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Abdelfadiel E, Gunta R, Villuri BK, Afosah DK, Sankaranarayanan NV, Desai UR. Designing Smaller, Synthetic, Functional Mimetics of Sulfated Glycosaminoglycans as Allosteric Modulators of Coagulation Factors. J Med Chem 2023; 66:4503-4531. [PMID: 37001055 PMCID: PMC10108365 DOI: 10.1021/acs.jmedchem.3c00132] [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: 01/23/2023] [Indexed: 04/03/2023]
Abstract
Natural glycosaminoglycans (GAGs) are arguably the most diverse collection of natural products. Unfortunately, this bounty of structures remains untapped. Decades of research has realized only one GAG-like synthetic, small-molecule drug, fondaparinux. This represents an abysmal output because GAGs present a frontier that few medicinal chemists, and even fewer pharmaceutical companies, dare to undertake. GAGs are heterogeneous, polymeric, polydisperse, highly water soluble, synthetically challenging, too rapidly cleared, and difficult to analyze. Additionally, GAG binding to proteins is not very selective and GAG-binding sites are shallow. This Perspective attempts to transform this negative view into a much more promising one by highlighting recent advances in GAG mimetics. The Perspective focuses on the principles used in the design/discovery of drug-like, synthetic, sulfated small molecules as allosteric modulators of coagulation factors, such as antithrombin, thrombin, and factor XIa. These principles will also aid the design/discovery of sulfated agents against cancer, inflammation, and microbial infection.
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Affiliation(s)
- Elsamani
I. Abdelfadiel
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rama Gunta
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Bharath Kumar Villuri
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Daniel K. Afosah
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nehru Viji Sankaranarayanan
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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Allosteric modulation of exosite 1 attenuates polyphosphate-catalyzed activation of factor XI by thrombin. JOURNAL OF THROMBOSIS AND HAEMOSTASIS : JTH 2023; 21:83-93. [PMID: 36695400 DOI: 10.1016/j.jtha.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/05/2022] [Accepted: 10/31/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Polyphosphate (polyP) promotes feedback activation of factor (F) XI by thrombin by serving as a template. The contribution of thrombin's exosites to these interactions is unclear. OBJECTIVES To determine the contribution of thrombin exosites 1 and 2 to polyP-induced potentiation of FXI activation by thrombin. METHODS The affinities of α-thrombin; K109E/110E-thrombin, an exosite 1 variant, or R93E-thrombin, an exosite 2 variant; FXI; and FXIa for polyP-70 were quantified using surface plasmon resonance in the absence or presence of exosite ligands. FXI was activated with α-thrombin or thrombin variants in the absence or presence of polyP-70 and exosite ligands. RESULTS α-Thrombin, K109/110E-thrombin, FXI, and FXIa bound polyP-70, whereas R93E-thrombin exhibited minimal binding. Exosite 1 and exosite 2 ligands attenuated thrombin binding to polyP-70. PolyP-70 accelerated the rate of FXI activation by α-thrombin and K109E/110E-thrombin but not R93E-thrombin up to 1500-fold in a bell-shaped, concentration-responsive manner. Exosite 1 and exosite 2 ligands had no impact on FXI activation by thrombin in the absence of polyP-70; however, in its presence, they attenuated activation by 40% to 65%. CONCLUSION PolyP-70 binds FXI and thrombin and promotes their interaction. Exosite 2 ligands attenuate activation because thrombin binds polyP-70 via exosite 2. Attenuation of FXI activation by exosite 1 ligands likely reflects allosteric modulation of exosite 2 and/or the active site of thrombin because exosite 1 is not directly involved in FXI activation. Therefore, allosteric modulation of thrombin's exosites may represent a novel strategy for downregulating FXI activation.
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Mo Z, Xiao Z, He C. Functional expression of a thrombin exosite I inhibitor triabin in Escherichia coli and elucidation of the role of key residues in its inhibitory activity. Biochimie 2022; 208:13-19. [PMID: 36580989 DOI: 10.1016/j.biochi.2022.12.013] [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: 09/16/2022] [Revised: 12/03/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Triabin, a lipocalin-like thrombin inhibitor from the saliva of the blood-sucking triatomine bug Triatoma pallidipennis, exhibits effective inhibition comparable to hirudin despite binding exclusively at exosite I. Interestingly, it was reported that higher triabin doses would not inhibit thrombin completely, which makes it a promising antithrombotic candidate agent with a larger therapeutic window. However, few structural and functional studies about triabin have been reported in the past three decades, mostly due to the lack of a reliable and practicable recombinant expression technology for this seemingly small protein. In this work, we have adopted the SUMO fusion technology for the expression of triabin in E. coli cells-with facile refolding and purification procedures-and the bioactive triabin was produced in ∼12 mg/L culture medium. Subsequently, the structure-function studies through extensive site-directed mutagenesis reveal that triabin's Phe-106 involved in the hydrophobic contacts plays a surprisingly important role in the thrombin inhibition, in contrast to the negatively charged residues Asp-135 or Glu-128 involved in the salt-bridge interaction. As such, this study complements our understanding of the interaction mechanism of natural thrombin inhibitors, which should facilitate the development of anticoagulant drugs with a novel mode of action against thrombin.
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Affiliation(s)
- Zeyuan Mo
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Zhenbang Xiao
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China.
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Zhong X, D’Antona AM. A potential antibody repertoire diversification mechanism through tyrosine sulfation for biotherapeutics engineering and production. Front Immunol 2022; 13:1072702. [PMID: 36569848 PMCID: PMC9774471 DOI: 10.3389/fimmu.2022.1072702] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
The diversity of three hypervariable loops in antibody heavy chain and light chain, termed the complementarity-determining regions (CDRs), defines antibody's binding affinity and specificity owing to the direct contact between the CDRs and antigens. These CDR regions typically contain tyrosine (Tyr) residues that are known to engage in both nonpolar and pi stacking interaction with antigens through their complementary aromatic ring side chains. Nearly two decades ago, sulfotyrosine residue (sTyr), a negatively charged Tyr formed by Golgi-localized membrane-bound tyrosylprotein sulfotransferases during protein trafficking, were also found in the CDR regions and shown to play an important role in modulating antibody-antigen interaction. This breakthrough finding demonstrated that antibody repertoire could be further diversified through post-translational modifications, in addition to the conventional genetic recombination. This review article summarizes the current advances in the understanding of the Tyr-sulfation modification mechanism and its application in potentiating protein-protein interaction for antibody engineering and production. Challenges and opportunities are also discussed.
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Stewart V, Ronald PC. Sulfotyrosine residues: interaction specificity determinants for extracellular protein-protein interactions. J Biol Chem 2022; 298:102232. [PMID: 35798140 PMCID: PMC9372746 DOI: 10.1016/j.jbc.2022.102232] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification, can determine and often enhance protein–protein interaction specificity. Sulfotyrosyl residues (sTyrs) are formed by the enzyme tyrosyl-protein sulfotransferase during protein maturation in the Golgi apparatus and most often occur singly or as a cluster within a six-residue span. With both negative charge and aromatic character, sTyr facilitates numerous atomic contacts as visualized in binding interface structural models, thus there is no discernible binding site consensus. Found exclusively in secreted proteins, in this review, we discuss the four broad sequence contexts in which sTyr has been observed: first, a solitary sTyr has been shown to be critical for diverse high-affinity interactions, such as between peptide hormones and their receptors, in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of cellular processes, including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters is found in conserved acidic sequences termed hirudin-like motifs that enable proteins to interact with thrombin; consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyrs for their activity. Finally, several proteins that interact with collagen or similar proteins contain one or more sTyrs within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in mass spectrometry and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
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Affiliation(s)
- Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, USA.
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, USA; Genome Center, University of California, Davis, USA.
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Tyrosine-O-sulfation is a widespread affinity enhancer among thrombin interactors. Biochem Soc Trans 2022; 50:387-401. [PMID: 34994377 DOI: 10.1042/bst20210600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/24/2022]
Abstract
Tyrosine-O-sulfation is a common post-translational modification (PTM) of proteins following the cellular secretory pathway. First described in human fibrinogen, tyrosine-O-sulfation has long been associated with the modulation of protein-protein interactions in several physiological processes. A number of relevant interactions for hemostasis are largely dictated by this PTM, many of which involving the serine proteinase thrombin (FIIa), a central player in the blood-clotting cascade. Tyrosine sulfation is not limited to endogenous FIIa ligands and has also been found in hirudin, a well-known and potent thrombin inhibitor from the medicinal leech, Hirudo medicinalis. The discovery of hirudin led to successful clinical application of analogs of leech-inspired molecules, but also unveiled several other natural thrombin-directed anticoagulant molecules, many of which undergo tyrosine-O-sulfation. The presence of this PTM has been shown to enhance the anticoagulant properties of these peptides from a range of blood-feeding organisms, including ticks, mosquitos and flies. Interestingly, some of these molecules display mechanisms of action that mimic those of thrombin's bona fide substrates.
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Lu ZC, Jiang F, Wu YD. Phosphate binding sites prediction in phosphorylation-dependent protein-protein interactions. Bioinformatics 2021; 37:4712-4718. [PMID: 34270697 DOI: 10.1093/bioinformatics/btab525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Phosphate binding plays an important role in modulating protein-protein interactions, which are ubiquitous in various biological processes. Accurate prediction of phosphate binding sites is an important but challenging task. Small size and diversity of phosphate binding sites lead to a substantial challenge for developing accurate prediction methods. RESULTS Here we present the phosphate binding site predictor (PBSP), a novel and accurate approach to identifying phosphate binding sites from protein structures. PBSP combines an energy-based ligand-binding sites identification method with reverse focused docking using a phosphate probe. We show that PBSP outperforms not only general ligand binding sites predictors but also other existing phospholigand-specific binding sites predictors. It achieves ∼95% success rate for top 10 predicted sites with an average Matthews correlation coefficient (MCC) value of 0.84 for successful predictions. PBSP can accurately predict phosphate binding modes, with average position error of 1.4 Å and 2.4 Å in bound and unbound datasets, respectively. Lastly, visual inspection of the predictions is conducted. Reasons for failed predictions are further analyzed and possible ways to improve the performance are provided. These results demonstrate a novel and accurate approach to phosphate binding sites identification in protein structures. AVAILABILITY The software and benchmark datasets are freely available at http://web.pkusz.edu.cn/wu/PBSP/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zheng-Chang Lu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Fan Jiang
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,NanoAI Biotech Co., Ltd, Shenzhen, 518118, China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,Shenzhen Bay Laboratory, Shenzhen, 518055, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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Li YR, Huang YN, Zhao B, Wu MF, Li TY, Zhang YL, Chen D, Yu M, Mo W. RGD-hirudin-based low molecular weight peptide prevents blood coagulation via subcutaneous injection. Acta Pharmacol Sin 2020; 41:753-762. [PMID: 31949293 PMCID: PMC7468311 DOI: 10.1038/s41401-019-0347-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/12/2019] [Indexed: 11/09/2022] Open
Abstract
Thromboembolic disease is a common cardio-cerebral vascular disease that threatens human life and health. Thrombin not only affects the exogenous coagulation pathway, but also the endogenous pathway. Thus, it becomes one of the most important targets of anticoagulant drugs. RGD-hirudin is an anticoagulant drug targeting thrombin, but it can only be administered intravenously. We designed a low molecular weight peptide based on RGD-hirudin that could prevent blood clots. We first used NMR to identify the key amino acid residues of RGD-hirudin that interacted with thrombin. Then, we designed a novel direct thrombin inhibitor peptide (DTIP) based on the structure and function of RGD-hirudin using homology modeling. Molecular docking showed that the targeting and binding of DTIP with thrombin were similar to those of RGD-hirudin, suggesting DTIP interacted directly with thrombin. The active amino acids of DTIP were identified by alanine scanning, and mutants were successfully constructed. In blood clotting time tests in vitro, we found that aPTT, PT, and TT in the rat plasma added with DTIP were greatly prolonged than in that added with the mutants. Subcutaneous injection of DTIP in rats also could significantly prolong the clotting time. Thrombelastography analysis revealed that DTIP significantly delayed blood coagulation. Bio-layer interferometry study showed that there were no significant differences between DTIP and the mutants in thrombin affinity constants, suggesting that it might bind to other sites of thrombin rather than to its active center. Our results demonstrate that DTIP with low molecular weight can prevent thrombosis via subcutaneous injection.
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Schmidt AE, Vadivel K, Whitelegge J, Bajaj SP. Plasmin-mediated proteolysis of human factor IXa in the presence of calcium/phospholipid: Conversion of procoagulant factor IXa to a fibrinolytic enhancer. J Thromb Haemost 2020; 18:1171-1182. [PMID: 32073726 PMCID: PMC7363452 DOI: 10.1111/jth.14773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/28/2020] [Accepted: 02/18/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Factor (F) IX/IXa inactivation by plasmin has been studied; however, whether plasmin converts FIXa to a fibrinolytic enhancer is not known. OBJECTIVE Investigate plasmin proteolysis site(s) in FIXa that inactivates and transforms it into a fibrinolytic enhancer. METHODS NH2 -terminal sequencing, mass spectrometry analysis, and functional assays. RESULTS Plasmin in the presence of Ca2+ /phospholipid (PL) rapidly cleaved FIXaβ at Lys316↓Gly317 to yield FIXaγ followed by a slow cleavage at Lys413↓Leu414 to yield FIXaδ. FIXaγ/FIXaδ migrated indistinguishably from FIXaβ in nondenaturing gel system indicating that C-terminal residues 317-415/317-413 of heavy chain remain noncovalently associated with FIXaγ/FIXaδ. However, as compared with FIXaβ, FIXaγ or FIXaγ/FIXaδ (25-75 mixture, 8-hour/24-hour incubation analysis by mass spectrometry) was impaired ~ 10-fold in hydrolyzing synthetic substrate CBS 31.39 (CH3-SO2-D-Leu-Gly-Arg-pNA), ~ 30-fold (~ 5-fold higher Km , ~ 6-fold lower kcat ) in activating FX in a system containing Ca2+ /PL, and ~ 650-fold in a system containing Ca2+ /PL and FVIIIa. Further, FIXaγ or FIXaγ/FIXaδ bound FVIIIa with ~ 60-fold reduced affinity compared with FIXaβ. Additionally, in ligand blots, plasminogen or diisopropylfluorophosphate-inhibited plasmin (DIP-plasmin) bound FIXaγ and FIXaδ but not FIXaβ. This interaction was prevented by ε-aminocaproic acid or carboxypeptidase B treatment suggesting that plasminogen/DIP-plasmin binds to FIXaγ/FIXaδ through newly generated C-terminal Lys316 and Lys413. Importantly, FIXaγ/FIXaδ mixture but not FIXaγ enhanced tissue plasminogen activator (tPA)-mediated plasminogen activation in a concentration dependent manner. Similarly, FIXaγ/FIXaδ mixture but not FIXaγ enhanced tPA-induced clot lysis in FIX-depleted plasma. CONCLUSION Plasmin cleavage at Lys316↓Gly317 abrogates FIXaβ coagulant activity, whereas additional cleavage at Lys413↓Leu414 converts it into a fibrinolytic enhancer.
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Affiliation(s)
- Amy E. Schmidt
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Kanagasabai Vadivel
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Julian Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - S. Paul Bajaj
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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Mehta AY, Heimburg-Molinaro J, Cummings RD, Goth CK. Emerging patterns of tyrosine sulfation and O-glycosylation cross-talk and co-localization. Curr Opin Struct Biol 2020; 62:102-111. [PMID: 31927217 DOI: 10.1016/j.sbi.2019.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Akul Y Mehta
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, 02215, USA
| | - Jamie Heimburg-Molinaro
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, 02215, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, 02215, USA
| | - Christoffer K Goth
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, 02215, USA
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De D, Bhattacharjee P, Das H, Kumar KS, Biswas SC, Bhattacharyya D. Destabilization of β-amyloid aggregates by thrombin derived peptide: plausible role of thrombin in neuroprotection. FEBS J 2020; 287:2386-2413. [PMID: 31747135 DOI: 10.1111/febs.15149] [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: 10/10/2018] [Revised: 09/04/2019] [Accepted: 11/19/2019] [Indexed: 01/06/2023]
Abstract
β-amyloid (Aβ) aggregates involved in Alzheimer's disease (AD) are resistant to proteases but could be destabilized by small peptides designed to target specific hydrophobic regions of Aβ that take part in aggregate assembly. Since thrombin and AD are intricately connected, and elastase modulates thrombin activity, elastase-digested thrombin peptides were verified for intervention in the Aβ-aggregation pathway. Intact or elastase-digested thrombin destabilized Aβ fibril, as demonstrated by thioflavin T assay. Peptides were synthesized employing thrombin as a template, of which, a hexapeptide (T3) showed maximum destabilization at 1 µm. ExPASy peptide cutter software coupled with mass spectrometric analysis confirmed the generation of T3 peptide from elastase-digested thrombin. TEM micrographs revealed that 30-day incubation of preformed Aβ fibrils or monomers with T3 resulted in destabilization or inhibition, respectively, leading mostly to particles of 1.74 ± 0.17 nm, which roughly corresponded to Aβ monomer. Surface plasmon resonance employing CM5 chip coupled with Aβ40 mouse monoclonal antibody showed a drop in response when T3 was incubated with Aβ fibrils between 2 and 8 h. 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide and confocal microscopy demonstrated the ability of T3 to rescue neuroblastoma cells from Aβ oligomer-induced cytotoxic damage. Although no [Aβ-T3] adduct could be detected by mass spectrometry, an initial interaction appeared to facilitate the process of destabilization/inhibition of aggregation. T3 was comparable to standard β-sheet breaker peptides, LPFFD and KLVFF in terms of Aβ aggregate destabilization. High hydrophobicity values coupled with recognition and breaking elements make T3 a potential candidate for future therapeutic applications.
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Affiliation(s)
- Debashree De
- Division of Structural Biology and Bioinformatics, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Payel Bhattacharjee
- Division of Structural Biology and Bioinformatics, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Hrishita Das
- Division of Cell Biology and Physiology, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Karri Suresh Kumar
- Central Instrument Facility, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Subhas Chandra Biswas
- Division of Cell Biology and Physiology, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Debasish Bhattacharyya
- Division of Structural Biology and Bioinformatics, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
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12
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Li J, Kim K, Jeong SY, Chiu J, Xiong B, Petukhov PA, Dai X, Li X, Andrews RK, Du X, Hogg PJ, Cho J. Platelet Protein Disulfide Isomerase Promotes Glycoprotein Ibα-Mediated Platelet-Neutrophil Interactions Under Thromboinflammatory Conditions. Circulation 2019; 139:1300-1319. [PMID: 30586735 DOI: 10.1161/circulationaha.118.036323] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Platelet-neutrophil interactions contribute to vascular occlusion and tissue damage in thromboinflammatory disease. Platelet glycoprotein Ibα (GPIbα), a key receptor for the cell-cell interaction, is believed to be constitutively active for ligand binding. Here, we established the role of platelet-derived protein disulfide isomerase (PDI) in reducing the allosteric disulfide bonds in GPIbα and enhancing the ligand-binding activity under thromboinflammatory conditions. METHODS Bioinformatic analysis identified 2 potential allosteric disulfide bonds in GPIbα. Agglutination assays, flow cytometry, surface plasmon resonance analysis, a protein-protein docking model, proximity ligation assays, and mass spectrometry were used to demonstrate a direct interaction between PDI and GPIbα and to determine a role for PDI in regulating GPIbα function and platelet-neutrophil interactions. Also, real-time microscopy and animal disease models were used to study the pathophysiological role of PDI-GPIbα signaling under thromboinflammatory conditions. RESULTS Deletion or inhibition of platelet PDI significantly reduced GPIbα-mediated platelet agglutination. Studies using PDI-null platelets and recombinant PDI or Anfibatide, a clinical-stage GPIbα inhibitor, revealed that the oxidoreductase activity of platelet surface-bound PDI was required for the ligand-binding function of GPIbα. PDI directly bound to the extracellular domain of GPIbα on the platelet surface and reduced the Cys4-Cys17 and Cys209-Cys248 disulfide bonds. Real-time microscopy with platelet-specific PDI conditional knockout and sickle cell disease mice demonstrated that PDI-regulated GPIbα function was essential for platelet-neutrophil interactions and vascular occlusion under thromboinflammatory conditions. Studies using a mouse model of ischemia/reperfusion-induced stroke indicated that PDI-GPIbα signaling played a crucial role in tissue damage. CONCLUSIONS Our results demonstrate that PDI-facilitated cleavage of the allosteric disulfide bonds tightly regulates GPIbα function, promoting platelet-neutrophil interactions, vascular occlusion, and tissue damage under thromboinflammatory conditions.
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Affiliation(s)
- Jing Li
- Department of Pharmacology, University of Illinois College of Medicine, Chicago (J.L., K.K., S.-Y.J, B.X., X. Du, J. Cho)
| | - Kyungho Kim
- Department of Pharmacology, University of Illinois College of Medicine, Chicago (J.L., K.K., S.-Y.J, B.X., X. Du, J. Cho).,Korean Medicine-Application Center, Korea Institute of Oriental Medicine, Daegu (K.K.)
| | - Si-Yeon Jeong
- Department of Pharmacology, University of Illinois College of Medicine, Chicago (J.L., K.K., S.-Y.J, B.X., X. Du, J. Cho)
| | - Joyce Chiu
- The Centenary Institute, Newtown, NSW, Australia (J. Chiu, P.J.H.).,National Health and Medical Research Council Clinical Trials Centre, University of Sydney, NSW, Australia (J. Chiu, P.J.H.)
| | - Bei Xiong
- Department of Pharmacology, University of Illinois College of Medicine, Chicago (J.L., K.K., S.-Y.J, B.X., X. Du, J. Cho)
| | - Pavel A Petukhov
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Chicago (P.A.P.)
| | - Xiangrong Dai
- Lee's Pharmaceutical Holdings Ltd, Shatin, Hong Kong (X. Dai, X.L.)
| | - Xiaoyi Li
- Lee's Pharmaceutical Holdings Ltd, Shatin, Hong Kong (X. Dai, X.L.)
| | - Robert K Andrews
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC (R.K.A.)
| | - Xiaoping Du
- Department of Pharmacology, University of Illinois College of Medicine, Chicago (J.L., K.K., S.-Y.J, B.X., X. Du, J. Cho)
| | - Philip J Hogg
- The Centenary Institute, Newtown, NSW, Australia (J. Chiu, P.J.H.).,National Health and Medical Research Council Clinical Trials Centre, University of Sydney, NSW, Australia (J. Chiu, P.J.H.)
| | - Jaehyung Cho
- Department of Pharmacology, University of Illinois College of Medicine, Chicago (J.L., K.K., S.-Y.J, B.X., X. Du, J. Cho)
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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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14
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The Glycoprotein Ib-IX-V Complex. Platelets 2019. [DOI: 10.1016/b978-0-12-813456-6.00010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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15
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Pryzdial ELG, Lee FMH, Lin BH, Carter RLR, Tegegn TZ, Belletrutti MJ. Blood coagulation dissected. Transfus Apher Sci 2018; 57:449-457. [PMID: 30049564 DOI: 10.1016/j.transci.2018.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hemostasis is the physiological control of bleeding and is initiated by subendothelial exposure. Platelets form the primary vascular seal in three stages (localization, stimulation and aggregation), which are triggered by specific interactions between platelet surface receptors and constituents of the subendothelial matrix. As a secondary hemostatic plug, fibrin clot formation is initiated and feedback-amplified to advance the seal and stabilize platelet aggregates comprising the primary plug. Once blood leakage has been halted, the fibrinolytic pathway is initiated to dissolve the clot and restore normal blood flow. Constitutive and induced anticoagulant and antifibrinolytic pathways create a physiological balance between too much and too little clot production. Hemostatic imbalance is a major burden to global healthcare, resulting in thrombosis or hemorrhage.
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Affiliation(s)
- Edward L G Pryzdial
- Centre for Innovation, Canadian Blood Services, Ottawa, ON, Canada; Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Frank M H Lee
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Bryan H Lin
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rolinda L R Carter
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tseday Z Tegegn
- Centre for Innovation, Canadian Blood Services, Ottawa, ON, Canada; Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark J Belletrutti
- Pediatric Hematology, Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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16
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14-3-3 proteins in platelet biology and glycoprotein Ib-IX signaling. Blood 2018; 131:2436-2448. [PMID: 29622550 DOI: 10.1182/blood-2017-09-742650] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/25/2018] [Indexed: 12/16/2022] Open
Abstract
Members of the 14-3-3 family of proteins function as adapters/modulators that recognize phosphoserine/phosphothreonine-based binding motifs in many intracellular proteins and play fundamental roles in signal transduction pathways of eukaryotic cells. In platelets, 14-3-3 plays a wide range of regulatory roles in phosphorylation-dependent signaling pathways, including G-protein signaling, cAMP signaling, agonist-induced phosphatidylserine exposure, and regulation of mitochondrial function. In particular, 14-3-3 interacts with several phosphoserine-dependent binding sites in the major platelet adhesion receptor, the glycoprotein Ib-IX complex (GPIb-IX), regulating its interaction with von Willebrand factor (VWF) and mediating VWF/GPIb-IX-dependent mechanosignal transduction, leading to platelet activation. The interaction of 14-3-3 with GPIb-IX also plays a critical role in enabling the platelet response to low concentrations of thrombin through cooperative signaling mediated by protease-activated receptors and GPIb-IX. The various functions of 14-3-3 in platelets suggest that it is a possible target for the treatment of thrombosis and inflammation.
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17
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Pontarollo G, Acquasaliente L, Peterle D, Frasson R, Artusi I, De Filippis V. Non-canonical proteolytic activation of human prothrombin by subtilisin from Bacillus subtilis may shift the procoagulant-anticoagulant equilibrium toward thrombosis. J Biol Chem 2017; 292:15161-15179. [PMID: 28684417 DOI: 10.1074/jbc.m117.795245] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/28/2017] [Indexed: 12/26/2022] Open
Abstract
Blood coagulation is a finely regulated physiological process culminating with the factor Xa (FXa)-mediated conversion of the prothrombin (ProT) zymogen to active α-thrombin (αT). In the prothrombinase complex on the platelet surface, FXa cleaves ProT at Arg-271, generating the inactive precursor prethrombin-2 (Pre2), which is further attacked at Arg-320-Ile-321 to yield mature αT. Whereas the mechanism of physiological ProT activation has been elucidated in great detail, little is known about the role of bacterial proteases, possibly released in the bloodstream during infection, in inducing blood coagulation by direct proteolytic ProT activation. This knowledge gap is particularly concerning, as bacterial infections are frequently complicated by severe coagulopathies. Here, we show that addition of subtilisin (50 nm to 2 μm), a serine protease secreted by the non-pathogenic bacterium Bacillus subtilis, induces plasma clotting by proteolytically converting ProT into active σPre2, a nicked Pre2 derivative with a single cleaved Ala-470-Asn-471 bond. Notably, we found that this non-canonical cleavage at Ala-470-Asn-471 is instrumental for the onset of catalysis in σPre2, which was, however, reduced about 100-200-fold compared with αT. Of note, σPre2 could generate fibrin clots from fibrinogen, either in solution or in blood plasma, and could aggregate human platelets, either isolated or in whole blood. Our findings demonstrate that alternative cleavage of ProT by proteases, even by those secreted by non-virulent bacteria such as B. subtilis, can shift the delicate procoagulant-anticoagulant equilibrium toward thrombosis.
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Affiliation(s)
- Giulia Pontarollo
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Laura Acquasaliente
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Daniele Peterle
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Roberta Frasson
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Ilaria Artusi
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Vincenzo De Filippis
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
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18
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Chen K, Stafford AR, Wu C, Yeh CH, Kim PY, Fredenburgh JC, Weitz JI. Exosite 2-Directed Ligands Attenuate Protein C Activation by the Thrombin–Thrombomodulin Complex. Biochemistry 2017; 56:3119-3128. [DOI: 10.1021/acs.biochem.7b00250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Chen
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Alan R. Stafford
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Chengliang Wu
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Calvin H. Yeh
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Paul Y. Kim
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - James C. Fredenburgh
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Jeffrey I. Weitz
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
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19
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A cluster of aspartic residues in the extracellular loop II of PAR 4 is important for thrombin interaction and activation of platelets. Thromb Res 2017; 154:84-92. [DOI: 10.1016/j.thromres.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022]
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20
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Petzold T, Thienel M, Konrad I, Schubert I, Regenauer R, Hoppe B, Lorenz M, Eckart A, Chandraratne S, Lennerz C, Kolb C, Braun D, Jamasbi J, Brandl R, Braun S, Siess W, Schulz C, Massberg S. Oral thrombin inhibitor aggravates platelet adhesion and aggregation during arterial thrombosis. Sci Transl Med 2016; 8:367ra168. [DOI: 10.1126/scitranslmed.aad6712] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 08/31/2016] [Indexed: 12/13/2022]
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21
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Molecular mapping of α-thrombin (αT)/β2-glycoprotein I (β2GpI) interaction reveals how β2GpI affects αT functions. Biochem J 2016; 473:4629-4650. [PMID: 27760842 DOI: 10.1042/bcj20160603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/07/2016] [Accepted: 10/14/2016] [Indexed: 01/15/2023]
Abstract
β2-Glycoprotein I (β2GpI) is the major autoantigen in the antiphospholipid syndrome, a thrombotic autoimmune disease. Nonetheless, the physiological role of β2GpI is still unclear. In a recent work, we have shown that β2GpI selectively inhibits the procoagulant functions of human α-thrombin (αT; i.e. prolongs fibrin clotting time, tc, and inhibits αT-induced platelet aggregation) without affecting the unique anticoagulant activity of the protease, i.e. the proteolytic generation of the anticoagulant protein C (PC) from the PC zymogen, which interacts with αT exclusively at the protease catalytic site. Here, we used several different biochemical/biophysical techniques and molecular probes for mapping the binding sites in the αT-β2GpI complex. Our results indicate that αT exploits the highly electropositive exosite-II, which is also responsible for anchoring αT on the platelet GpIbα (platelet receptor glycoprotein Ibα) receptor, for binding to a continuous negative region on β2GpI structure, spanning domain IV and (part of) domain V, whereas the protease active site and exosite-I (i.e. the fibrinogen-binding site) remain accessible for substrate/ligand binding. Furthermore, we provided evidence that the apparent increase in tc, previously observed with β2GpI, is more likely caused by alteration in the ensuing fibrin structure rather than by the inhibition of fibrinogen hydrolysis. Finally, we produced a theoretical docking model of αT-β2GpI interaction, which was in agreement with the experimental results. Altogether, these findings help to understand how β2GpI affects αT interactions and suggest that β2GpI may function as a scavenger of αT for binding to the GpIbα receptor, thus impairing platelet aggregation while enabling normal cleavage of fibrinogen and PC.
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22
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Coagulation Factors in the Interstitial Space. Protein Sci 2016. [DOI: 10.1201/9781315374307-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Dabigatran and Argatroban Diametrically Modulate Thrombin Exosite Function. PLoS One 2016; 11:e0157471. [PMID: 27305147 PMCID: PMC4909201 DOI: 10.1371/journal.pone.0157471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022] Open
Abstract
Thrombin is a highly plastic molecule whose activity and specificity are regulated by exosites 1 and 2, positively-charged domains that flank the active site. Exosite binding by substrates and cofactors regulates thrombin activity by localizing thrombin, guiding substrates, and by inducing allosteric changes at the active site. Although inter-exosite and exosite-to-active-site allostery have been demonstrated, the impact of active site ligation on exosite function has not been examined. To address this gap, we used surface plasmon resonance to determine the effects of dabigatran and argatroban, active site-directed inhibitors, on thrombin binding to immobilized γA/γA-fibrin or glycoprotein Ibα peptide via exosite 1 and 2, respectively, and thrombin binding to γA/γ′-fibrin or factor Va, which is mediated by both exosites. Whereas dabigatran attenuated binding, argatroban increased thrombin binding to γA/γA- and γA/γ′-fibrin and to factor Va. The results with immobilized fibrin were confirmed by examining the binding of radiolabeled thrombin to fibrin clots. Thus, dabigatran modestly accelerated the dissociation of thrombin from γA/γA-fibrin clots, whereas argatroban attenuated dissociation. Dabigatran had no effect on thrombin binding to glycoprotein Ibα peptide, whereas argatroban promoted binding. These findings not only highlight functional effects of thrombin allostery, but also suggest that individual active site-directed thrombin inhibitors uniquely modulate exosite function, thereby identifying potential novel mechanisms of action.
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24
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Allosteric Partial Inhibition of Monomeric Proteases. Sulfated Coumarins Induce Regulation, not just Inhibition, of Thrombin. Sci Rep 2016; 6:24043. [PMID: 27053426 PMCID: PMC4823711 DOI: 10.1038/srep24043] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/14/2016] [Indexed: 11/26/2022] Open
Abstract
Allosteric partial inhibition of soluble, monomeric proteases can offer major regulatory advantages, but remains a concept on paper to date; although it has been routinely documented for receptors and oligomeric proteins. Thrombin, a key protease of the coagulation cascade, displays significant conformational plasticity, which presents an attractive opportunity to discover small molecule probes that induce sub-maximal allosteric inhibition. We synthesized a focused library of some 36 sulfated coumarins to discover two agents that display sub-maximal efficacy (~50%), high potency (<500 nM) and high selectivity for thrombin (>150-fold). Michaelis-Menten, competitive inhibition, and site-directed mutagenesis studies identified exosite 2 as the site of binding for the most potent sulfated coumarin. Stern-Volmer quenching of active site-labeled fluorophore suggested that the allosteric regulators induce intermediate structural changes in the active site as compared to those that display ~80–100% efficacy. Antithrombin inactivation of thrombin was impaired in the presence of the sulfated coumarins suggesting that allosteric partial inhibition arises from catalytic dysfunction of the active site. Overall, sulfated coumarins represent first-in-class, sub-maximal inhibitors of thrombin. The probes establish the concept of allosteric partial inhibition of soluble, monomeric proteins. This concept may lead to a new class of anticoagulants that are completely devoid of bleeding.
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25
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Mehta AY, Mohammed BM, Martin EJ, Brophy DF, Gailani D, Desai UR. Allosterism-based simultaneous, dual anticoagulant and antiplatelet action: allosteric inhibitor targeting the glycoprotein Ibα-binding and heparin-binding site of thrombin. J Thromb Haemost 2016; 14:828-38. [PMID: 26748875 PMCID: PMC4828251 DOI: 10.1111/jth.13254] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/24/2015] [Indexed: 12/01/2022]
Abstract
BACKGROUND Allosteric inhibition is a promising approach for developing a new group of anticoagulants with potentially reduced bleeding consequences. Recently, we designed sulfated β-O4 lignin (SbO4L) as an allosteric inhibitor that targets exosite 2 of thrombin to reduce fibrinogen cleavage through allostery and compete with glycoprotein Ibα to reduce platelet activation. OBJECTIVE To assess: (i) the antithrombotic potential of a novel approach of simultaneous exosite 2-dependent allosteric inhibition of thrombin and competitive inhibition of platelet activation; and (ii) the promise of SbO4L as the first-in-class antithrombotic agent. METHODS A combination of whole blood thromboelastography, hemostasis analysis, mouse arterial thrombosis models and mouse tail bleeding studies were used to assess antithrombotic potential. RESULTS AND CONCLUSIONS SbO4L extended the clot initiation time, and reduced maximal clot strength, platelet contractile force, and the clot elastic modulus, suggesting dual anticoagulant and antiplatelet effects. These effects were comparable to those observed with enoxaparin. A dose of 1 mg of SbO4L per mouse prevented occlusion in 100% of arteries, and lower doses resulted in a proportionally reduced response. Likewise, the time to occlusion increased by ~ 70% with a 0.5-mg dose in the mouse Rose Bengal thrombosis model. Finally, tail bleeding studies demonstrated that SbO4L does not increase bleeding propensity. In comparison, a 0.3-mg dose of enoxaparin increased the bleeding time and blood volume loss. Overall, this study highlights the promise of the allosteric inhibition approach, and presents SbO4L as a novel anticoagulant with potentially reduced bleeding side effects.
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Affiliation(s)
- Akul Y. Mehta
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Bassem M. Mohammed
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University, Richmond, VA 23298, USA
- Department of Clinical Pharmacy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Erika J. Martin
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Donald F. Brophy
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - David Gailani
- Department of Pathology, Immunology and Microbiology, Vanderbilt University Medical Center, Nashville, TN 37203
| | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
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26
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The Importance of Thrombin in Cerebral Injury and Disease. Int J Mol Sci 2016; 17:ijms17010084. [PMID: 26761005 PMCID: PMC4730327 DOI: 10.3390/ijms17010084] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 12/31/2022] Open
Abstract
There is increasing evidence that prothrombin and its active derivative thrombin are expressed locally in the central nervous system. So far, little is known about the physiological and pathophysiological functions exerted by thrombin in the human brain. Extra-hepatic prothrombin expression has been identified in neuronal cells and astrocytes via mRNA measurement. The actual amount of brain derived prothrombin is expected to be 1% or less compared to that in the liver. The role in brain injury depends upon its concentration, as higher amounts cause neuroinflammation and apoptosis, while lower concentrations might even be cytoprotective. Its involvement in numerous diseases like Alzheimer’s, multiple sclerosis, cerebral ischemia and haemorrhage is becoming increasingly clear. This review focuses on elucidation of the cerebral thrombin expression, local generation and its role in injury and disease of the central nervous system.
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27
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Hou Y, Carrim N, Wang Y, Gallant RC, Marshall A, Ni H. Platelets in hemostasis and thrombosis: Novel mechanisms of fibrinogen-independent platelet aggregation and fibronectin-mediated protein wave of hemostasis. J Biomed Res 2015; 29:437. [PMID: 26541706 PMCID: PMC4662204 DOI: 10.7555/jbr.29.20150121] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/12/2015] [Indexed: 12/31/2022] Open
Abstract
Platelets are small anucleate cells generated from megakaryocytes in the bone marrow. Although platelet generation, maturation, and clearance are still not fully understood, significant progress has been made in the last 1-2 decades. In blood circulation, platelets can quickly adhere and aggregate at sites of vascular injury, forming the platelet plug (i.e. the first wave of hemostasis). Activated platelets can also provide negatively charged phosphatidylserinerich membrane surface that enhances cell-based thrombin generation, which facilitates blood coagulation (i.e. the second wave of hemostasis). Platelets therefore play central roles in hemostasis. However, the same process of hemostasis may also cause thrombosis and vessel occlusion, which are the most common mechanisms leading to heart attack and stroke following ruptured atherosclerotic lesions. In this review, we will introduce the classical mechanisms and newly discovered pathways of platelets in hemostasis and thrombosis, including fibrinogen-independent platelet aggregation and thrombosis, and the plasma fibronectin-mediated "protein wave" of hemostasis that precedes the classical first wave of hemostasis. Furthermore, we briefly discuss the roles of platelets in inflammation and atherosclerosis and the potential strategies to control atherothrombosis.
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Affiliation(s)
- Yan Hou
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital and Toronto Platelet Immunobiology Group, Toronto, M5B 1W8, Ontario, Canada
- Jilin Provincial Center for Disease Control and Prevention, Changchun, Jilin, 130062 China
| | - Naadiya Carrim
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital and Toronto Platelet Immunobiology Group, Toronto, M5B 1W8, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Canadian Blood Services, Toronto, Ontario M5B 1W8, Canada
| | - Yiming Wang
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital and Toronto Platelet Immunobiology Group, Toronto, M5B 1W8, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Canadian Blood Services, Toronto, Ontario M5B 1W8, Canada
| | - Reid C Gallant
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital and Toronto Platelet Immunobiology Group, Toronto, M5B 1W8, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Alexandra Marshall
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital and Toronto Platelet Immunobiology Group, Toronto, M5B 1W8, Ontario, Canada
| | - Heyu Ni
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital and Toronto Platelet Immunobiology Group, Toronto, M5B 1W8, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Department of Medicine and Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A1, Canada.
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28
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Adams TE, Huntington JA. Structural transitions during prothrombin activation: On the importance of fragment 2. Biochimie 2015; 122:235-42. [PMID: 26365066 PMCID: PMC4756804 DOI: 10.1016/j.biochi.2015.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 09/08/2015] [Indexed: 01/01/2023]
Abstract
Prothrombin is activated to thrombin by the prothrombinase complex through sequential cleavage at two distinct sites. This occurs at sites of vascular injury in a highly regulated cascade of serine protease and cofactor activation, where activated platelets provide a suitable surface for protease/cofactor/substrate assembly. The precise structural and conformational changes undergone during the transition from prothrombin to thrombin have been studied for decades, and several structures of prothrombin fragments along the activation pathway have been solved. Here we present a new structure analyzed in context of other recent structures and biochemical studies. What emerges is an unexpected mechanism that involves a change in the mode of binding of the F2 domain (fragment 2) on the catalytic domain after cleavage at Arg320, and a subsequent reorientation of the linker between the F2 and catalytic domain to present the Arg271 site for cleavage. The catalytic domain of thrombin precursors binds to its F2 domain by two distinct modes. Cleavage of prothrombin at either Arg271 or Arg320 results in shift from mode 2 to mode 1. After cleavage at Arg320, movement of F2 helps to present the second cleavage site at Arg271.
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Affiliation(s)
- Ty E Adams
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - James A Huntington
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, United Kingdom.
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29
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Substantial non-electrostatic forces are needed to induce allosteric disruption of thrombin's active site through exosite 2. Biochem Biophys Res Commun 2014; 452:813-6. [PMID: 25201728 DOI: 10.1016/j.bbrc.2014.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/01/2014] [Indexed: 11/20/2022]
Abstract
Sulfated β-O4 lignin (SbO4L), a non-saccharide glycosaminoglycan mimetic, was recently disclosed as a novel exosite 2-directed thrombin inhibitor with the capability of mimicking sulfated tyrosine sequences of glycoprotein Ibα resulting in dual anticoagulant and antiplatelet activities. SbO4L engages essentially the same residues of exosite 2 as heparin and yet induces allosteric inhibition. Fluorescence spectroscopic studies indicate that SbO4L reduces access of the active site to molecular probes and affinity studies at varying salt concentrations show nearly 6 ionic interactions, similar to heparin, but much higher non-ionic contribution. The results suggest that subtle increase in non-electrostatic forces arising from SbO4L's aromatic scaffold appear to be critical for inducing allosteric dysfunction of thrombin's active site.
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Mehta AY, Thakkar JN, Mohammed BM, Martin EJ, Brophy DF, Kishimoto T, Desai UR. Targeting the GPIbα binding site of thrombin to simultaneously induce dual anticoagulant and antiplatelet effects. J Med Chem 2014; 57:3030-9. [PMID: 24635452 PMCID: PMC4203406 DOI: 10.1021/jm4020026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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Exosite 2 of human thrombin contributes
to two opposing pathways, the anticoagulant pathway and the platelet
aggregation pathway. We reasoned that an exosite 2 directed allosteric
thrombin inhibitor should simultaneously induce anticoagulant and
antiplatelet effects. To assess this, we synthesized SbO4L based on
the sulfated tyrosine-containing sequence of GPIbα. SbO4L was
synthesized in three simple steps in high yield and found to be a
highly selective, direct inhibitor of thrombin. Michelis–Menten
kinetic studies indicated a noncompetitive mechanism of inhibition.
Competitive inhibition studies suggested ideal competition with heparin
and glycoprotein Ibα, as predicted. Studies with site-directed
mutants of thrombin indicated that SbO4L binds to Arg233, Lys235,
and Lys236 of exosite 2. SbO4L prevented thrombin-mediated platelet
activation and aggregation as expected on the basis of competition
with GPIbα. SbO4L presents a novel paradigm of simultaneous
dual anticoagulant and antiplatelet effects achieved through the GPIbα
binding site of thrombin.
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Affiliation(s)
- Akul Y Mehta
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , Richmond, Virginia 23219, United States
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