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Yu HS, Gao C, Lupyan D, Wu Y, Kimura T, Wu C, Jacobson L, Harder E, Abel R, Wang L. Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics. J Chem Inf Model 2019; 59:3955-3967. [PMID: 31425654 DOI: 10.1021/acs.jcim.9b00268] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covalent inhibitors have emerged as an important drug class in recent years, largely due to their many unique advantages as compared to noncovalent inhibitors, including longer duration of action, lower prolonged systemic exposure, higher potency, and selectivity. However, the potential off-target toxicity of covalent inhibitors, particularly of irreversible covalent inhibitors, represents a great challenge in covalent drug development. Therefore, accurate calculation of protein covalent inhibitor reaction kinetics to guide the design of selective inhibitors would greatly benefit covalent drug discovery efforts. In the present paper, we present a computational method to calculate the relative reaction kinetics between congeneric irreversible covalent inhibitors and their protein receptors. The method combines density functional theory calculations of the transition state barrier height of the rate-limiting step for reaction between the warhead of the inhibitor and a single protein residue, and molecular-mechanics-based free energy calculations to account for the interactions between the ligand in the transition state and the protein environment. The method was tested on four pharmaceutically interesting irreversible covalent binding systems involving 28 ligands; the mean unsigned error (MUE) of the relative reaction rate for all pairs of ligands between the predictions and experimental results for these tested systems is 0.79 log unit. This is to our knowledge the first time where the reaction kinetics of protein irreversible covalent inhibition have been directly calculated with physics-based free energy calculation methods and transition state theory. We anticipate the outstanding accuracy demonstrated here across a broad range of target classes will have a strong impact on the design of selective covalent inhibitors.
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Affiliation(s)
- Haoyu S Yu
- Schrodinger, Inc. , 120 West 45th Street , New York , New York 10036 , United States
| | - Cen Gao
- Eli Lilly and Company , Lilly Corporate Center , Indianapolis , Indiana 46285 , United States
| | - Dmitry Lupyan
- Schrodinger, Inc. , 120 West 45th Street , New York , New York 10036 , United States
| | - Yujie Wu
- Schrodinger, Inc. , 120 West 45th Street , New York , New York 10036 , United States
| | - Takayuki Kimura
- Schrodinger, Inc. , 101 SW Main Street, Suite 1300 , Portland , Oregon 97204 , United States
| | - Chuanjie Wu
- Schrodinger, Inc. , 120 West 45th Street , New York , New York 10036 , United States
| | - Leif Jacobson
- Schrodinger, Inc. , 120 West 45th Street , New York , New York 10036 , United States
| | - Edward Harder
- Schrodinger, Inc. , 120 West 45th Street , New York , New York 10036 , United States
| | - Robert Abel
- Schrodinger, Inc. , 120 West 45th Street , New York , New York 10036 , United States
| | - Lingle Wang
- Schrodinger, Inc. , 120 West 45th Street , New York , New York 10036 , United States
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Pharmacological actions of miltirone in the modulation of platelet function. Acta Pharmacol Sin 2019; 40:199-207. [PMID: 29795134 DOI: 10.1038/s41401-018-0010-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/30/2017] [Accepted: 01/25/2018] [Indexed: 01/27/2023] Open
Abstract
Salvia miltiorrhiza Bunge contains various active constituents, some of which have been developed as commercially available medicine. Moreover, some other ingredients in Salvia miltiorrhiza play roles in anti-platelet activity. The aim of the present study was to investigate the effects and the underlying mechanism of miltirone, a lipophilic compound of Salvia miltiorrhiza Bunge. The ability of miltirone to modulate platelet function was investigated by a variety of in vitro and in vivo experiments. Platelet aggregation and dense granule secretion induced by various agonists were measured with platelet aggregometer. Clot retraction and spreading were imaged by digital camera and fluorescence microscope. Ferric chloride-induced carotid injury model and pulmonary thromboembolism model were used to check miltirone antithrombotic effect in vivo. To elucidate the mechanisms of anti-platelet activity of miltirone, flow cytometry and western blotting were performed. Miltirone (2, 4, 8 µM) was shown to suppress platelet aggregation, dense granule, and α granule secretion in a dose-dependent manner. Meanwhile, miltirone inhibited the clot retraction and spreading of washed platelets. It reduced the phosphorylation of PLCγ2, PKC, Akt, GSK3β and ERK1/2 in the downstream signal pathway of collagen receptor. It also reduced the phosphorylation of Src and FAK in the integrin αIIbβ3-mediated "outside-in" signaling, while it did not suppress the phosphorylation of β3. In addition, miltirone prolonged the occlusion time and reduced collagen/epinephrine-induced pulmonary thrombi. Miltirone suppresses platelet "inside-out" and "outside-in" signaling by affecting PLCγ2/PKC/ERK1/2, PI3K/Akt, and Src/FAK signaling. Therefore, miltirone might represent a potential anti-platelet candidate for the prevention of thrombotic disorders.
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Fuentes E, Fuentes M, Caballero J, Palomo I, Hinz S, El-Tayeb A, Müller CE. Adenosine A 2A receptor agonists with potent antiplatelet activity. Platelets 2017; 29:292-300. [PMID: 28504052 DOI: 10.1080/09537104.2017.1306043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Selected adenosine A2A receptor agonists (PSB-15826, PSB-12404, and PSB-16301) have been evaluated as new antiplatelet agents. In addition, radioligand-binding studies and receptor-docking experiments were performed in order to explain their differential biological effects on a molecular level. Among the tested adenosine derivatives, PSB-15826 was the most potent compound to inhibit platelet aggregation (EC50 0.32 ± 0.05 µmol/L) and platelet P-selectin cell-surface localization (EC50 0.062 ± 0.2 µmol/L), and to increase intraplatelets cAMP levels (EC50 0.24 ± 0.01 µmol/L). The compound was more active than CGS21680 (EC50 0.97±0.07 µmol/L) and equipotent to NECA (EC50 0.31 ± 0.05 µmol/L) in platelet aggregation induced by ADP. In contrast to the results from cAMP assays, Ki values determined in radioligand-binding studies were not predictive of the A2A agonists' antiplatelet activity. Docking studies revealed the key molecular determinants of this new family of adenosine A2A receptor agonists: differences in activities are related to π-stacking interactions between the ligands and the residue His264 in the extracellular loop of the adenosine A2A receptor which may result in increased residence times. In conclusion, these results provide an improved understanding of the requirements of antiplatelet adenosine A2A receptor agonists.
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Affiliation(s)
- Eduardo Fuentes
- a Platelet Research Laboratory, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences , Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), Universidad de Talca , Talca , Chile.,b Núcleo Científico Multidisciplinario , Universidad de Talca , Talca , Chile
| | - Manuel Fuentes
- a Platelet Research Laboratory, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences , Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), Universidad de Talca , Talca , Chile
| | - Julio Caballero
- c Centro de Bioinformatica y Simulacion Molecular (CBSM) , Universidad de Talca , Talca , Chile
| | - Iván Palomo
- a Platelet Research Laboratory, Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences , Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), Universidad de Talca , Talca , Chile
| | - Sonja Hinz
- d PharmaCenter Bonn , Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , Bonn , Germany
| | - Ali El-Tayeb
- d PharmaCenter Bonn , Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , Bonn , Germany
| | - Christa E Müller
- d PharmaCenter Bonn , Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn , Bonn , Germany
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Angiolillo DJ, Roffi M, Fernandez-Ortiz A. Tackling the thrombotic burden in patients with acute coronary syndrome and diabetes mellitus. Expert Rev Cardiovasc Ther 2014; 9:697-710. [DOI: 10.1586/erc.11.76] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Bonello L, Lemesle G, De Labriolle A, Barragan P, Camoin-Jau L, Paganelli F. Personalized antiplatelet therapy for coronary artery disease patients: is this the future? Expert Rev Cardiovasc Ther 2014; 7:1525-32. [DOI: 10.1586/erc.09.146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Palekar RU, Myerson JW, Schlesinger PH, Sadler JE, Pan H, Wickline SA. Thrombin-targeted liposomes establish a sustained localized anticlotting barrier against acute thrombosis. Mol Pharm 2013; 10:4168-75. [PMID: 24063304 DOI: 10.1021/mp400210q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The goal of the present work was to design and test an acute-use nanoparticle-based antithrombotic agent that exhibits sustained local inhibition of thrombin without requiring a systemic anticoagulant effect to function against acute arterial thrombosis. To demonstrate proof of concept, we functionalized the surface of liposomes with multiple copies of the direct thrombin inhibitor, d-phenylalanyl-l-prolyl-l-arginyl-chloromethyl ketone (PPACK), which exhibits high affinity for thrombin as a free agent but manifests too rapid clearance in vivo to be effective alone. The PPACK-liposomes were formulated as single unilamellar vesicles, with a diameter of 170.78 ± 10.59 nm and a near neutral charge. In vitro models confirmed the inhibitory activity of PPACK-liposomes, demonstrating a KI' of 172.6 nM. In experimental clots in vitro, treatment of formed clots completely abrogated any further clotting upon exposure to human plasma. The liposomes were evaluated in vivo in a model of photochemical-induced carotid artery injury, resulting in significantly prolonged arterial occlusion time over that of controls (69.06 ± 5.65 min for saline treatment, N = 6, 71.33 ± 9.46 min for free PPACK treated; N = 4, 85.75 ± 18.24 min for precursor liposomes; N = 4, 139.75 ± 20.46 min for PPACK-liposomes; P = 0.0049, N = 6). Systemic anticoagulant profiles revealed a rapid return to control levels within 50 min, while still maintaining antithrombin activity at the injury site. The establishment of a potent and long-acting anticoagulant surface over a newly forming clot with the use of thrombin targeted nanoparticles that do not require systemic anticoagulation to be effective offers an alternative site-targeted approach to the management of acute thrombosis.
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Affiliation(s)
- Rohun U Palekar
- Department of Biomedical Engineering, ‡Department of Cell Biology and Physiology, §Department of Medicine, and ∥Department of Physics, Washington University in St. Louis, Consortium for Translational Research in Advanced Imaging and Nanomedicine , 4320 Forest Park Avenue, St. Louis, Missouri 63108, United States
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Apostolakis S, Lip GYH, Shantsila E. Pharmacokinetic considerations for antithrombotic therapies in stroke. Expert Opin Drug Metab Toxicol 2013; 9:1335-47. [DOI: 10.1517/17425255.2013.808331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
Non-ST elevation (NSTE) myocardial infarction and unstable angina are the most common clinical presentations of acute coronary syndrome (ACS). Platelet activation is central to the pathogenesis of NSTE-ACS and consensus guidelines that advocate early revascularization supported by intensive antiplatelet therapy. This review examines the drugs used concurrently with aspirin as dual antiplatelet therapy in the NSTE-ACS setting. Clopidogrel represented an important therapeutic advance. However, variations in platelet response and a relatively slow onset of action compromise outcomes with clopidogrel. Evidence reviewed in this article shows that in NSTE-ACS patients, ticagrelor and prasugrel are more effective than clopidogrel and are relatively well tolerated, with an acceptable and manageable bleeding risk. The literature suggests several differences between ticagrelor and prasugrel that should allow clinicians to better tailor treatment to the patient. Head-to-head comparisons are now needed to compare directly the risks and benefits of ticagrelor and prasugrel in NSTE-ACS. Further studies also need to address other outstanding issues such as the benefits and risks of prasugrel pre-treatment and to stratify efficacy and tolerability according to diabetes mellitus (DM) and other co-morbidities. In the meantime, the issues discussed in this review should enhance clinicians' ability to optimize and individualize NSTE-ACS treatment, thereby further reducing the morbidity and mortality associated with this common cardiovascular condition.
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Affiliation(s)
- G Cayla
- Institut de Cardiologie, Bureau 236, Pitié-Salpêtrière University Hospital, 47-83, Bld de l'Hôpital, 75013 Paris, France
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Wouter Jukema J, Collet JP, De Luca L. Antiplatelet therapy in patients with ST-elevation myocardial infarction undergoing myocardial revascularisation: beyond clopidogrel. Curr Med Res Opin 2012; 28:203-11. [PMID: 22181345 DOI: 10.1185/03007995.2011.651526] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Despite revascularisation, outcomes among patients presenting with ST-elevation myocardial infarction (STEMI) remain suboptimal. SCOPE This review compares clopidogrel, ticagrelor and prasugrel as antiplatelet strategies with a particular focus on STEMI. Medline and Google Scholar were searched for relevant terms and citations from these articles were also assessed. FINDINGS While clopidogrel represented an important therapeutic advance, variations in platelet response and a relatively slow onset of action compromise outcomes in some patients. Ticagrelor and prasugrel are more effective than clopidogrel, although essentially only one large study supports each drug. Nevertheless, a detailed examination of the evidence reveals several issues that may influence the decision to prescribe ticagrelor instead of prasugrel and vice versa. Arguably, prasugrel could be the preferred strategy in STEMI, reflecting the drugs' efficacy in clopidogrel-naïve patients, the most common group in clinical practice. Conversely, ticagrelor may be a better option than clopidogrel in clopidogrel-pretreated patients showing a mortality benefit irrespective of clopidogrel pre-treatment. The clinical benefits offered by prasugrel and ticagrelor need to be offset against the increased cost and we suggest an algorithm for using these new compounds in the primary percutaneous coronary intervention (PCI) setting. The risk of bleeding associated with prasugrel is similar to that of clopidogrel and ticagrelor following exclusion of at-risk patients. Nevertheless, prasugrel may be especially appropriate for STEMI patients undergoing PCI who are considered to be at high risk of ischaemia. Conversely, ticagrelor's short half-life, while potentially a limitation during maintenance therapy, may reduce bleeding risk if the patient undergoes CABG during the same hospital admission, although confirmatory studies are needed. CONCLUSION Future studies also need to address several other outstanding issues, such as the subsequent approach if patients do not undergo PCI, and to overcome limitations in and differences between the primary studies. In particular, head-to-head comparisons need to compare directly the risks and benefits of ticagrelor and prasugrel in STEMI patients. These caveats notwithstanding, ticagrelor and prasugrel markedly improve the prognosis for patients with STEMI.
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Affiliation(s)
- J Wouter Jukema
- Department of Cardiology, Leiden University Medical Centre, Leiden, The Netherlands.
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Rodrigues APC, Costa LMM, Santos BLR, Maia RC, Miranda ALP, Barreiro EJ, Fraga CAM. Novel furfurylidene N-acylhydrazones derived from natural safrole: discovery of LASSBio-1215, a new potent antiplatelet prototype. J Enzyme Inhib Med Chem 2011; 27:101-9. [PMID: 21612374 DOI: 10.3109/14756366.2011.578575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe herein the discovery of (E)-N-methyl-N'-((5-nitrofuran-2-yl)methylene)benzo[d]( 1 , 3 ) dioxole-5-carbohydrazide (9e), named LASSBio-1215, as a novel antiplatelet agent belonging to the N-methyl-N-acylhydrazone class, which exert their antiaggregating actions on human and rabbit platelets induced by different agonists, through cyclooxygenase-1 (COX-1) or thromboxane synthase inhibition. This compound was elected after screening of a series of functionalized furyl N-acylhydrazone derivatives, synthesized from natural safrole 10. In vitro assays showed that compound 9e presents platelet-aggregating activity in rabbit platelet-rich plasma (PRP) induced by arachidonic acid (IC(50) = 0.7 µM) and collagen (IC(50) = 4.5 µM). Moreover, LASSBio-1215 also inhibited almost completely the second wave of adenosine diphosphate-induced platelet aggregation in human PRP, and this effect was correlated with their ability to block the production of pro-aggregating autacoid thromboxane A(2).
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Affiliation(s)
- Ana Paula C Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Gehrig SM, Lynch GS. Emerging drugs for treating skeletal muscle injury and promoting muscle repair. Expert Opin Emerg Drugs 2011; 16:163-82. [DOI: 10.1517/14728214.2010.524743] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Breivik H, Bang U, Jalonen J, Vigfússon G, Alahuhta S, Lagerkranser M. Nordic guidelines for neuraxial blocks in disturbed haemostasis from the Scandinavian Society of Anaesthesiology and Intensive Care Medicine. Acta Anaesthesiol Scand 2010; 54:16-41. [PMID: 19839941 DOI: 10.1111/j.1399-6576.2009.02089.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Central neuraxial blocks (CNBs) for surgery and analgesia are an important part of anaesthesia practice in the Nordic countries. More active thromboprophylaxis with potent antihaemostatic drugs has increased the risk of bleeding into the spinal canal. National guidelines for minimizing this risk in patients who benefit from such blocks vary in their recommendations for safe practice. METHODS The Scandinavian Society of Anaesthesiology and Intensive Care Medicine (SSAI) appointed a task force of experts to establish a Nordic consensus on recommendations for best clinical practice in providing effective and safe CNBs in patients with an increased risk of bleeding. We performed a literature search and expert evaluation of evidence for (1) the possible benefits of CNBs on the outcome of anaesthesia and surgery, for (2) risks of spinal bleeding from hereditary and acquired bleeding disorders and antihaemostatic drugs used in surgical patients for thromboprophylaxis, for (3) risk evaluation in published case reports, and for (4) recommendations in published national guidelines. Proposals from the taskforce were available for feedback on the SSAI web-page during the summer of 2008. RESULTS Neuraxial blocks can improve comfort and reduce morbidity (strong evidence) and mortality (moderate evidence) after surgical procedures. Haemostatic disorders, antihaemostatic drugs, anatomical abnormalities of the spine and spinal blood vessels, elderly patients, and renal and hepatic impairment are risk factors for spinal bleeding (strong evidence). Published national guidelines are mainly based on experts' opinions (weak evidence). The task force reached a consensus on Nordic guidelines, mainly based on our experts' opinions, but we acknowledge different practices in heparinization during vascular surgery and peri-operative administration of non-steroidal anti-inflammatory drugs during neuraxial blocks. CONCLUSIONS Experts from the five Nordic countries offer consensus recommendations for safe clinical practice of neuraxial blocks and how to minimize the risks of serious complications from spinal bleeding. A brief version of the recommendations is available on http://www.ssai.info.
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Affiliation(s)
- H Breivik
- Section for Anaesthesiology and Intensive Care Medicine, University of Oslo, Rikshospitalet, Oslo, Norway.
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Glycoprotein Ibalpha inhibitor complex structure reveals a combined steric and allosteric mechanism of von Willebrand factor antagonism. Blood 2009; 114:4883-5. [PMID: 19726719 DOI: 10.1182/blood-2009-05-224170] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Platelet glycoprotein Ibalpha (GpIbalpha) interactions with von Willebrand factor (VWF) are a critical early event in platelet adhesion, which contributes to hemostasis and thrombosis. Here we report the structure of a complex between GpIbalpha and a potent peptide inhibitor. The cyclic peptide (CTERMALHNLC) was isolated from a cysteine-constrained phage display library, and in the complex this forms one and a half turns of an amphipathic alpha-helix, the curvature of which facilitates contacts with the curved concave face of the GpIbalpha leucine-rich repeats. The peptide has only limited overlap with the VWF binding site. It effectively inhibits by stabilizing an alternative alpha-helical conformation of a regulatory loop that forms an extended beta-hairpin upon VWF binding. The structure defines a previously unrecognized binding site within GpIbalpha and represents a clear strategy for developing antiplatelet agents targeting the GpIbalpha-VWF interaction allosterically.
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