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Thrombin, derived from zymogen prothrombin (ProT), is a serine protease involved in procoagulation, anticoagulation, and platelet activation. Thrombin's actions are regulated through anion-binding exosites I and II (ABE I and ABE II) that undergo maturation during activation. Mature ABEs can utilize exosite-based communication to fulfill thrombin functions. However, the conformational basis behind such long-range communication and the resultant ligand binding affinities are not well understood. Protease activated receptors (PARs), involved in platelet activation and aggregation, are known to target thrombin ABE I. Unexpectedly, PAR3 (44-56) can already bind to pro-ABE I of ProT. Nuclear magnetic resonance (NMR) ligand-enzyme titrations were used to characterize how individual PAR1 (49-62) residues interact with pro-ABE I and mature ABE I. 1D proton line broadening studies demonstrated that binding affinities for native PAR1P (49-62, P54) and for the weak binding variant PAR1G (49-62, P54G) increased as ProT was converted to mature thrombin. 1H,15N-HSQC titrations revealed that PAR1G residues K51, E53, F55, D58, and E60 exhibited less affinity to pro-ABE I than comparable residues in PAR3G (44-56, P51G). Individual PAR1G residues then displayed tighter binding upon exosite maturation. Long-range communication between thrombin exosites was examined by saturating ABE II with phosphorylated GpIbα (269-282, 3Yp) and monitoring the binding of PAR1 and PAR3 peptides to ABE I. Individual PAR residues exhibited increased affinities in this dual-ligand environment supporting the presence of interexosite allostery. Exosite maturation and beneficial long-range allostery are proposed to help stabilize an ABE I conformation that can effectively bind PAR ligands.
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Affiliation(s)
- Ramya Billur
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center , University of Louisville , Louisville , Kentucky 40202 , United States
| | - Muriel C Maurer
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
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43
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Takenouchi T, Shimada H, Uehara T, Kanai Y, Takahashi T, Kosaki K. A paradoxical thrombogenic mutation in factor II at the target site of arthropod bleeding toxin. Eur J Med Genet 2019; 62:93-95. [DOI: 10.1016/j.ejmg.2018.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/09/2018] [Accepted: 06/02/2018] [Indexed: 10/14/2022]
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44
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Abstract
Activated factor XIIa (FXIIa) is a serine protease that has received a great deal of interest in recent years as a potential target for the development of new antithrombotics. Despite the strong interest in obtaining structural information, only the structure of the FXIIa catalytic domain in its zymogen conformation is available. In this work, reproducible experimental conditions found for the crystallization of human plasma β-FXIIa and crystal growth optimization have led to determination of the first structure of the active form of the enzyme. Two crystal structures of human plasma β-FXIIa complexed with small molecule inhibitors are presented herein. The first is the noncovalent inhibitor benzamidine. The second is an aminoisoquinoline containing a boronic acid-reactive group that targets the catalytic serine. Both benzamidine and the aminoisoquinoline bind in a canonical fashion typical of synthetic serine protease inhibitors, and the protease domain adopts a typical chymotrypsin-like serine protease active conformation. This novel structural data explains the basis of the FXII activation, provides insights into the enzymatic properties of β-FXIIa, and is a great aid toward the further design of protease inhibitors for human FXIIa.
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45
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46
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Gogoi D, Pal A, Chattopadhyay P, Paul S, Deka RC, Mukherjee AK. First Report of Plant-Derived β-Sitosterol with Antithrombotic, in Vivo Anticoagulant, and Thrombus-Preventing Activities in a Mouse Model. JOURNAL OF NATURAL PRODUCTS 2018; 81:2521-2530. [PMID: 30406661 DOI: 10.1021/acs.jnatprod.8b00574] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Inhibitors of thrombin, a key enzyme in the blood coagulation cascade, are of great interest because of their selective specificity and effectiveness in anticoagulation therapy against cardiovascular disorders. The natural soybean phytosterol, β-sitosterol (BSS) demonstrated anticoagulant activity by dose-dependent inhibition of thrombin in an uncompetitive manner with a Ki value of 0.267 μM as well as by partial inhibition of thrombin-catalyzed platelet aggregation with a half-maximal inhibitory concentration (IC50) value of 10.45 ± 2.88 μM against platelet-rich plasma and 9.2 ± 1.2 μM against washed platelets. An in silico study indicated binding of BSS to thrombin, which was experimentally verified by spectrofluorometric and isothermal calorimetric analyses. Under in vitro conditions, BSS demonstrated thrombolytic activity by activating plasminogen, albeit it is devoid of protease (fibrinogenolytic) activity. BSS was noncytotoxic to mammalian cells, nonhemolytic, demonstrated its in vivo anticoagulant activity when administered orally, and inhibited k-carrageen-induced thrombus formation in the tails of mice. Our results suggest that dietary supplementation of BSS may help to prevent thrombosis-associated cardiovascular disorders.
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Affiliation(s)
| | - Anirban Pal
- In-vivo Testing Laboratory, Molecular Bioprospection Department , Central Institute of Medicinal and Aromatic Plants , Lucknow , India
| | - Pronobesh Chattopadhyay
- Division of Pharmaceutical Technology , Defense Research Laboratory , Tezpur , Assam , India
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47
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Li B, Billur R, Maurer MC, Kohler HP, Raddatz Müller P, Alberio L, Schroeder V. Proline 36 of the Factor XIII Activation Peptide Plays a Crucial Role in Substrate Recognition and Zymogen Activation. Thromb Haemost 2018; 118:2037-2045. [PMID: 30419598 DOI: 10.1055/s-0038-1675600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The activation peptide of blood coagulation factor XIII (AP-FXIII) has important functions in stabilizing the FXIII-A2 dimer and regulating FXIII activation. Contributions of many of its 37 amino acids to these functions have been described. However, the role of proline 36, which is adjacent to the thrombin cleavage site at Arg37, has not yet been studied in detail. We approached this question when we came across a patient with congenital FXIII deficiency in whom we detected a novel Pro36Ser mutation. We expressed the mutant FXIII-A Pro36Ser protein in Chinese hamster ovary cells and found that this mutation does not influence FXIII-A expression but significantly inhibits proteolytic activation by thrombin. The enzymatic transglutaminase activity is not affected as it can be induced in the presence of high Ca2+ concentrations. We performed nuclear magnetic resonance analysis to investigate AP-FXIII-thrombin interactions, which showed that the mutant Ser36 peptide binds less well to the thrombin surface than the native Pro36 peptide. The Arg37 at the P1 position still makes strong interactions with the active site cleft but the P4-P2 residues (34VVS36) appear to be less well positioned to contact the neighbouring thrombin active site region. In conclusion, we have characterized a novel mutation in AP-FXIII representing only the fourth case of the rare FXIII-A type II deficiency. This case served as a perfect in vivo model to shed light on the crucial role of Pro36 in the proteolytic activation of FXIII-A. Our results contribute to the understanding of structure-function relationship in FXIII.
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Affiliation(s)
- Bojun Li
- Experimental Haemostasis Group, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Ramya Billur
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States
| | - Muriel C Maurer
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States
| | - Hans P Kohler
- Experimental Haemostasis Group, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Pascale Raddatz Müller
- Division of Haematology and Central Haematology Laboratory, Luzerner Kantonsspital, Lucerne, Switzerland
| | - Lorenzo Alberio
- Division of Haematology and Central Haematology Laboratory, Lausanne University Hospital, Lausanne, Switzerland.,Faculté de Biologie et Médecine, University of Lausanne, Lausanne, Switzerland
| | - Verena Schroeder
- Experimental Haemostasis Group, Department for BioMedical Research, University of Bern, Bern, Switzerland
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48
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De Filippis V, Pozzi N, Acquasaliente L, Artusi I, Pontarollo G, Peterle D. Protein engineering by chemical methods: Incorporation of nonnatural amino acids as a tool for studying protein folding, stability, and function. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Nicola Pozzi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Ilaria Artusi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
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49
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Takagi Y, Murata M, Kozuka T, Nakata Y, Hasebe R, Tamura S, Takagi A, Matsushita T, Saito H, Kojima T. Missense mutations in the gene encoding prothrombin corresponding to Arg596 cause antithrombin resistance and thrombomodulin resistance. Thromb Haemost 2018; 116:1022-1031. [DOI: 10.1160/th16-03-0223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/15/2016] [Indexed: 11/05/2022]
Abstract
SummaryAntithrombin (AT) and thrombomodulin (TM) play important roles in the process of natural anticoagulation in vivo. Recently, we reported that the prothrombin Yukuhashi mutation (p.Arg596Leu) was associated with AT and TM resistance-related thrombophilia. To assess the AT and TM resistances associated with other missense mutations by single base substitution in the Arg596 codon, we generated recombinant variants (596Gln, 596Trp, 596Gly, and 596Pro) and investigated the effects on AT and TM anticoagulant functions. All variants except 596Pro were secreted in amounts comparable to that of the wild-type but exhibited variable procoagulant activities. After a 30-minute inactivation by AT, the relative residual activity of wild-type thrombin decreased to 15 ± 4.0%, in contrast to values of all variants were maintained at above 80%. The thrombin–AT complex formation, as determined by enzyme-linked immunosorbent assay, was reduced with all tested variants in the presence and absence of heparin. In the presence of soluble TM (sTM), the relative fibrinogen clotting activity of wild-type thrombin decreased to 16 ± 0.12%, whereas that of tested variants was 37%–56%. In a surface plasmon resonance assay, missense Arg596 mutations reduced thrombin–TM affinity to an extent similar to the reduction of fibrinogen clotting inhibition. In the presence of sTM or cultured endothelial-like cells, APC generation was enhanced differently by variant thrombins in a thrombin–TM affinity- dependent manner. These data indicate that prothrombin Arg596 missense mutations lead to AT and TM resistance in the variant thrombins and suggest that prothrombin Arg596 is important for AT- and TM- mediated anticoagulation.
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50
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Chakraborty P, Acquasaliente L, Pelc LA, Di Cera E. Interplay between conformational selection and zymogen activation. Sci Rep 2018; 8:4080. [PMID: 29511224 PMCID: PMC5840343 DOI: 10.1038/s41598-018-21728-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/09/2018] [Indexed: 11/09/2022] Open
Abstract
Trypsin-like proteases are synthesized as zymogens and activated through a mechanism that folds the active site for efficient binding and catalysis. Ligand binding to the active site is therefore a valuable source of information on the changes that accompany zymogen activation. Using the physiologically relevant transition of the clotting zymogen prothrombin to the mature protease thrombin, we show that the mechanism of ligand recognition follows selection within a pre-existing ensemble of conformations with the active site accessible (E) or inaccessible (E*) to binding. Prothrombin exists mainly in the E* conformational ensemble and conversion to thrombin produces two dominant changes: a progressive shift toward the E conformational ensemble triggered by removal of the auxiliary domains upon cleavage at R271 and a drastic drop of the rate of ligand dissociation from the active site triggered by cleavage at R320. Together, these effects produce a significant (700-fold) increase in binding affinity. Limited proteolysis reveals how the E*-E equilibrium shifts during prothrombin activation and influences exposure of the sites of cleavage at R271 and R320. These new findings on the molecular underpinnings of prothrombin activation are relevant to other zymogens with modular assembly involved in blood coagulation, complement and fibrinolysis.
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Affiliation(s)
- Pradipta Chakraborty
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Laura Acquasaliente
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
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