1
|
Koenekoop L, Åqvist J. Computational Analysis of Heat Capacity Effects in Protein-Ligand Binding. J Chem Theory Comput 2024; 20:5708-5716. [PMID: 38870420 PMCID: PMC11238534 DOI: 10.1021/acs.jctc.4c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Heat capacity effects in protein-ligand binding as measured by calorimetric experiments have recently attracted considerable attention, particularly in the field of enzyme inhibitor design. A significant negative heat capacity change upon ligand binding implies a marked temperature dependence of the binding enthalpy, which is of high relevance for attempts to optimize protein-ligand interactions. In this work, we address the question of how well such heat capacity changes can be predicted by computer simulations. We examine a series of human thrombin inhibitors that all bind with ΔCp values of about -0.4 kcal/mol/K and calculate heat capacity changes from plain molecular dynamics simulations of the bound and free states of the enzyme and ligand. The results show that accurate ΔCp estimates within a few tenths of a kcal/mol/K of the experimental values can be obtained with this approach. This allows us to address the structural and energetic origin of the negative heat capacity changes for the thrombin inhibitors, and it is found that conformational equilibria of the free ligands in solution make a major contribution to the observed effect.
Collapse
Affiliation(s)
- Lucien Koenekoop
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| |
Collapse
|
2
|
Hanessian S. My 50-Plus Years of Academic Research Collaborations with Industry. A Retrospective. J Org Chem 2024; 89:9147-9186. [PMID: 38865159 DOI: 10.1021/acs.joc.4c00652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
A retrospective is presented highlighting the synthesis of selected "first-in-kind" natural products, their synthetic analogues, structure elucidations, and rationally designed bioactive synthetic compounds that were accomplished because of collaborations with past and present pharmaceutical and agrochemical companies. Medicinal chemistry projects involving structure-based design exploiting cocrystal structures of small molecules with biologically relevant enzymes, receptors, and bacterial ribosomes with synthetic small molecules leading to marketed products, clinical candidates, and novel drug prototypes were realized in collaboration. Personal reflections, historical insights, behind the scenes stories from various long-term projects are shared in this retrospective article.
Collapse
Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ. Centre-ville, Montréal, Québec, Canada H3C 3J7
- Department of Pharmaceutical Sciences, University of California, Irvine, California 91266, United States
| |
Collapse
|
3
|
Krause KD, Rees K, Darwish GH, Bernal-Escalante J, Algar WR. Bait and Cleave: Exosite-Binding Peptides on Quantum Dots Selectively Accelerate Protease Activity for Sensing with Enhanced Sensitivity. ACS NANO 2024; 18:17018-17030. [PMID: 38845136 DOI: 10.1021/acsnano.4c03265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The advantageous optical properties of quantum dots (QDs) motivate their use in a wide variety of applications related to imaging and bioanalysis, including the detection of proteases and their activity. Recent studies have shown that surface chemistry on QDs is able to modulate protease activity, but only nonspecifically. Here, we present a strategy to selectively accelerate the activity of a particular target protease by as much as two orders of magnitude. Exosite-binding "bait" peptides were derived from proteins that span a range of biological roles─substrate, receptor, and inhibitor─and were used to increase the affinity of the QD-peptide conjugates for either thrombin or factor Xa, resulting in increased rates of proteolysis for coconjugated substrates. Unlike effects from QD surface chemistry, the acceleration was specific to the target protease with negligible acceleration of other proteases. Benefits of this "bait and cleave" sensing approach included detection limits that improved by more than an order of magnitude, reenabled detection of target protease against an overwhelming background of nontarget proteolysis, and mitigation of the action of inhibitors. The cumulative results point to a generalizable strategy, where the mechanism of acceleration, considerations for the design of bait peptides and conjugates, and routes to expanding the scope of this approach are discussed. Overall, this research represents a major step forward in the rational design of nanoparticle-based enzyme sensors that enhance sensitivity and selectivity.
Collapse
Affiliation(s)
- Katherine D Krause
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| | - Kelly Rees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| | - Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| | - Jasmine Bernal-Escalante
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| |
Collapse
|
4
|
Yu H, Kumar S, Frederiksen JW, Kolyadko VN, Pitoc G, Layzer J, Yan A, Rempel R, Francis S, Krishnaswamy S, Sullenger BA. Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors. Nat Commun 2024; 15:3977. [PMID: 38730234 PMCID: PMC11087511 DOI: 10.1038/s41467-024-48211-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Potent and selective inhibition of the structurally homologous proteases of coagulation poses challenges for drug development. Hematophagous organisms frequently accomplish this by fashioning peptide inhibitors combining exosite and active site binding motifs. Inspired by this biological strategy, we create several EXACT inhibitors targeting thrombin and factor Xa de novo by linking EXosite-binding aptamers with small molecule ACTive site inhibitors. The aptamer component within the EXACT inhibitor (1) synergizes with and enhances the potency of small-molecule active site inhibitors by many hundred-fold (2) can redirect an active site inhibitor's selectivity towards a different protease, and (3) enable efficient reversal of inhibition by an antidote that disrupts bivalent binding. One EXACT inhibitor, HD22-7A-DAB, demonstrates extraordinary anticoagulation activity, exhibiting great potential as a potent, rapid onset anticoagulant to support cardiovascular surgeries. Using this generalizable molecular engineering strategy, selective, potent, and rapidly reversible EXACT inhibitors can be created against many enzymes through simple oligonucleotide conjugation for numerous research and therapeutic applications.
Collapse
Affiliation(s)
- Haixiang Yu
- Department of Surgery, Duke University, Durham, NC, USA
| | - Shekhar Kumar
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Vladimir N Kolyadko
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - George Pitoc
- Department of Surgery, Duke University, Durham, NC, USA
| | | | - Amy Yan
- Department of Surgery, Duke University, Durham, NC, USA
| | - Rachel Rempel
- Department of Surgery, Duke University, Durham, NC, USA
| | - Samuel Francis
- Department of Emergency Medicine, Duke University Hospital, Durham, NC, USA
| | - Sriram Krishnaswamy
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Bruce A Sullenger
- Department of Surgery, Duke University, Durham, NC, USA.
- Departments of Pharmacology & Cancer Biology and Biomedical Engineering, Duke University, Durham, NC, USA.
| |
Collapse
|
5
|
Kirsch ZJ, Vachet RW. Proteins Can Withstand More Extensive Labeling while Providing Accurate Structural Information in Covalent Labeling-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1030-1039. [PMID: 38581471 PMCID: PMC11167616 DOI: 10.1021/jasms.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
Diethylpyrocarbonate (DEPC) covalent labeling-mass spectrometry (CL-MS) has been extensively utilized to study protein structure and interactions owing to its ease of use, commercial availability, and broad labeling of nucleophilic residues. During typical CL-MS experiments with DEPC, the extent of labeling is kept low to avoid any structural perturbations resulting from covalent modification of the protein. In this study, we demonstrate that proteins can be labeled more extensively via DEPC and still provide accurate structural information. To show this, we modeled labeling kinetics over a range of DEPC concentrations and used molecular dynamics simulations to investigate the molecular-level effects of extensive labeling on the protein structure. Our results indicate that higher extents of DEPC labeling do not significantly perturb the protein structure and can lead to improved precision, detectability of labeled peptides, and protein structural resolution. Furthermore, higher extents of labeling enable better identification of protein-ligand binding sites where lower extents of modification provide ambiguous results.
Collapse
Affiliation(s)
- Zachary J. Kirsch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| |
Collapse
|
6
|
Wu D, Prem A, Xiao J, Salsbury FR. Thrombin - A Molecular Dynamics Perspective. Mini Rev Med Chem 2024; 24:1112-1124. [PMID: 37605420 DOI: 10.2174/1389557523666230821102655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/08/2023] [Accepted: 07/15/2023] [Indexed: 08/23/2023]
Abstract
Thrombin is a crucial enzyme involved in blood coagulation, essential for maintaining circulatory system integrity and preventing excessive bleeding. However, thrombin is also implicated in pathological conditions such as thrombosis and cancer. Despite the application of various experimental techniques, including X-ray crystallography, NMR spectroscopy, and HDXMS, none of these methods can precisely detect thrombin's dynamics and conformational ensembles at high spatial and temporal resolution. Fortunately, molecular dynamics (MD) simulation, a computational technique that allows the investigation of molecular functions and dynamics in atomic detail, can be used to explore thrombin behavior. This review summarizes recent MD simulation studies on thrombin and its interactions with other biomolecules. Specifically, the 17 studies discussed here provide insights into thrombin's switch between 'slow' and 'fast' forms, active and inactive forms, the role of Na+ binding, the effects of light chain mutation, and thrombin's interactions with other biomolecules. The findings of these studies have significant implications for developing new therapies for thrombosis and cancer. By understanding thrombin's complex behavior, researchers can design more effective drugs and treatments that target thrombin.
Collapse
Affiliation(s)
- Dizhou Wu
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Athul Prem
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
- Freenome, South San Francisco, CA, 94080, USA
| | - Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| |
Collapse
|
7
|
Krause KD, Rees K, Algar WR. Assessing the Steric Impact of Surface Ligands on the Proteolytic Turnover of Quantum Dot-Peptide Conjugates. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 38047551 DOI: 10.1021/acsami.3c12665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Proteases are important biomarkers and targets for the diagnosis and treatment of disease. The advantageous properties of semiconductor quantum dots (QDs) have made these nanoparticles useful as probes for protease activity; however, the effects of QD surface chemistry on protease activity are not yet fully understood. Here, we present a systematic study of the impact of sterics on the proteolysis of QD-peptide conjugates. The study utilized eight proteases (chymotrypsin, trypsin, endoproteinase Lys C, papain, endoproteinase Arg C, thrombin, factor Xa, and plasmin) and 41 distinct surface chemistries. The latter included three molecular weights of each of three macromolecular ligands derived from dextran and polyethylene glycol, as well as anionic and zwitterionic small-molecule ligands, and an array of mixed coatings of macromolecular and small-molecule ligands. These surface chemistries spanned a diversity of thicknesses, densities, and packing organization, as characterized by gel electrophoresis, capillary electrophoresis, dynamic light scattering, and infrared spectroscopy. The macromolecular ligands decreased the adsorption of proteases on the QDs and decelerated proteolysis of the QD-peptide conjugates via steric hindrance. The properties of the QD surface chemistry, rather than the protease properties, were the main factor in determining the magnitude of deceleration. The broad scope of this study provides insights into the many ways in which QD surface chemistry affects protease activity, and will inform the development of optimized nanoparticle-peptide conjugates for sensing of protease activity and resistance to unwanted proteolysis.
Collapse
Affiliation(s)
- Katherine D Krause
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelly Rees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| |
Collapse
|
8
|
Strijbis VJF, Vatandoost J, Bos MHA. Crippling down factor IX for therapeutic gain. J Thromb Haemost 2023; 21:3287-3291. [PMID: 37678545 DOI: 10.1016/j.jtha.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Affiliation(s)
- Viola J F Strijbis
- Department of Internal Medicine, Division of Thrombosis and Hemostasis, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands. https://twitter.com/ViolaStrijbis
| | - Jafar Vatandoost
- Department of Biology, Hakim Sabzevari University, Sabzevar, Iran
| | - Mettine H A Bos
- Department of Internal Medicine, Division of Thrombosis and Hemostasis, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands.
| |
Collapse
|
9
|
Yasmin R, Chanchal S, Ashraf MZ, Doley R. Daboxin P, a phospholipase A 2 of Indian Daboia russelii venom, modulates thrombin-mediated platelet aggregation. J Biochem Mol Toxicol 2023; 37:e23476. [PMID: 37466159 DOI: 10.1002/jbt.23476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/12/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Daboxin P, reported earlier from the venom of Daboia russellii, disturbs the blood coagulation cascade by targeting factor X and factor Xa. The present study exhibits that Daboxin P also inhibits platelet aggregation induced by various agonists. The thrombin-induced platelet aggregation was inhibited maximum whereas inhibition of collagen-induced platelet aggregation was found to be 50% and no inhibition of adenosine diphosphate (ADP) and arachidonic acid-induced aggregation was observed. Daboxin P dose-dependently inhibited the thrombin-induced platelet aggregation with Anti-Aggregation 50 (AD50 ) dose of 55.166 nM and also reduced the thrombin-mediated calcium influx. In-silico interaction studies suggested that Daboxin P binds to thrombin and blocks its interaction with its receptor on the platelet surface. Quenching of thrombin's emission spectrum by Daboxin P and electrophoretic profiles of pull-down assay further reveals the binding between Daboxin P and thrombin. Thus, the present study demonstrates that Daboxin P inhibits thrombin-induced platelet aggregation by binding to thrombin.
Collapse
Affiliation(s)
- Rafika Yasmin
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Shankar Chanchal
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, New Delhi, India
| | - Mohammad Zahid Ashraf
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, New Delhi, India
| | - Robin Doley
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| |
Collapse
|
10
|
Ferguson TEG, Reihill JA, Martin SL, Walker B. Novel inhibitors and activity-based probes targeting serine proteases. Front Chem 2022; 10:1006618. [PMID: 36247662 PMCID: PMC9555310 DOI: 10.3389/fchem.2022.1006618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Serine proteases play varied and manifold roles in important biological, physiological, and pathological processes. These include viral, bacterial, and parasitic infection, allergic sensitization, tumor invasion, and metastasis. The use of activity-based profiling has been foundational in pinpointing the precise roles of serine proteases across this myriad of processes. A broad range of serine protease-targeted activity-based probe (ABP) chemotypes have been developed and we have recently introduced biotinylated and "clickable" peptides containing P1 N-alkyl glycine arginine N-hydroxy succinimidyl (NHS) carbamates as ABPs for detection/profiling of trypsin-like serine proteases. This present study provides synthetic details for the preparation of additional examples of this ABP chemotype, which function as potent irreversible inhibitors of their respective target serine protease. We describe their use for the activity-based profiling of a broad range of serine proteases including trypsin, the trypsin-like protease plasmin, chymotrypsin, cathepsin G, and neutrophil elastase (NE), including the profiling of the latter protease in clinical samples obtained from patients with cystic fibrosis.
Collapse
Affiliation(s)
| | | | | | - Brian Walker
- Biomolecular Sciences Research Group, School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
| |
Collapse
|
11
|
Shestopal SA, Parunov LA, Olivares P, Chun H, Ovanesov MV, Pettersson JR, Sarafanov AG. Isolated Variable Domains of an Antibody Can Assemble on Blood Coagulation Factor VIII into a Functional Fv-like Complex. Int J Mol Sci 2022; 23:ijms23158134. [PMID: 35897712 PMCID: PMC9330781 DOI: 10.3390/ijms23158134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022] Open
Abstract
Single-chain variable fragments (scFv) are antigen-recognizing variable fragments of antibodies (FV) where both subunits (VL and VH) are connected via an artificial linker. One particular scFv, iKM33, directed against blood coagulation factor VIII (FVIII) was shown to inhibit major FVIII functions and is useful in FVIII research. We aimed to investigate the properties of iKM33 enabled with protease-dependent disintegration. Three variants of iKM33 bearing thrombin cleavage sites within the linker were expressed using a baculovirus system and purified by two-step chromatography. All proteins retained strong binding to FVIII by surface plasmon resonance, and upon thrombin cleavage, dissociated into VL and VH as shown by size-exclusion chromatography. However, in FVIII activity and low-density lipoprotein receptor-related protein 1 binding assays, the thrombin-cleaved iKM33 variants were still inhibitory. In a pull-down assay using an FVIII-affinity sorbent, the isolated VH, a mixture of VL and VH, and intact iKM33 were carried over via FVIII analyzed by electrophoresis. We concluded that the isolated VL and VH assembled into scFv-like heterodimer on FVIII, and the isolated VH alone also bound FVIII. We discuss the potential use of both protease-cleavable scFvs and isolated Fv subunits retaining high affinity to the antigens in various practical applications such as therapeutics, diagnostics, and research.
Collapse
|
12
|
Modrzycka S, Kołt S, Polderdijk SGI, Adams TE, Potoczek S, Huntington JA, Kasperkiewicz P, Drąg M. Parallel imaging of coagulation pathway proteases activated protein C, thrombin, and factor Xa in human plasma. Chem Sci 2022; 13:6813-6829. [PMID: 35774156 PMCID: PMC9200056 DOI: 10.1039/d2sc01108e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022] Open
Abstract
Activated protein C (APC), thrombin, and factor (f) Xa are vitamin K-dependent serine proteases that are key factors in blood coagulation. Moreover, they play important roles in inflammation, apoptosis, fibrosis, angiogenesis, and viral infections. Abnormal activity of these coagulation factors has been related to multiple conditions, such as bleeding and thrombosis, Alzheimer's disease, sepsis, multiple sclerosis, and COVID-19. The individual activities of APC, thrombin, and fXa in coagulation and in various diseases are difficult to establish since these proteases are related and have similar substrate preferences. Therefore, the development of selective chemical tools that enable imaging and discrimination between coagulation factors in biological samples may provide better insight into their roles in various conditions and potentially aid in the establishment of novel diagnostic tests. In our study, we used a large collection of unnatural amino acids, and this enabled us to extensively explore the binding pockets of the enzymes' active sites. Based on the specificity profiles obtained, we designed highly selective substrates, inhibitors, and fluorescent activity-based probes (ABPs) that were used for fast, direct, and simultaneous detection of APC, thrombin, and fXa in human plasma. Using a collection of natural and unnatural amino acids, we synthesized a set of fluorescent activity-based probes for the fast, direct, and simultaneous detection of coagulation factors in human plasma.![]()
Collapse
Affiliation(s)
- Sylwia Modrzycka
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Stéphanie G I Polderdijk
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Ty E Adams
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Stanisław Potoczek
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Wrocław Medical University Pasteura 1 50-367 Wrocław Poland
| | - James A Huntington
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| |
Collapse
|
13
|
Vecchio FL, Bisceglia P, Imbimbo BP, Lozupone M, Latino RR, Resta E, Leone M, Solfrizzi V, Greco A, Daniele A, Watling M, Panza F, Seripa D. Are apolipoprotein E fragments a promising new therapeutic target for Alzheimer’s disease? Ther Adv Chronic Dis 2022; 13:20406223221081605. [PMID: 35321401 PMCID: PMC8935560 DOI: 10.1177/20406223221081605] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/28/2022] [Indexed: 11/17/2022] Open
Abstract
Human apolipoprotein E (ApoE) is a 299-amino acid secreted glycoprotein that binds cholesterol and phospholipids. ApoE exists as three common isoforms (ApoE2, ApoE3, and ApoE4) and heterozygous carriers of the ε4 allele of the gene encoding ApoE (APOE) have a fourfold greater risk of developing Alzheimer’s disease (AD). The enzymes thrombin, cathepsin D, α-chymotrypsin-like serine protease, and high-temperature requirement serine protease A1 are responsible for ApoE proteolytic processing resulting in bioactive C-terminal-truncated fragments that vary depending on ApoE isoforms, brain region, aging, and neural injury. The objectives of the present narrative review were to describe ApoE processing, discussing current hypotheses about the potential role of various ApoE fragments in AD pathophysiology, and reviewing the current development status of different anti-ApoE drugs. The exact mechanism by which APOE gene variants increase/decrease AD risk and the role of ApoE fragments in the deposition are not fully understood, but APOE is known to directly affect tau-mediated neurodegeneration. ApoE fragments co-localize with neurofibrillary tangles and amyloid β (Aβ) plaques, and may cause neurodegeneration. Among anti-ApoE approaches, a fascinating strategy may be to therapeutically overexpress ApoE2 in APOE ε4/ε4 carriers through vector administration or liposomal delivery systems. Another approach involves reducing ApoE4 expression by intracerebroventricular antisense oligonucleotides that significantly decreased Aβ pathology in transgenic mice. Differences in the proteolytic processing of distinct ApoE isoforms and the use of ApoE fragments as mimetic peptides in AD treatment are also under investigation. Treatment with peptides that mimic the structural and biological properties of native ApoE may reduce Aβ deposition, tau hyperphosphorylation, and glial activation in mouse models of Aβ pathology. Alternative strategies involve the use of ApoE4 structure correctors, passive immunization to target a certain form of ApoE, conversion of the ApoE4 aminoacid sequence into that of ApoE3 or ApoE2, and inhibition of the ApoE-Aβ interaction.
Collapse
Affiliation(s)
- Filomena Lo Vecchio
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia 71013, Italy
| | - Paola Bisceglia
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Raffaela Rita Latino
- Complex Structure of Neurology, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuela Resta
- Translational Medicine and Management of Health Systems, University of Foggia, Foggia, Italy
| | - Maurizio Leone
- Complex Structure of Neurology, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Vincenzo Solfrizzi
- ‘Cesare Frugoni’ Internal and Geriatric Medicine and Memory Unit, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Antonio Greco
- Department of Neuroscience, Catholic University of the Sacred Heart, Rome, Italy; Neurology Unit, IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Mark Watling
- CNS & Pain Department, TranScrip Ltd, Reading, UK
| | - Francesco Panza
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
- Population Health Unit, Healthy Aging Phenotypes Research Unit, ‘Salus in Apulia Study’, National Institute of Gastroenterology ‘Saverio de Bellis’, Research Hospital, Castellana Grotte, Bari 70013, Italy
| | - Davide Seripa
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Hematology and Stem Cell Transplant Unit, ‘Vito Fazzi’ Hospital, Lecce, Italy
| |
Collapse
|
14
|
Kosinski R, Perez JM, Schöneweiß EC, Ruiz-Blanco YB, Ponzo I, Bravo-Rodriguez K, Erkelenz M, Schlücker S, Uhlenbrock G, Sanchez-Garcia E, Saccà B. The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease. SCIENCE ADVANCES 2022; 8:eabk0425. [PMID: 34985948 PMCID: PMC8730604 DOI: 10.1126/sciadv.abk0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/10/2021] [Indexed: 06/04/2023]
Abstract
DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.
Collapse
Affiliation(s)
- Richard Kosinski
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joel Mieres Perez
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elisa-C. Schöneweiß
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Irene Ponzo
- Dynamic Biosensors GmbH, 82152 Martinsried, Germany
| | | | - Michael Erkelenz
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Elsa Sanchez-Garcia
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| |
Collapse
|
15
|
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.
Collapse
|
16
|
Peacock RB, McGrann T, Zaragoza S, Komives EA. How Thrombomodulin Enables W215A/E217A Thrombin to Cleave Protein C but Not Fibrinogen. Biochemistry 2022; 61:77-84. [PMID: 34978431 DOI: 10.1021/acs.biochem.1c00635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The W215A/E217A mutant thrombin is called "anticoagulant thrombin" because its activity toward its procoagulant substrate, fibrinogen, is reduced more than 500-fold whereas in the presence of thrombomodulin (TM) its activity toward its anticoagulant substrate, protein C, is reduced less than 10-fold. To understand how these mutations so dramatically alter one activity over the other, we compared the backbone dynamics of wild type thrombin to those of the W215A/E217A mutant thrombin by hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS). Our results show that the mutations cause the 170s, 180s, and 220s C-terminal β-barrel loops near the sites of mutation to exchange more, suggesting that the structure of this region is disrupted. Far from the mutation sites, residues at the N-terminus of the heavy chain, which need to be buried in the Ile pocket for correct structuring of the catalytic triad, also exchange much more than in wild type thrombin. TM binding causes reduced H/D exchange in these regions and also alters the dynamics of the β-strand that links the TM binding site to the catalytic Asp 102 in both wild type thrombin and in the W215A/E217A mutant thrombin. In contrast, whereas TM binding reduces the dynamics the 170, 180 and 220 s C-terminal β-barrel loops in WT thrombin, this region remains disordered in the W215A/E217A mutant thrombin. Thus, TM partially restores the catalytic activity of W215A/E217A mutant thrombin by allosterically altering its dynamics in a manner similar to that of wild type thrombin.
Collapse
Affiliation(s)
- Riley B Peacock
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Taylor McGrann
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Sofia Zaragoza
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| |
Collapse
|
17
|
Chen J, Chen M, Zhu TF. Directed evolution and selection of biostable L-DNA aptamers with a mirror-image DNA polymerase. Nat Biotechnol 2022; 40:1601-1609. [PMID: 35668324 PMCID: PMC9646512 DOI: 10.1038/s41587-022-01337-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/28/2022] [Indexed: 12/30/2022]
Abstract
Mirror-image aptamers made from chirally inverted nucleic acids are nuclease-resistant and exceptionally biostable, opening up opportunities for unique applications. However, the directed evolution and selection of mirror-image aptamers directly from large randomized L-DNA libraries has, to our knowledge, not been demonstrated previously. Here, we developed a 'mirror-image selection' scheme for the directed evolution and selection of biostable L-DNA aptamers with a mirror-image DNA polymerase. We performed iterative rounds of enrichment and mirror-image polymerase chain reaction (PCR) amplification of L-DNA sequences that bind native human thrombin, in conjunction with denaturing gradient gel electrophoresis (DGGE) to isolate individual aptamers and L-DNA sequencing-by-synthesis to determine their sequences. Based on the selected L-DNA aptamers, we designed biostable thrombin sensors and inhibitors, which remained functional in physiologically relevant nuclease-rich environments, even in the presence of human serum that rapidly degraded D-DNA aptamers. Mirror-image selection of biostable L-DNA aptamers directly from large randomized L-DNA libraries greatly expands the range of biomolecules that can be targeted, broadening their applications as biostable sensors, therapeutics and basic research tools.
Collapse
Affiliation(s)
- Ji Chen
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Mengyin Chen
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Ting F. Zhu
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China
| |
Collapse
|
18
|
Lu S, Tirloni L, Oliveira MB, Bosio CF, Nardone GA, Zhang Y, Hinnebusch BJ, Ribeiro JM, Andersen JF. Identification of a substrate-like cleavage-resistant thrombin inhibitor from the saliva of the flea Xenopsylla cheopis. J Biol Chem 2021; 297:101322. [PMID: 34688666 PMCID: PMC8573170 DOI: 10.1016/j.jbc.2021.101322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
The salivary glands of the flea Xenopsylla cheopis, a vector of the plague bacterium, Yersinia pestis, express proteins and peptides thought to target the hemostatic and inflammatory systems of its mammalian hosts. Past transcriptomic analyses of salivary gland tissue revealed the presence of two similar peptides (XC-42 and XC-43) having no extensive similarities to any other deposited sequences. Here we show that these peptides specifically inhibit coagulation of plasma and the amidolytic activity of α-thrombin. XC-43, the smaller of the two peptides, is a fast, tight-binding inhibitor of thrombin with a dissociation constant of less than 10 pM. XC-42 exhibits similar selectivity as well as kinetic and binding properties. The crystal structure of XC-43 in complex with thrombin shows that despite its substrate-like binding mode, XC-43 is not detectably cleaved by thrombin and that it interacts with the thrombin surface from the enzyme catalytic site through the fibrinogen-binding exosite I. The low rate of hydrolysis was verified in solution experiments with XC-43, which show the substrate to be largely intact after 2 h of incubation with thrombin at 37 °C. The low rate of XC-43 cleavage by thrombin may be attributable to specific changes in the catalytic triad observable in the crystal structure of the complex or to extensive interactions in the prime sites that may stabilize the binding of cleavage products. Based on the increased arterial occlusion time, tail bleeding time, and blood coagulation parameters in rat models of thrombosis XC-43 could be valuable as an anticoagulant.
Collapse
Affiliation(s)
- Stephen Lu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Lucas Tirloni
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA; Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Markus Berger Oliveira
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Christopher F Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - Glenn A Nardone
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Yixiang Zhang
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - B Joseph Hinnebusch
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, USA
| | - José M Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - John F Andersen
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA.
| |
Collapse
|
19
|
Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
Collapse
|
20
|
Malecka K, Ferapontova EE. Femtomolar Detection of Thrombin in Serum and Cerebrospinal Fluid via Direct Electrocatalysis of Oxygen Reduction by the Covalent G4-Hemin-Aptamer Complex. ACS APPLIED MATERIALS & INTERFACES 2021; 13:37979-37988. [PMID: 33878266 DOI: 10.1021/acsami.1c03784] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Thrombin, a serine protease playing a central role in the coagulation cascade reactions and a potent neurotoxin produced by injured brain endothelial cells, is a recognized cardiac biomarker and a critical biomarker for Alzheimer's disease development. Both in vivo and in vitro, its low physiological concentrations and nonspecific binding of other components of physiological fluids complicate electroanalysis of thrombin. Here, femtomolar levels of thrombin in serum and an artificial cerebrospinal fluid (CSF) were detected by the indicator-free electrochemical methodology exploiting the O2 reduction reaction directly, with no electron transfer mediators, electrocatalyzed by the covalent G4-hemin DNAzyme complex naturally self-assembling upon thrombin binding to the hemin-modified 29-mer DNA aptamer sequence tethered to gold via an alkanethiol linker. Coadsorbed PEG inhibited nonspecific protein binding and allowed the sought signal resolution. The proposed assay exploiting the "oxidase" activity of G4-hemin DNAzyme does not require any coreactants necessary for the traditional peroxidase activity-based assays with this DNAzyme, such as H2O2 and redox mediators, or solution deaeration and allows fast, overall 30 min analysis of thrombin in aerated buffer, CSF, and 1% human serum solutions. This pioneer approach exploiting the oxidase activity G4-hemin DNAzyme is simple, sensitive, and selective and represents a new tool for ultrasensitive electrocatalytic assays based on simple and efficient O2-dependent DNAzyme labels.
Collapse
Affiliation(s)
- Kamila Malecka
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, Aarhus C DK-8000, Denmark
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn 10-748, Poland
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, Aarhus C DK-8000, Denmark
| |
Collapse
|
21
|
Lu Y, Villoutreix BO, Biswas I, Ding Q, Wang X, Rezaie AR. Antithrombin Resistance Rescues Clotting Defect of Homozygous Prothrombin-Y510N Dysprothrombinemia. Thromb Haemost 2021; 122:679-691. [PMID: 34256393 PMCID: PMC8755856 DOI: 10.1055/a-1549-6407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A patient with hematuria in our clinic was diagnosed with urolithiasis. Analysis of the patient's plasma clotting time indicated that both activated partial thromboplastin time (52.6 seconds) and prothrombin time (19.4 seconds) are prolonged and prothrombin activity is reduced to 12.4% of normal, though the patient exhibited no abnormal bleeding phenotype and a prothrombin antigen level of 87.9%. Genetic analysis revealed the patient is homozygous for prothrombin Y510N mutation. We expressed and characterized the prothrombin-Y510N variant in appropriate coagulation assays and found that the specificity constant for activation of the mutant zymogen by factor Xa is impaired approximately fivefold. Thrombin generation assay using patient's plasma and prothrombin-deficient plasma supplemented with either wild-type or prothrombin-Y510N revealed that both peak height and time to peak for the prothrombin mutant are decreased; however, the endogenous thrombin generation potential is increased. Further analysis indicated that the thrombin mutant exhibits resistance to antithrombin and is inhibited by the serpin with approximately 12-fold slower rate constant. Protein C activation by thrombin-Y510N was also decreased by approximately 10-fold; however, thrombomodulin overcame the catalytic defect. The Na+-concentration-dependence of the amidolytic activities revealed that the dissociation constant for the interaction of Na+ with the mutant has been elevated approximately 20-fold. These results suggest that Y510 (Y184a in chymotrypsin numbering) belongs to network of residues involved in binding Na+. A normal protein C activation by thrombin-Y510N suggests that thrombomodulin modulates the conformation of the Na+-binding loop of thrombin. The clotting defect of thrombin-Y510N appears to be compensated by its markedly lower reactivity with antithrombin, explaining patient's normal hemostatic phenotype.
Collapse
Affiliation(s)
- Yeling Lu
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States.,Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bruno O Villoutreix
- INSERM 1141, NeuroDiderot, Université de Paris, Hôpital Robert-Debré, Paris, France
| | - Indranil Biswas
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Alireza R Rezaie
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States.,Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
| |
Collapse
|
22
|
De-Simone SG, Lechuga GC, Napoleão-Pêgo P, Gomes LR, Provance DW, Nirello VD, Sodero ACR, Guedes HLDM. Small Angle X-ray Scattering, Molecular Modeling, and Chemometric Studies from a Thrombin-Like (Lmr-47) Enzyme of Lachesis m. rhombeata Venom. Molecules 2021; 26:3930. [PMID: 34203140 PMCID: PMC8271572 DOI: 10.3390/molecules26133930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Snakebite envenomation is considered a neglected tropical disease, and SVTLEs critical elements are involved in serious coagulopathies that occur on envenoming. Although some enzymes of this group have been structurally investigated, it is essential to characterize other proteins to better understand their unique properties such as the Lachesis muta rhombeata 47 kDa (Lmr-47) venom serine protease. METHODS The structure of Lmr-47 was studied in solution, using SAXS, DLS, CD, and in silico by homology modeling. Molecular docking experiments simulated 21 competitive inhibitors. RESULTS At pH 8.0, Lmr-47 has an Rg of 34.5 ± 0.6 Å, Dmax of 130 Å, and SR of 50 Å, according to DLS data. Kratky plot analysis indicates a rigid shape at pH 8.0. Conversely, the pH variation does not change the center of mass's intrinsic fluorescence, possibly indicating the absence of fluorescent amino acids in the regions affected by pH variation. CD experiments show a substantially random coiled secondary structure not affected by pH. The low-resolution model of Lmr-47 presented a prolate elongated shape at pH 8.0. Using the 3D structure obtained by molecular modeling, docking experiments identified five good and three suitable competitive inhibitors. CONCLUSION Together, our work provided insights into the structure of the Lmr-47 and identified inhibitors that may enhance our understanding of thrombin-like family proteins.
Collapse
Affiliation(s)
- Salvatore Giovanni De-Simone
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
- Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil
| | - Guilherme Curty Lechuga
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
| | - Paloma Napoleão-Pêgo
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
| | - Larissa Rodrigues Gomes
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
| | - David William Provance
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute/FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
| | - Vinícius Dias Nirello
- Faculty of Pharmacy, Federal of Rio de Janeiro University, Rio de Janeiro 21949-900, Brazil; (V.D.N.); (A.C.R.S.)
| | - Ana Carolina Rennó Sodero
- Faculty of Pharmacy, Federal of Rio de Janeiro University, Rio de Janeiro 21949-900, Brazil; (V.D.N.); (A.C.R.S.)
| | - Herbert Leonel de Mattos Guedes
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute/FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
- Laboratory of Immunopharmacology, Federal of Rio de Janeiro University, Duque de Caxias 25245-390, Brazil
| |
Collapse
|
23
|
Peacock RB, Komives EA. Hydrogen/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin. Biochemistry 2021; 60:3441-3448. [PMID: 34159782 DOI: 10.1021/acs.biochem.1c00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A deeper understanding of how hydrogen/deuterium exchange mass spectrometry (HDX-MS) reveals allostery is important because HDX-MS can reveal allostery in systems that are not amenable to nuclear magnetic resonance (NMR) spectroscopy. We were able to study thrombin and its complex with thrombomodulin, an allosteric regulator, by both HDX-MS and NMR. In this Perspective, we compare and contrast the results from both experiments and from molecular dynamics simulations. NMR detects changes in the chemical environment around the protein backbone N-H bond vectors, providing residue-level information about the conformational exchange between distinct states. HDX-MS detects changes in amide proton solvent accessibility and H-bonding. Taking advantage of NMR relaxation dispersion measurements of the time scale of motions, we draw conclusions about the motions reflected in HDX-MS experiments. Both experiments detect allostery, but they reveal different components of the allosteric transition. The insights gained from integrating NMR and HDX-MS into thrombin dynamics enable a clearer interpretation of the evidence for allostery revealed by HDX-MS in larger protein complexes and assemblies that are not amenable to NMR.
Collapse
Affiliation(s)
- Riley B Peacock
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| |
Collapse
|
24
|
Mansory EM, Bhai P, Stuart A, Laudenbach L, Sadikovic B, Lazo-Langner A. A case of congenital prothrombin deficiency with two concurrent mutations in the prothrombin gene. Res Pract Thromb Haemost 2021; 5:e12510. [PMID: 33977210 PMCID: PMC8105154 DOI: 10.1002/rth2.12510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 11/06/2022] Open
Abstract
Congenital prothrombin deficiency is an extremely rare, autosomal recessive bleeding disorder with a prevalence of 1 in 2 million individuals. Here, we report a case of congenital prothrombin deficiency with two concurrent mutations in the prothrombin gene (F2), affecting the heavy B chain. The patient presented with a history of multiple bleeding events in his youth that are mostly trauma associated, with a family history of prothrombin deficiency. Laboratory analysis showed a prolonged activated partial thromboplastin time and a prothrombin activity level of 5%. Genetic analysis of the F2 gene identified two heterozygous variants; one is a previously reported pathogenic deletion (c.1814_1815del; p.His605Argfs*13), and the other is a novel missense variant (c.1147C>T; p.Arg383Trp). In silico analysis predicted that p.Arg383Trp is likely to be disease causing, as it affects one of the anion-binding exosites-I of the B chain. This case highlights the significance of molecular findings in confirming the diagnosis of patients with congenital prothrombin deficiency.
Collapse
Affiliation(s)
- Eman M Mansory
- Division of Hematology Department of Medicine Western University London ON Canada.,Department of Hematology King Abdulaziz University Jeddah Saudi Arabia
| | - Pratibha Bhai
- Molecular Diagnostics Division Department of Pathology and Laboratory Medicine Western University London ON Canada
| | - Alan Stuart
- Molecular Diagnostics Division Department of Pathology and Laboratory Medicine Western University London ON Canada
| | - Lori Laudenbach
- Bleeding Disorders Program London Health Sciences Program London ON Canada
| | - Bekim Sadikovic
- Molecular Diagnostics Division Department of Pathology and Laboratory Medicine Western University London ON Canada
| | - Alejandro Lazo-Langner
- Division of Hematology Department of Medicine Western University London ON Canada.,Department of Epidemiology and Biostatistics Western University London ON Canada
| |
Collapse
|
25
|
Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex. Sci Rep 2021; 11:9354. [PMID: 33931701 PMCID: PMC8087772 DOI: 10.1038/s41598-021-88432-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/07/2021] [Indexed: 01/04/2023] Open
Abstract
Serine proteases catalyze a multi-step covalent catalytic mechanism of peptide bond cleavage. It has long been assumed that serine proteases including thrombin carry-out catalysis without significant conformational rearrangement of their stable two-β-barrel structure. We present nuclear magnetic resonance (NMR) and hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments on the thrombin-thrombomodulin (TM) complex. Thrombin promotes procoagulative fibrinogen cleavage when fibrinogen engages both the anion binding exosite 1 (ABE1) and the active site. It is thought that TM promotes cleavage of protein C by engaging ABE1 in a similar manner as fibrinogen. Thus, the thrombin-TM complex may represent the catalytically active, ABE1-engaged thrombin. Compared to apo- and active site inhibited-thrombin, we show that thrombin-TM has reduced μs-ms dynamics in the substrate binding (S1) pocket consistent with its known acceleration of protein C binding. Thrombin-TM has increased μs-ms dynamics in a β-strand connecting the TM binding site to the catalytic aspartate. Finally, thrombin-TM had doublet peaks indicative of dynamics that are slow on the NMR timescale in residues along the interface between the two β-barrels. Such dynamics may be responsible for facilitating the N-terminal product release and water molecule entry that are required for hydrolysis of the acyl-enzyme intermediate.
Collapse
|
26
|
Kovach IM. Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System. Life (Basel) 2021; 11:396. [PMID: 33925363 PMCID: PMC8146069 DOI: 10.3390/life11050396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Inquiries into the participation of short hydrogen bonds in stabilizing transition states and intermediate states in the thrombin, factor Xa, plasmin and activated protein C-catalyzed reactions revealed that specific binding of effectors at Sn, n = 1-4 and S'n, n = 1-3 and at remote exosites elicit complex patterns of hydrogen bonding and involve water networks. The methods employed that yielded these discoveries include; (1) kinetics, especially partial or full kinetic deuterium solvent isotope effects with short cognate substrates and also with the natural substrates, (2) kinetic and structural probes, particularly low-field high-resolution nuclear magnetic resonance (1H NMR), of mechanism-based inhibitors and substrate-mimic peptide inhibitors. Short hydrogen bonds form at the transition states of the catalytic reactions at the active site of the enzymes as they do with mechanism-based covalent inhibitors of thrombin. The emergence of short hydrogen bonds at the binding interface of effectors and thrombin at remote exosites has recently gained recognition. Herein, I describe our contribution, a confirmation of this discovery, by low-field 1H NMR. The principal conclusion of this review is that proton sharing at distances below the sum of van der Waals radii of the hydrogen and both donor and acceptor atoms contribute to the remarkable catalytic prowess of serine proteases of the blood clotting system and other enzymes that employ acid-base catalysis. Proton bridges also play a role in tight binding in proteins and at exosites, i.e., allosteric sites, of enzymes.
Collapse
Affiliation(s)
- Ildiko M Kovach
- Department of Chemistry, The Catholic University of America, Washington, DC 20064, USA
| |
Collapse
|
27
|
Camire RM. Blood coagulation factor X: molecular biology, inherited disease, and engineered therapeutics. J Thromb Thrombolysis 2021; 52:383-390. [PMID: 33886037 DOI: 10.1007/s11239-021-02456-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/13/2021] [Indexed: 12/19/2022]
Abstract
Blood coagulation factor X/Xa sits at a pivotal point in the coagulation cascade and has a role in each of the three major pathways (intrinsic, extrinsic and the common pathway). Due to this central position, it is an attractive therapeutic target to either enhance or dampen thrombin generation. In this brief review, I will summarize key developments in the molecular understanding of this critical clotting factor and discuss the molecular basis of FX deficiency, highlight difficulties in expressing recombinant factor X, and detail two factor X variants evaluated clinically.
Collapse
Affiliation(s)
- Rodney M Camire
- Division of Hematology and the Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
28
|
Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021; 12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Proteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays. Characterizing proteases in their native environment is still challenging. Here, the authors develop a proteomics workflow for analyzing protease-specific peptides from cell lysates in 96-well format, providing mechanistic insights into blood proteases and enabling the prediction of protease substrates.
Collapse
|
29
|
Lu Y, Biswas I, Villoutreix BO, Rezaie AR. Role of Gly197 in the structure and function of protein C. Biochim Biophys Acta Gen Subj 2021; 1865:129892. [PMID: 33722640 DOI: 10.1016/j.bbagen.2021.129892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
We previously demonstrated that heterozygous Gly197 to Arg mutation in PROC is associated with venous thrombosis due to the mutation abrogating both zymogenic and enzymatic activities of protein C and activated protein C (APC). In this study, we investigated the role of Gly197 on the structure and function of protein C by replacing it with Ala, Lys and Glu in separate constructs. Characterization of protein C mutants indicated their activation by thrombin is improved ~5-20-fold with the order of PC-G197K > PC-G197E > PC-G197A > PC-WT. Interestingly, the cofactor function of thrombomodulin (TM) in promoting the activation of zymogens by thrombin followed the reverse order of PC-WT > PC-G197A > PC-G197E > PC-G197K. The thrombin-generation inhibitory profiles of zymogens in a tissue factor-mediated thrombin generation assay using protein C-deficient plasma with or without supplementation with TM followed the same order of zymogen activation in the purified system. Evaluation of anticoagulant activities of APC derivatives by prothrombinase and aPTT assays revealed a normal activity for APC-G197A but dramatically impaired activity for the other two mutants. In the endothelial cell permeability assay, APC-G197A exhibited normal antiinflammatory activity, but the other two mutants were nearly inactive. These results suggest that Gly197 plays a key role in TM cofactor-dependent protein C activation by thrombin. It facilitates the recognition of protein C by thrombin in the presence of TM but impedes it in the absence of the cofactor. In APC, a small residue at this position is required for the proper folding/reactivity of the active-site pocket of the protease, a hypothesis supported by structural modeling.
Collapse
Affiliation(s)
- Yeling Lu
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America; Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Indranil Biswas
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Bruno O Villoutreix
- INSERM 1141, NeuroDiderot, Université de Paris, Hôpital Robert-Debré, F-75019 Paris, France
| | - Alireza R Rezaie
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America.
| |
Collapse
|
30
|
Li ZL, Buck M. Beyond history and "on a roll": The list of the most well-studied human protein structures and overall trends in the protein data bank. Protein Sci 2021; 30:745-760. [PMID: 33550681 DOI: 10.1002/pro.4038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Of the roughly 20,000 canonical human protein sequences, as of January 20, 2021, 7,077 proteins have had their full or partial, medium- to high-resolution structures determined by x-ray crystallography or other methods. Which of these proteins dominate the protein data bank (the PDB) and why? In this paper, we list the 273 top human protein structures based on the number of their PDB entries. This set of proteins accounts for more than 40% of all available human PDB entries and represent past trends as well as current status for protein structural biology. We briefly discuss the relationship which some of the prominent protein structures have with protein research as a whole and mention their relevance to human diseases. The top-10 soluble and membrane proteins are all well-known (most of their first structures being deposited more than 30 years ago). Overall, there is no dramatic change in recent trends in the PDB. Remarkably, the number of structure depositions has grown nearly exponentially over the last 10 or more years (with a doubling time of 7 years for proteins, obtained from any organism). Growth in human protein structures is slightly faster (at 5.9 years). The information in this paper may be informative to senior scientists but also inspire researchers who are new to protein science, providing the year 2021 snap-shot for the state of protein structural biology.
Collapse
Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA.,Department of Pharmacology; Department of Neurosciences and Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| |
Collapse
|
31
|
Sandner A, Ngo K, Schiebel J, Pizarroso AIM, Schmidt L, Wenzel B, Steinmetzer T, Ostermann A, Heine A, Klebe G. How a Fragment Draws Attention to Selectivity Discriminating Features between the Related Proteases Trypsin and Thrombin. J Med Chem 2021; 64:1611-1625. [PMID: 33471524 DOI: 10.1021/acs.jmedchem.0c01809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the S1 pocket, the serine proteases thrombin and trypsin commonly feature Asp189 and a Ala190Ser and Glu192Gln exchange. Nevertheless, thrombin cleaves peptide chains solely after Arg, and trypsin after Lys and Arg. Thrombin exhibits a Na+-binding site next to Asp189, which is missing in trypsin. The fragment benzylamine shows direct H-bonding to Asp189 in trypsin, while in thrombin, it forms an H-bond to Glu192. A series of fragments and expanded ligands were studied against both enzymes and mutated variants by crystallography and ITC. The selectivity-determining features of both S1 pockets are difficult to assign to one dominating factor. The Ala190Ser and Glu192Gln replacements may be regarded as highly conserved as no structural and affinity changes are observed between both proteases. With respect to charge distribution, Glu192, together with the thrombin-specific sodium ion, helps in creating an electrostatic gradient across the S1 pocket. This feature is definitely absent in trypsin but important for selectivity along with solvation-pattern differences in the S1 pocket.
Collapse
Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | | | - Linda Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Benjamin Wenzel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Torsten Steinmetzer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| |
Collapse
|
32
|
Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H. A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail. Angew Chem Int Ed Engl 2020; 59:18619-18626. [PMID: 32533629 DOI: 10.1002/anie.202005505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 11/08/2022]
Abstract
DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.
Collapse
Affiliation(s)
- Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| |
Collapse
|
33
|
Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H. A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chad R. Simmons
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| |
Collapse
|
34
|
Jackson CM, Esnouf P, Duewer DL. Thrombin: An Approach to Developing a Higher-Order Reference Material and Reference Measurement Procedure for Substance Identity, Amount, and Biological Activities. JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY 2020; 125:125021. [PMID: 39035347 PMCID: PMC10871826 DOI: 10.6028/jres.125.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 07/23/2024]
Abstract
Thrombin, the proteolytic enzyme that catalyzes the transformation of soluble fibrinogen to the polymerized fibrin clot, participates in multiple reactions in blood coagulation in addition to the clotting reaction. Although reference materials have existed for many years, structural characterization and measurement of biological activity have never been sufficient to permit claims of clear metrological traceability for the thrombin preparations. Our current state-of-the-art methods for protein characterization and determination of the catalytic properties of thrombin now make it practical to develop and characterize a metrologically acceptable reference material and reference measurement procedure for thrombin. Specifically, α-thrombin, the biologically produced protease formed during prothrombin activation, is readily available and has been extensively characterized. Dependences of thrombin proteolytic and peptide hydrolytic activities on a variety of substrates, pH, specific ions, and temperature are established, although variability remains for the kinetic parameters that describe thrombin enzymatic action. The roles of specific areas on the surface of the thrombin molecule (exosites) in substrate recognition and catalytic efficiency are described and characterized. It is opportune to develop reference materials of high metrological order and technical feasibility. In this article, we review the properties of α-thrombin important for its preparation and suggest an approach suitable for producing a reference material and a reference measurement procedure that is sensitive to thrombin’s catalytic competency on a variety of substrates.
Collapse
Affiliation(s)
| | | | - David L. Duewer
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| |
Collapse
|
35
|
Biembengut ÍV, de Souza TDACB. Coagulation modifiers targeting SARS-CoV-2 main protease Mpro for COVID-19 treatment: an in silico approach. Mem Inst Oswaldo Cruz 2020; 115:e200179. [PMID: 32490889 PMCID: PMC7265679 DOI: 10.1590/0074-02760200179] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/18/2020] [Indexed: 11/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection depends on viral polyprotein processing, catalysed by the main proteinase (Mpro). The solution of the SARS-CoV-2 Mpro structure allowed the investigation of potential inhibitors. This work aims to provide first evidences of the applicability of commercially approved drugs to treat coronavirus disease-19 (COVID-19). We screened 4,334 compounds to found potential inhibitors of SARS-CoV-2 replication using an in silico approach. Our results evidenced the potential use of coagulation modifiers in COVID-19 treatment due to the structural similarity of SARS-CoV-2 Mpro and human coagulation factors thrombin and Factor Xa. Further in vitro and in vivo analysis are needed to corroborate these results.
Collapse
Affiliation(s)
- Ísis Venturi Biembengut
- Laboratório de Proteômica Estrutural e Computacional, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | | |
Collapse
|
36
|
Lu Y, Giri H, Villoutreix BO, Ding Q, Wang X, Rezaie AR. Gly197Arg mutation in protein C causes recurrent thrombosis in a heterozygous carrier. J Thromb Haemost 2020; 18:1141-1153. [PMID: 32078247 PMCID: PMC7192786 DOI: 10.1111/jth.14777] [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: 09/23/2019] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Activated protein C (APC) downregulates thrombin generation by inactivating procoagulant cofactors Va and VIIIa by limited proteolysis. We identified two protein C-deficient patients both of whom carry a heterozygous Gly197 to Arg (G197R) mutation in PROC and experience venous thrombosis. OBJECTIVE The objective of this study was to determine the molecular basis of the clotting defect in patients carrying the G197R mutation. METHODS We expressed protein C-G197R in mammalian cells and characterized its properties in established coagulation and anti-inflammatory assay systems. RESULTS The activation of protein C-G197R by thrombin was improved ~10-fold; however, its activation by thrombin was not promoted by thrombomodulin (TM). In a tissue factor-mediated thrombin generation assay, the addition of soluble TM to protein C-deficient plasma, supplemented with protein C-G197R, did not have a significant inhibitory effect on thrombin generation parameters. APC-G197R did not exhibit a significant anticoagulant activity in either purified or plasma-based assay systems. APC-G197R was essentially inactive because it showed no activity in an aPTT assay. Anti-inflammatory activity of APC-G197R was also dramatically impaired as determined by an endothelial cell permeability assay. Structural modeling predicted that the side-chain of Arg cannot be accommodated at this site of APC without a major distortion of the local structure that appears to propagate and adversely affect the reactivity/folding of the catalytic pocket. CONCLUSION The G197R mutation in patients appears to be functionally equivalent to a heterozygous protein C knockout with half of the protein having no significant activity and thus causing thrombosis.
Collapse
Affiliation(s)
- Yeling Lu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City
| | - Hemant Giri
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City
| | - Bruno O. Villoutreix
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Alireza R. Rezaie
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| |
Collapse
|
37
|
Chandankere R, Chelliah J, Subban K, Shanadrahalli VC, Parvez A, Zabed HM, Sharma YC, Qi X. Pleiotropic Functions and Biological Potentials of Silver Nanoparticles Synthesized by an Endophytic Fungus. Front Bioeng Biotechnol 2020; 8:95. [PMID: 32154230 PMCID: PMC7047737 DOI: 10.3389/fbioe.2020.00095] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/03/2020] [Indexed: 11/13/2022] Open
Abstract
In recent years, the biological synthesis of silver nanoparticles (AgNPs) from microorganisms has become an emerging trend for developing biocompatible nanomaterials that finds applications in nano and biomedical sectors. In the present study, we demonstrated a facile, green and eco-friendly method for AgNPs synthesis using the endophytic fungi (Colletotrichum incarnatum DM16.3) isolated from medicinal plant Datura metel and its in vitro antithrombin and cytotoxic activity. At first, biosynthesis of colloidal AgNPs was predicted by visual observation of color change and UV-visible spectra demonstrated specific surface plasmon resonance peak at 420 nm which confirmed the presence of nanoparticles. Microscopic analyses revealed the structure of highly aggregated, spherical and crystalline AgNPs in the diameter range of 5–25 nm. Transform infrared spectroscopy (FT-IR) spectral analysis confirmed the presence of probable biomolecules required for the reduction of silver ions. In vitro evaluation of thrombin activity demonstrates that AgNPs could exert strong inhibition against both thrombin activity (87%) and thrombin generation (84%), respectively. Further, in silico based mechanistic analysis yielded a better insight in understanding the probable amino acids responsible for AgNPs binding with thrombin protein. Similarly, in vitro cytotoxicity of synthesized AgNPs on human epithelial cells using MTT assay did not produce any substantial effects after 24 h exposure which indicates excellent biocompatibility nature, whereas notable toxicity was observed on human cancerous (HeLa) cells at 50 μg/mL (IC50 value). In addition, assessment of AgNPs at 10 μg/mL concentration via crystal violet method on biofilm forming Gram-positive (Vibrio cholerae) and Gram-negative bacteria (Bacillus cereus) revealed inhibition up to 85 and 46%, respectively. Overall, this study showed the possibility of microbially synthesized AgNPs as a potent inhibitor for managing acute thrombosis and highlighted their role for other biomedical applications.
Collapse
Affiliation(s)
- Radhika Chandankere
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China.,Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | | - Kamalraj Subban
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | | - Amreesh Parvez
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hossain M Zabed
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yogesh C Sharma
- Department of Chemistry, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| |
Collapse
|
38
|
Sodium-induced population shift drives activation of thrombin. Sci Rep 2020; 10:1086. [PMID: 31974511 PMCID: PMC6978324 DOI: 10.1038/s41598-020-57822-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/06/2020] [Indexed: 02/04/2023] Open
Abstract
The equilibrium between active E and inactive E* forms of thrombin is assumed to be governed by the allosteric binding of a Na+ ion. Here we use molecular dynamics simulations and Markov state models to sample transitions between active and inactive states. With these calculations we are able to compare thermodynamic and kinetic properties depending on the presence of Na+. For the first time, we directly observe sodium-induced conformational changes in long-timescale computer simulations. Thereby, we are able to explain the resulting change in activity. We observe a stabilization of the active form in presence of Na+ and a shift towards the inactive form in Na+-free simulations. We identify key structural features to quantify and monitor this conformational shift. These include the accessibility of the S1 pocket and the reorientation of W215, of R221a and of the Na+ loop. The structural characteristics exhibit dynamics at various timescales: Conformational changes in the Na+ binding loop constitute the slowest observed movement. Depending on its orientation, it induces conformational shifts in the nearby substrate binding site. Only after this shift, residue W215 is able to move freely, allowing thrombin to adopt a binding-competent conformation.
Collapse
|
39
|
Sandner A, Hüfner-Wulsdorf T, Heine A, Steinmetzer T, Klebe G. Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J Med Chem 2019; 62:9753-9771. [PMID: 31633354 DOI: 10.1021/acs.jmedchem.9b01196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation in solution and complex formation have been characterized by crystallography, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations. First, we show why these preorganizing modifications do not affect the overall binding mode and how key interactions are preserved. Next, we demonstrate how preorganization thermodynamics can be largely dominated by enthalpy rather than entropy because of the significant population of low-energy conformations. Furthermore, a salt bridge is shielded by actively reducing its surface exposure, thus leading to an enhanced enthalpic binding profile. Our results suggest that the consideration of the ligand solution ensemble by MD simulation is necessary to predict preorganizing modifications that enhance the binding behavior of already promising binders.
Collapse
Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Torsten Steinmetzer
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| |
Collapse
|
40
|
Kelley M, Leiderman K. A Mathematical Model of Bivalent Binding Suggests Physical Trapping of Thrombin within Fibrin Fibers. Biophys J 2019; 117:1442-1455. [PMID: 31586524 DOI: 10.1016/j.bpj.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/14/2019] [Accepted: 09/06/2019] [Indexed: 01/21/2023] Open
Abstract
Thrombin is an enzyme that plays many important roles in the blood clotting process; it activates platelets, cleaves coagulation proteins within feedback loops, and cleaves fibrinogen into fibrin, which polymerizes into fibers to form a stabilizing gel matrix in and around growing clots. Thrombin also binds to the formed fibrin matrix, but this interaction is not well understood. Thrombin-fibrin binding is often described as two independent, single-step binding events, one high-affinity and one low-affinity. However, kinetic schemes describing these single-step binding events do not explain experimentally-observed residency times of fibrin-bound thrombin. In this work, we study a bivalent, sequential-step binding scheme as an alternative to the high-affinity event and, in addition to the low-affinity one. We developed mathematical models for the single- and sequential-step schemes consisting of reaction-diffusion equations to compare to each other and to experimental data. We then used Bayesian inference, in the form of Markov chain Monte Carlo, to learn model parameter distributions from previously published experimental data. For the model to best fit the data, we made an additional assumption that thrombin was irreversibly sequestered; we hypothesized that this could be due to thrombin becoming physically trapped within fibrin fibers as they formed. We further estimated that ∼30% of thrombin in the experiments to which we compare our model output became physically trapped. The notion of physically trapped thrombin may provide new insights into conflicting observations regarding the speed of fibrinolysis. Finally, we show that our new model can be used to further probe scenarios dealing with thrombin allostery.
Collapse
Affiliation(s)
- Michael Kelley
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado
| | - Karin Leiderman
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado.
| |
Collapse
|
41
|
Chen H, Cheng S, Fan F, Tu M, Xu Z, Du M. Identification and molecular mechanism of antithrombotic peptides from oyster proteins released in simulated gastro-intestinal digestion. Food Funct 2019; 10:5426-5435. [PMID: 31402368 DOI: 10.1039/c9fo01433k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this study, oyster (Crassostrea gigas) proteins were digested under in vitro gastrointestinal conditions to screen potential antithrombotic peptides. The sequences of the released peptides in the intestinal digestion phase were identified by ultra-performance liquid chromatography coupled to quadrupole time-of-flight MS (UPLC-Q-TOF-MS/MS). According to the antithrombotic activity analysis, the inhibitory ratio of oyster peptides showed an increasing trend, reaching up to 35.80% for a digestion period of 4 h. The APTT (activated partial thromboplastin time) and TT (thromboplastin time) were increased by oyster peptides for human serum in vitro. Oyster peptides showed a competitive inhibition effect on thrombin, based on Lineweaver-Burk plot analysis. Molecular docking between the antithrombotic peptides and thrombin (PDB: ) was conducted using Discovery Studio 2017. Potential inhibitors against thrombin and the mechanism of antithrombotic activity were predicted using the algorithm of CDOCKER. There are fourteen potential antithrombotic peptides, whose affinity with thrombin is higher than that of hirudin, as indicated by the "-CDOCKER energy" score (181.491). Peptide LSKEEIEEAKEV is similar in sequence to thrombin inhibitors. The binding sites of potential antithrombotic peptides against thrombin at the S1 pocket were compared with hirudin variant-2 (GDFEEIPEEYLQ). In addition, the peptides containing the RG/RGD sequence were identified, which can be hydrolyzed by thrombin as a substrate. Consequently, the oyster peptides released in simulated gastrointestinal digestion probably inhibit thrombin in two ways, not only as the inhibitor against the active site, but also as the substrate of thrombin. These results maybe be attributed to the potentially strong antithrombotic activity in the human digestive system.
Collapse
Affiliation(s)
- Hui Chen
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| | - Shuzhen Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Fengjiao Fan
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Maolin Tu
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| | - Zhe Xu
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| | - Ming Du
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
| |
Collapse
|
42
|
Pathak M, Manna R, Li C, Kaira BG, Hamad BK, Belviso BD, Bonturi CR, Dreveny I, Fischer PM, Dekker LV, Oliva MLV, Emsley J. Crystal structures of the recombinant β-factor XIIa protease with bound Thr-Arg and Pro-Arg substrate mimetics. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:578-591. [DOI: 10.1107/s2059798319006910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/13/2019] [Indexed: 11/10/2022]
Abstract
Coagulation factor XII (FXII) is a key initiator of the contact pathway, which contributes to inflammatory pathways. FXII circulates as a zymogen, which when auto-activated forms factor XIIa (FXIIa). Here, the production of the recombinant FXIIa protease domain (βFXIIaHis) with yields of ∼1–2 mg per litre of insect-cell culture is reported. A second construct utilized an N-terminal maltose-binding protein (MBP) fusion (MBP-βFXIIaHis). Crystal structures were determined of MBP-βFXIIaHisin complex with the inhibitor D-Phe-Pro-Arg chloromethyl ketone (PPACK) and of βFXIIaHisin isolation. The βFXIIaHisstructure revealed that the S2 and S1 pockets were occupied by Thr and Arg residues, respectively, from an adjacent molecule in the crystal. The Thr-Arg sequence mimics the P2–P1 FXIIa cleavage-site residues present in the natural substrates prekallikrein and FXII, and Pro-Arg (from PPACK) mimics the factor XI cleavage site. A comparison of the βFXIIaHisstructure with the available crystal structure of the zymogen-like FXII protease revealed large conformational changes centred around the S1 pocket and an alternate conformation for the 99-loop, Tyr99 and the S2 pocket. Further comparison with activated protease structures of factors IXa and Xa, which also have the Tyr99 residue, reveals that a more open form of the S2 pocket only occurs in the presence of a substrate mimetic. The FXIIa inhibitors EcTI and infestin-4 have Pro-Arg and Phe-Arg P2–P1 sequences, respectively, and the interactions that these inhibitors make with βFXIIa are also described. These structural studies of βFXIIa provide insight into substrate and inhibitor recognition and establish a scaffold for the structure-guided drug design of novel antithrombotic and anti-inflammatory agents.
Collapse
|
43
|
Cheng S, Tu M, Chen H, Xu Z, Wang Z, Liu H, Zhao G, Zhu B, Du M. Identification and inhibitory activity against α-thrombin of a novel anticoagulant peptide derived from oyster (Crassostrea gigas) protein. Food Funct 2019; 9:6391-6400. [PMID: 30457135 DOI: 10.1039/c8fo01635f] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A newly discovered anticoagulant peptide was isolated, purified and identified from the pepsin hydrolysate of oyster (Crassostrea gigas) which could potently prolong the activated partial thromboplastin time and the thrombin time. The anticoagulant peptide with a 1264.36 Da molecular mass was similar to the amino acid sequence of the C-terminal segment (DFEEIPEEYLQ) of hirudin (a potent thrombin inhibitor). The peptide specifically inhibited a vital blood coagulation factor: thrombin. The molecular docking energy scores of the anticoagulant peptide with the active site, exosite-I and exosite-II of thrombin were 132.355 kcal mol-1, 151.266 kcal mol-1 and 147.317 kcal mol-1, respectively. The anticoagulant peptide interacted with thrombin by competing with fibrinogen for an anion-binding exosite I. In the anticoagulant peptide-thrombin complex, there are seven hydrogen bonds and reciprocity exists between hydrogen atoms and oxygen atoms, and electrostatic and hydrophobic interactions are also involved. Such abundant interactions may be accountable for the high affinity and specificity of the anticoagulant peptide.
Collapse
Affiliation(s)
- Shuzhen Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Li CY, de Veer SJ, White AM, Chen X, Harris JM, Swedberg JE, Craik DJ. Amino Acid Scanning at P5' within the Bowman-Birk Inhibitory Loop Reveals Specificity Trends for Diverse Serine Proteases. J Med Chem 2019; 62:3696-3706. [PMID: 30888159 DOI: 10.1021/acs.jmedchem.9b00211] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sunflower trypsin inhibitor-1 (SFTI-1) is a 14-amino acid cyclic peptide that shares an inhibitory loop with a sequence and structure similar to a larger family of serine protease inhibitors, the Bowman-Birk inhibitors. Here, we focus on the P5' residue in the Bowman-Birk inhibitory loop and produce a library of SFTI variants to characterize the P5' specificity of 11 different proteases. We identify seven amino acids that are generally preferred by these enzymes and also correlate with P5' sequence diversity in naturally occurring Bowman-Birk inhibitors. Additionally, we show that several enzymes have divergent specificities that can be harnessed in engineering studies. By optimizing the P5' residue, we improve the potency or selectivity of existing inhibitors for kallikrein-related peptidase 5 and show that a variant with substitutions at 7 of the scaffold's 14 residues retains a similar structure to SFTI-1. These findings provide new insights into P5' specificity requirements for the Bowman-Birk inhibitory loop.
Collapse
Affiliation(s)
- Choi Yi Li
- Institute for Molecular Bioscience , The University of Queensland , Brisbane QLD 4072 , Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane QLD 4072 , Australia
| | - Andrew M White
- Institute for Molecular Bioscience , The University of Queensland , Brisbane QLD 4072 , Australia
| | - Xingchen Chen
- Institute of Health and Biomedical Innovation , Queensland University of Technology , Brisbane QLD 4059 , Australia
| | - Jonathan M Harris
- Institute of Health and Biomedical Innovation , Queensland University of Technology , Brisbane QLD 4059 , Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience , The University of Queensland , Brisbane QLD 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane QLD 4072 , Australia
| |
Collapse
|
45
|
Cheng S, Tu M, Liu H, Zhao G, Du M. Food-derived antithrombotic peptides: Preparation, identification, and interactions with thrombin. Crit Rev Food Sci Nutr 2019; 59:S81-S95. [PMID: 30740983 DOI: 10.1080/10408398.2018.1524363] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thromboembolism and its sequelae have been the leading causes of morbidity and mortality throughout the world. Food-derived antithrombotic peptides, as potential ingredients in health-promoting functional foods targeting thrombus, have attracted increasing attention because of their high biological activities, low toxicity, and ease of metabolism in the human body. This review presents the conventional workflow of preparation, isolation and identification of antithrombotic peptides from various kinds of food materials. More importantly, to analyze the antithrombotic effects and mechanism of antithrombotic peptides, methods for interaction of anticoagulant peptides and thrombin, the main participant in thrombosis, were analyzed from biochemistry, solution chemistry and crystal chemistry. The present study is intended to highlight the recent advances in research of food-derived antithrombotic peptide as a novel vehicle in the field of food science and nutrition. Future outlooks are highlighted with the aim to suggest a research line to be followed in further studies with the introduced research approach.
Collapse
Affiliation(s)
- Shuzheng Cheng
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Maolin Tu
- c Department of Food Science and Engineering , Harbin Institute of Technology , Harbin , Heilongjiang , China
| | - Hanxiong Liu
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China
| | - Guanghua Zhao
- b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Ming Du
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China
| |
Collapse
|
46
|
Markwick PRL, Peacock RB, Komives EA. Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery. Biophys J 2018; 116:49-56. [PMID: 30558884 DOI: 10.1016/j.bpj.2018.11.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022] Open
Abstract
Amide hydrogen/deuterium exchange mass spectrometry (HDXMS) of proteins has become extremely popular for identifying ligand-binding sites, protein-protein interactions, intrinsic disorder, and allosteric changes upon protein modification. Such phenomena are revealed when amide exchange is measured in the fast limit, that is, within a few minutes of exchange in deuterated buffer. The HDXMS data have a resolution of the length of peptides and are difficult to interpret because many different phenomena lead to changes in hydrogen/deuterium exchange. We present a quantitative analysis of accelerated molecular dynamics simulations that provides impressive agreement with peptide-length HDXMS data. Comparative analysis of thrombin and a single-point mutant reveals that the simulation analysis can distinguish the subtle differences in exchange due to mutation. In addition, the results provide a deeper understanding of the underlying changes in dynamics revealed by the HDXMS that extend far from the site of mutation.
Collapse
Affiliation(s)
- Phineus R L Markwick
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California
| | - Riley B Peacock
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California.
| |
Collapse
|
47
|
Pal S, Paul S. Conformational deviation of Thrombin binding G-quadruplex aptamer (TBA) in presence of divalent cation Sr 2+: A classical molecular dynamics simulation study. Int J Biol Macromol 2018; 121:350-363. [PMID: 30308284 DOI: 10.1016/j.ijbiomac.2018.09.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 11/28/2022]
Abstract
Thrombin binding TBA-G-quadruplex aptamer (TBA) plays a major role in blood coagulation cascade. The 15-mer TBA sequence tends to form four-stranded TBA-G-quadruplex structure. In this research work, a series of explicit solvent classical MD simulations of the TBA is carried out using different salt (SrCl2) concentrations (0, 50, 100 and 200 mM). Here we have also testified the effect of salt concentration of divalent cation Sr2+ on the conformational change of quadruplex DNA. The structural deviations, fluctuations, torsional angles and the affinity of the ion are explored at different salt concentrations. It is found that the conformation of TBA-G-quadruplex at 0 mM and 50 mM salt concentrations, is very much different than the other salt concentrations (100 mM and 200 mM). Also observed are as follows: (i) no exchange of Sr2+ ion between inside and outside of the channel, (ii) an enhancement in the Sr2+ ion density around the phosphate region of the loop residues as salt concentration increases and (iii) the stacking of T3 and T4 residues of loop-1 that appears up to 50 mM concentration, vanishes as the salt concentration is increased further.
Collapse
Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
| |
Collapse
|
48
|
Hochscherf J, Pietsch M, Tieu W, Kuan K, Abell AD, Gütschow M, Niefind K. Crystal structure of highly glycosylated human leukocyte elastase in complex with an S2' site binding inhibitor. Acta Crystallogr F Struct Biol Commun 2018; 74:480-489. [PMID: 30084397 PMCID: PMC6096481 DOI: 10.1107/s2053230x1800537x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/05/2018] [Indexed: 11/10/2022] Open
Abstract
Glycosylated human leukocyte elastase (HLE) was crystallized and structurally analysed in complex with a 1,3-thiazolidine-2,4-dione derivative that had been identified as an HLE inhibitor in preliminary studies. In contrast to previously described HLE structures with small-molecule inhibitors, in this structure the inhibitor does not bind to the S1 and S2 substrate-recognition sites; rather, this is the first HLE structure with a synthetic inhibitor in which the S2' site is blocked that normally binds the second side chain at the C-terminal side of the scissile peptide bond in a substrate protein. The inhibitor also induces the formation of crystalline HLE dimers that block access to the active sites and that are also predicted to be stable in solution. Neither such HLE dimers nor the corresponding crystal packing have been observed in previous HLE crystal structures. This novel crystalline environment contributes to the observation that comparatively large parts of the N-glycan chains of HLE are defined by electron density. The final HLE structure contains the largest structurally defined carbohydrate trees among currently available HLE structures.
Collapse
Affiliation(s)
- Jennifer Hochscherf
- Department of Chemistry, Institute of Biochemistry, Universität zu Köln, Zülpicher Str. 47, 50674 Cologne, Germany
| | - Markus Pietsch
- Centre of Pharmacology, Medical Faculty, Universität zu Köln, Gleueler Str. 24, 50931 Cologne, Germany
| | - William Tieu
- Department of Chemistry and Centre for Nanoscale BioPhotonics (CNBP), The University of Adelaide, North Terrace, Adelaide 5005, Australia
| | - Kevin Kuan
- Department of Chemistry and Centre for Nanoscale BioPhotonics (CNBP), The University of Adelaide, North Terrace, Adelaide 5005, Australia
| | - Andrew D. Abell
- Department of Chemistry and Centre for Nanoscale BioPhotonics (CNBP), The University of Adelaide, North Terrace, Adelaide 5005, Australia
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Karsten Niefind
- Department of Chemistry, Institute of Biochemistry, Universität zu Köln, Zülpicher Str. 47, 50674 Cologne, Germany
| |
Collapse
|
49
|
Lim CH, Adav SS, Sze SK, Choong YK, Saravanan R, Schmidtchen A. Thrombin and Plasmin Alter the Proteome of Neutrophil Extracellular Traps. Front Immunol 2018; 9:1554. [PMID: 30038618 PMCID: PMC6046383 DOI: 10.3389/fimmu.2018.01554] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/22/2018] [Indexed: 12/12/2022] Open
Abstract
Neutrophil extracellular traps (NETs) consist of a decondensed DNA scaffold decorated with neutrophil-derived proteins. The proteome of NETs, or "NETome," has been largely elucidated in vitro. However, components such as plasma and extracellular matrix proteins may affect the NETome under physiological conditions. Here, using a reductionistic approach, we explored the effects of two proteases active during injury and wounding, human thrombin and plasmin, on the NETome. Using high-resolution mass spectrometry, we identified a total of 164 proteins, including those previously not described in NETs. The serine proteases, particularly thrombin, were also found to interact with DNA and bound to NETs in vitro. Among the most abundant proteins were those identified previously, including histones, neutrophil elastase, and antimicrobial proteins. We observed reduced histone (H2B, H3, and H4) and neutrophil elastase levels upon the addition of the two proteases. Analyses of NET-derived tryptic peptides identified subtle changes upon protease treatments. Our results provide evidence that exogenous proteases, present during wounding and inflammation, influence the NETome. Taken together, regulation of NETs and their proteins under different physiological conditions may affect their roles in infection, inflammation, and the host response.
Collapse
Affiliation(s)
- Chun Hwee Lim
- Interdisciplinary Graduate School, NTU Institute for Health Technologies, Nanyang Technological University, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sunil S Adav
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yeu Khai Choong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Rathi Saravanan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Artur Schmidtchen
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Lund, Sweden
| |
Collapse
|
50
|
Yesudasan S, Wang X, Averett RD. Fibrin polymerization simulation using a reactive dissipative particle dynamics method. Biomech Model Mechanobiol 2018; 17:1389-1403. [PMID: 29796957 DOI: 10.1007/s10237-018-1033-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 05/14/2018] [Indexed: 12/31/2022]
Abstract
The study on the polymerization of fibrinogen molecules into fibrin monomers and eventually a stable, mechanically robust fibrin clot is a persistent and enduring topic in the field of thrombosis and hemostasis. Despite many research advances in fibrin polymerization, the change in the structure of fibrin clots and its influence on the formation of a fibrous protein network are still poorly understood. In this paper, we develop a new computational method to simulate fibrin clot polymerization using dissipative particle dynamics simulations. With an effective combination of reactive molecular dynamics formularies and many body dissipative particle dynamics principles, we constructed the reactive dissipative particle dynamics (RDPD) model to predict the complex network formation of fibrin clots and branching of the fibrin network. The 340 kDa fibrinogen molecule is converted into a spring-bead coarse-grain system with 11 beads using a topology representing network algorithm, and using RDPD, we simulated polymerization and formation of the fibrin clot. The final polymerized structure of the fibrin clot qualitatively agrees with experimental results from the literature, and to the best of our knowledge this is the first molecular-based study that simulates polymerization and structure of fibrin clots.
Collapse
Affiliation(s)
- Sumith Yesudasan
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, 597 D.W. Brooks Drive, Athens, GA, 30602, USA
| | - Xianqiao Wang
- School of Environmental, Civil, Agricultural and Mechanical Engineering, University of Georgia, 597 D.W. Brooks Drive, Athens, GA, 30602, USA
| | - Rodney D Averett
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, 597 D.W. Brooks Drive, Athens, GA, 30602, USA.
| |
Collapse
|