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Khan A, Siddiqui U, Fatima S, Rehman A, Jairajpuri M. Protein disulfide isomerase uses thrombin-antithrombin complex as a template to bind its target protein and alter the blood coagulation rates. Biosci Rep 2024; 44:BSR20231540. [PMID: 38660763 PMCID: PMC11096647 DOI: 10.1042/bsr20231540] [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: 09/16/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
During inflammation and situations of cellular stress protein disulfide isomerase (PDI) is released in the blood plasma from the platelet and endothelial cells to influence thrombosis. The addition of exogenous PDI makes the environment pro-thrombotic by inducing disulfide bond formation in specific plasma protein targets like vitronectin, factor V, and factor XI. However, the mechanistic details of PDI interaction with its target remain largely unknown. A decrease in the coagulation time was detected in activated partial thromboplastin time (APTT), prothrombin time (PT), and thrombin time (TT) on addition of the purified recombinant PDI (175 nM). The coagulation time can be controlled using an activator (quercetin penta sulfate, QPS) or an inhibitor (quercetin 3-rutinoside, Q3R) of PDI activity. Likewise, the PDI variants that increase the PDI activity (H399R) decrease, and the variant with low activity (C53A) increases the blood coagulation time. An SDS-PAGE and Western blot analysis showed that the PDI does not form a stable complex with either thrombin or antithrombin (ATIII) but it uses the ATIII-thrombin complex as a template to bind and maintain its activity. A complete inhibition of thrombin activity on the formation of ATIII-thrombin-PDI complex, and the complex-bound PDI-catalyzed disulfide bond formation of the target proteins may control the pro- and anti-thrombotic role of PDI.
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Affiliation(s)
- Abdul Burhan Khan
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Urfi Siddiqui
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Sana Fatima
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ahmed Abdur Rehman
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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Lauster D, Osterrieder K, Haag R, Ballauff M, Herrmann A. Respiratory viruses interacting with cells: the importance of electrostatics. Front Microbiol 2023; 14:1169547. [PMID: 37440888 PMCID: PMC10333706 DOI: 10.3389/fmicb.2023.1169547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
The COVID-19 pandemic has rekindled interest in the molecular mechanisms involved in the early steps of infection of cells by viruses. Compared to SARS-CoV-1 which only caused a relatively small albeit deadly outbreak, SARS-CoV-2 has led to fulminant spread and a full-scale pandemic characterized by efficient virus transmission worldwide within a very short time. Moreover, the mutations the virus acquired over the many months of virus transmission, particularly those seen in the Omicron variant, have turned out to result in an even more transmissible virus. Here, we focus on the early events of virus infection of cells. We review evidence that the first decisive step in this process is the electrostatic interaction of the spike protein with heparan sulfate chains present on the surface of target cells: Patches of cationic amino acids located on the surface of the spike protein can interact intimately with the negatively charged heparan sulfate chains, which results in the binding of the virion to the cell surface. In a second step, the specific interaction of the receptor binding domain (RBD) within the spike with the angiotensin-converting enzyme 2 (ACE2) receptor leads to the uptake of bound virions into the cell. We show that these events can be expressed as a semi-quantitative model by calculating the surface potential of different spike proteins using the Adaptive Poison-Boltzmann-Solver (APBS). This software allows visualization of the positive surface potential caused by the cationic patches, which increased markedly from the original Wuhan strain of SARS-CoV-2 to the Omicron variant. The surface potential thus enhanced leads to a much stronger binding of the Omicron variant as compared to the original wild-type virus. At the same time, data taken from the literature demonstrate that the interaction of the RBD of the spike protein with the ACE2 receptor remains constant within the limits of error. Finally, we briefly digress to other viruses and show the usefulness of these electrostatic processes and calculations for cell-virus interactions more generally.
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Affiliation(s)
- Daniel Lauster
- Institut für Pharmazie, Biopharmazeutika, Freie Universität Berlin, Berlin, Germany
| | | | - Rainer Haag
- Institut für Chemie und Biochemie, SupraFAB, Freie Universität Berlin, Berlin, Germany
| | - Matthias Ballauff
- Institut für Chemie und Biochemie, SupraFAB, Freie Universität Berlin, Berlin, Germany
| | - Andreas Herrmann
- Institut für Chemie und Biochemie, SupraFAB, Freie Universität Berlin, Berlin, Germany
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Bano S, Khan AB, Fatima S, Rashid Q, Prakash A, Gupta N, Ahmad I, Ansari S, Lynn AM, Abid M, Jairajpuri MA. Mannose 2, 3, 4, 5, 6- O-pentasulfate (MPS): a partial activator of human heparin cofactor II with anticoagulation potential. J Biomol Struct Dyn 2023; 41:3717-3727. [PMID: 35343865 DOI: 10.1080/07391102.2022.2053749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
Abstract
Thromboembolic diseases are a major cause of mortality in human and the currently available anticoagulants are associated with various drawbacks, therefore the search for anticoagulants that have better safety profile is highly desirable. Compounds that are part of the dietary routine can be modified to possibly increase their anticoagulant potential. We show mannose 2,3,4,5,6-O-pentasulfate (MPS) as a synthetically modified form of mannose that has appreciable anticoagulation properties. An in silico study identified that mannose in sulfated form can bind effectively to the heparin-binding site of antithrombin (ATIII) and heparin cofactor II (HCII). Mannose was sulfated using a simple sulfation strategy-involving triethylamine-sulfur trioxide adduct. HCII and ATIII were purified from human plasma and the binding analysis using fluorometer and isothermal calorimetry showed that MPS binds at a unique site. A thrombin inhibition analysis using the chromogenic substrate showed that MPS partially enhances the activity of HCII. Further an assessment of in vitro blood coagulation assays using human plasma showed that the activated partial thromboplastin time (APTT) and prothrombin time (PT) were prolonged in the presence of MPS. A molecular dynamics simulation analysis of the HCII-MPS complex showed fluctuations in a N-terminal loop and the cofactor binding site of HCII. The results indicate that MPS is a promising lead due to its effect on the in vitro coagulation rate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shadabi Bano
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Abdul Burhan Khan
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Sana Fatima
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Qudsia Rashid
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Amresh Prakash
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Neha Gupta
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Irshad Ahmad
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shoyab Ansari
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Andrew M Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
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Afosah DK, Fayyad RM, Puliafico VR, Merrell S, Langmia EK, Diagne SR, Al-Horani RA, Desai UR. Homogeneous, Synthetic, Non-Saccharide Glycosaminoglycan Mimetics as Potent Inhibitors of Human Cathepsin G. Biomolecules 2023; 13:760. [PMID: 37238630 PMCID: PMC10216581 DOI: 10.3390/biom13050760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Cathepsin G (CatG) is a pro-inflammatory neutrophil serine protease that is important for host defense, and has been implicated in several inflammatory disorders. Hence, inhibition of CatG holds much therapeutic potential; however, only a few inhibitors have been identified to date, and none have reached clinical trials. Of these, heparin is a well-known inhibitor of CatG, but its heterogeneity and bleeding risk reduce its clinical potential. We reasoned that synthetic small mimetics of heparin, labeled as non-saccharide glycosaminoglycan mimetics (NSGMs), would exhibit potent CatG inhibition while being devoid of bleeding risks associated with heparin. Hence, we screened a focused library of 30 NSGMs for CatG inhibition using a chromogenic substrate hydrolysis assay and identified nano- to micro-molar inhibitors with varying levels of efficacy. Of these, a structurally-defined, octasulfated di-quercetin NSGM 25 inhibited CatG with a potency of ~50 nM. NSGM 25 binds to CatG in an allosteric site through an approximately equal contribution of ionic and nonionic forces. Octasulfated 25 exhibits no impact on human plasma clotting, suggesting minimal bleeding risk. Considering that octasulfated 25 also potently inhibits two other pro-inflammatory proteases, human neutrophil elastase and human plasmin, the current results imply the possibility of a multi-pronged anti-inflammatory approach in which these proteases are likely to simultaneously likely combat important conditions, e.g., rheumatoid arthritis, emphysema, or cystic fibrosis, with minimal bleeding risk.
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Affiliation(s)
- Daniel K. Afosah
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Rawan M. Fayyad
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Valerie R. Puliafico
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Spencer Merrell
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Eltice K. Langmia
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Sophie R. Diagne
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Rami A. Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
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Abdelfadiel E, Gunta R, Villuri BK, Afosah DK, Sankaranarayanan NV, Desai UR. Designing Smaller, Synthetic, Functional Mimetics of Sulfated Glycosaminoglycans as Allosteric Modulators of Coagulation Factors. J Med Chem 2023; 66:4503-4531. [PMID: 37001055 PMCID: PMC10108365 DOI: 10.1021/acs.jmedchem.3c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Indexed: 04/03/2023]
Abstract
Natural glycosaminoglycans (GAGs) are arguably the most diverse collection of natural products. Unfortunately, this bounty of structures remains untapped. Decades of research has realized only one GAG-like synthetic, small-molecule drug, fondaparinux. This represents an abysmal output because GAGs present a frontier that few medicinal chemists, and even fewer pharmaceutical companies, dare to undertake. GAGs are heterogeneous, polymeric, polydisperse, highly water soluble, synthetically challenging, too rapidly cleared, and difficult to analyze. Additionally, GAG binding to proteins is not very selective and GAG-binding sites are shallow. This Perspective attempts to transform this negative view into a much more promising one by highlighting recent advances in GAG mimetics. The Perspective focuses on the principles used in the design/discovery of drug-like, synthetic, sulfated small molecules as allosteric modulators of coagulation factors, such as antithrombin, thrombin, and factor XIa. These principles will also aid the design/discovery of sulfated agents against cancer, inflammation, and microbial infection.
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Affiliation(s)
- Elsamani
I. Abdelfadiel
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rama Gunta
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Bharath Kumar Villuri
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Daniel K. Afosah
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nehru Viji Sankaranarayanan
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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6
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Yamada Y, Onda T, Hamada K, Kikkawa Y, Nomizu M. Effect of Amino Acid Substitution on Cell Adhesion Properties of Octa-arginine. Biol Pharm Bull 2022; 45:1537-1543. [PMID: 36184513 DOI: 10.1248/bpb.b22-00430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Octa-arginine (R8) is a cell-permeable peptide with excellent cell adhesion properties. Surface-immobilized R8 mediates cell attachment via cell surface receptors, such as heparan sulfate proteoglycans and integrin β1, and promotes cell spreading and proliferation. However, it is not clear how these properties are affected by specific peptide composition and if they could be improved. Here, we synthesized XR8 peptides, in which half of the original R8 arginine residues were replaced with another amino acid (X). We then aimed to investigate the effect of the substitution on cell adhesion and proliferation on XR8-conjugated agarose matrices. The XR8-matrix showed slightly better cell attachment when X was a hydrophobic or aromatic amino acid. However, hydrophobic XR8-matrices tended to promote cell proliferation to a less extent. Eventually, YR8-matrix most efficiently promoted cell adhesion, spreading, and proliferation among the XR8-matrices tested. Collectively, these observations indicate that the properties of residue X play a major role in the biological activity of XR8-matrices and shed light on the interaction between small peptides and the cell membrane. Further, YR8 is a promising cell-adhesive peptide for the development of cell culture substrates and biomaterials.
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Affiliation(s)
- Yuji Yamada
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
| | - Toru Onda
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
| | - Keisuke Hamada
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
| | - Yamato Kikkawa
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
| | - Motoyoshi Nomizu
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
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7
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Malicka W, Haag R, Ballauff M. Interaction of Heparin with Proteins: Hydration Effects. J Phys Chem B 2022; 126:6250-6260. [PMID: 35960645 DOI: 10.1021/acs.jpcb.2c04928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a thermodynamic investigation of the interaction of heparin with lysozyme in the presence of potassium glutamate (KGlu). The binding constant Kb is measured by isothermal titration calorimetry (ITC) in a temperature range from 288 to 310 K for concentrations of KGlu between 25 and 175 mM. The free energy of binding ΔGb derived from Kb is strongly decreasing with increasing concentration of KGlu, whereas the dependence of ΔGb on temperature T is found to be small. The decrease of ΔGb can be explained in terms of counterion release: Binding of lysozyme to the strong polyelectrolyte heparin liberates approximately three of the condensed counterions of heparin, thus increasing the entropy of the system. The dependence of ΔGb on T, on the other hand, is traced back to a change of hydration of the protein and the polyelectrolyte upon complex formation. This dependence is quantitatively described by the parameter Δw that depends on T and vanishes at a characteristic temperature T0. A comparison of the complex formation in the presence of KGlu with the one in the presence of NaCl demonstrates that the parameters related to hydration are changed considerably. The characteristic temperature T0 in the presence of KGlu solutions is considerably smaller than that in the presence of NaCl solutions. The change of specific heat Δcp is found to become more negative with increasing salt concentration: This finding agrees with the model-free analysis by the generalized van't Hoff equation. The entire analysis reveals a small but important change of the free energy of binding by hydration. It shows that these ion-specific Hofmeister effects can be modeled quantitatively in terms of a characteristic temperature T0 and a parameter describing the dependence of Δcp on salt concentration.
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Affiliation(s)
- Weronika Malicka
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Rainer Haag
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Matthias Ballauff
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
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Abdolahpur Monikh F, Chupani L, Karkossa I, Gardian Z, Arenas-Lago D, von Bergen M, Schubert K, Piackova V, Zuskova E, Jiskoot W, Vijver MG, Peijnenburg WJGM. An environmental ecocorona influences the formation and evolution of the biological corona on the surface of single-walled carbon nanotubes. NANOIMPACT 2021; 22:100315. [PMID: 35559972 DOI: 10.1016/j.impact.2021.100315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/27/2021] [Accepted: 03/27/2021] [Indexed: 06/15/2023]
Abstract
Nanomaterials (NMs) taken up from the environment carry a complex ecocorona consisting of dissolved organic matter. An ecocorona is assumed to influence the interactions between NMs and endogenous biomolecules and consequently affects the formation of a biological corona (biocorona) and the biological fate of the NMs. This study shows that biomolecules in fish plasma attach immediately (within <5 min) to the surface of SWCNTs and the evolution of the biocorona is a size dependent phenomenon. Quantitative proteomics data revealed that the nanotube size also influences the plasma protein composition on the surface of SWCNTs. The presence of a pre-attached ecocorona on the surface of SWCNTs eliminated the influence of nanotube size on the formation and evolution of the biocorona. Over time, endogenous biomolecules from the plasma partially replaced the pre-attached ecocorona as measured using a fluorescently labelled ecocorona. The presence of an ecocorona offers a unique surface composition to each nanotube. This suggests that understanding the biological fate of NMs taken up from the environment by organisms to support the environmental risk assessment of NMs is a challenging task because each NM may have a unique surface composition in the body of an organism.
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Affiliation(s)
- Fazel Abdolahpur Monikh
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, Netherlands; Department of Environmental & Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland.
| | - Latifeh Chupani
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Isabel Karkossa
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Zdenko Gardian
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, University of South Bohemia, Faculty of Science, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Daniel Arenas-Lago
- Department of Plant Biology and soil Science, University of Vigo, As Lagoas, Ourense, Spain
| | - Martin von Bergen
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany; Institute of Biochemistry, Leipzig University, Permoserstraße 15, 04318 Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Veronika Piackova
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Eliska Zuskova
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Wim Jiskoot
- Division of BioTherapeutics, Leiden University, Einsteinweg 55, 2333, CC, Leiden, the Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, Netherlands
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Bilthoven, the Netherlands
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Chandika P, Heo SY, Oh GW, Choi IW, Park WS, Jung WK. Antithrombin III-mediated blood coagulation inhibitory activity of chitosan sulfate derivatized with different functional groups. Int J Biol Macromol 2020; 161:1552-1558. [PMID: 32791278 DOI: 10.1016/j.ijbiomac.2020.08.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/26/2022]
Abstract
Acylated chitosan sulfate (ChS1), a sulfated polysaccharide with high anticoagulant activity, was chemically synthesized and structurally characterized using FT-IR analysis. The beneficial structural properties and high availability of the sulfate group in ChS1 led to greater anticoagulant activity through both the intrinsic and common pathways with antithrombin III (AT III)-mediated inhibition, particularly involving coagulation factors FXa and FIIa. The analysis of the binding affinities using surface plasma resonance found that the equilibrium dissociation constant (KD) of ChS1 for FXa and FIIa in the presence of AT III was 67.4 nM and 112.6 nM, respectively, indicating the stronger interaction of the AT III/ChS1 complex with the ligands and the inhibition of activated FX and FII. The results of amidolytic assays further demonstrated the stronger inhibition of the proteolytic conversion of factor X by the intrinsic FXase complex and of FII by the prothrombinase complex. Molecular docking analysis further validated the protein-ligand interactions of ChS1 with AT III and their binding affinity.
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Affiliation(s)
- Pathum Chandika
- Department of Biomedical Engineering, Center for Marine-Integrated Biomedical Technology (BK21 Plus) Pukyong National University, Busan 48513, Republic of Korea
| | - Seong-Yeong Heo
- Department of Biomedical Engineering, Center for Marine-Integrated Biomedical Technology (BK21 Plus) Pukyong National University, Busan 48513, Republic of Korea
| | - Gun-Woo Oh
- Department of Biomedical Engineering, Center for Marine-Integrated Biomedical Technology (BK21 Plus) Pukyong National University, Busan 48513, Republic of Korea
| | - Il-Whan Choi
- Department of Microbiology, College of Medicine, Inje University, Busan 47392, Republic of Korea
| | - Won Sun Park
- Institute of Medical Sciences, Department of Physiology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Won-Kyo Jung
- Department of Biomedical Engineering, Center for Marine-Integrated Biomedical Technology (BK21 Plus) Pukyong National University, Busan 48513, Republic of Korea; Ingram School of Engineering, Texas State University, San Marcos, TX 78666, United States of America.
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10
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Balogh G, Komáromi I, Bereczky Z. The mechanism of high affinity pentasaccharide binding to antithrombin, insights from Gaussian accelerated molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:4718-4732. [PMID: 31686597 DOI: 10.1080/07391102.2019.1688194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The activity of antithrombin (AT), a serpin protease inhibitor, is enhanced by heparin and heparin analogs against its target proteases, mainly thrombin, factors Xa and IXa. Considerable amount of information is available on the multistep mechanism of the heparin pentasaccharide binding and conformational activation. However, much of the details were inferred from 'static' structures obtained by X-ray diffraction. Moreover, limited information is available for the early steps of binding mechanism other than kinetic studies with various ligands. To gain insights into these processes, we performed enhanced sampling molecular dynamics (MD) simulations using the Gaussian Accelerated Molecular Dynamics (GAMD) method, applied previously in drug binding studies. We were able to observe the binding of the pentasaccharide idraparinux to a 'non-activated' AT conformation in two separate trajectories with low root mean square deviation (RMSD) values compared to X-ray structures of the bound state. These trajectories along with further simulations of the AT-pentasaccharide complex provided insights into the mechanisms of multiple conformational transitions, including the expulsion of the hinge region, the extension of helix D and the conformational behavior of the reactive center loop (RCL). We could also confirm the high stability of helix P in non-activated AT conformations, such states might play an important role in heparin binding. 'Generalized correlation' matrices revealed possible paths of allosteric signal propagation to the binding sites for the target proteases, factors Xa and IXa. Enhanced MD simulations of ligand binding to AT may assist the design of new anticoagulant drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gábor Balogh
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Kálmán Laki Doctoral School, University of Debrecen, Debrecen, Hungary
| | - István Komáromi
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsuzsanna Bereczky
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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11
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Deciphering the role of trehalose in hindering antithrombin polymerization. Biosci Rep 2019; 39:BSR20182259. [PMID: 30886063 PMCID: PMC6449516 DOI: 10.1042/bsr20182259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 11/17/2022] Open
Abstract
Serine protease inhibitors (serpins) family have a complex mechanism of inhibition that requires a large scale conformational change. Antithrombin (AT), a member of serpin superfamily serves as a key regulator of the blood coagulation cascade, deficiency of which leads to thrombosis. In recent years, a handful of studies have identified small compounds that retard serpin polymerization but abrogated the normal activity. Here, we screened small molecules to find potential leads that can reduce AT polymer formation. We identified simple sugar molecules that successfully blocked polymer formation without a significant loss of normal activity of AT under specific buffer and temperature conditions. Of these, trehalose proved to be most promising as it showed a marked decrease in the bead like polymeric structures of AT shown by electron microscopic analysis. A circular dichroism (CD) analysis indicated alteration in the secondary structure profile and an increased thermal stability of AT in the presence of trehalose. Guanidine hydrochloride (GdnHCl)-based unfolding studies of AT show the formation of a different intermediate in the presence of trehalose. A time-dependent fluorescence study using 1,1′-bi(4-anilino)naphthalene-5,5′-disulfonic acid (Bis-ANS) shows that trehalose affects the initial conformational change step in transition from native to polymer state through its binding to exposed hydrophobic residues on AT thus making AT less polymerogenic. In conclusion, trehalose holds promise by acting as an initial scaffold that can be modified to design similar compounds with polymer retarding propensity.
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12
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Wang C, Wu YB, Wang AP, Jiang JD, Kong WJ. Evaluation of Anticoagulant and Antithrombotic Activities of Berberine: A Focus on the Ameliorative Effect on Blood Hypercoagulation. INT J PHARMACOL 2018. [DOI: 10.3923/ijp.2018.1087.1098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Ahmad I, Sharma S, Gupta N, Rashid Q, Abid M, Ashraf MZ, Jairajpuri MA. Antithrombotic potential of esculin 7, 3', 4', 5', 6'-O-pentasulfate (EPS) for its role in thrombus reduction using rat thrombosis model. Int J Biol Macromol 2018; 119:360-368. [PMID: 30009901 DOI: 10.1016/j.ijbiomac.2018.07.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022]
Abstract
Currently available anticoagulants for prevention and treatment of thrombosis have several limitations, thus, small organic scaffolds that can dissolve clots in vivo in a dose dependent manner with lesser side effects are highly desirable. Here we report the synthesis of esculin pentasulfate (EPS) and assessment of its in vitro, in vivo and ex vivo anticoagulant and antithrombotic potential. Assessment of in vitro clotting times showed prolonged activated partial thromboplastin time (APTT), prothrombin time (PT) and thrombin time (TT) in the presence of EPS. EPS also showed remarkable reduction in thrombus formation when administered in occlusion induced thrombotic rats at a low dose (2.5 mg/kg). Further, assessment of clot rate with plasma isolated from EPS treated rats confirmed its anticoagulation potential. EPS at varying concentrations showed no significant cytotoxic effect on HEK293 cell line. Further, molecular docking analysis of EPS with known anticoagulant proteins [(antithrombin (ATIII) and heparin cofactor II (HCF II)] that require heparin revealed good binding affinity (-7.9 kcal/mol) with ATIII but not with HCF II. ATIII when incubated with EPS showed increased fluorescence intensity, with no change in secondary structure. Overall, our results clearly show the in vivo modulation of thrombus formation using a modified natural scaffold EPS.
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Affiliation(s)
- Irshad Ahmad
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Swati Sharma
- Defence Institute of Physiology & Allied Sciences, Timarpur, New Delhi 110 054, India
| | - Neha Gupta
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Qudsia Rashid
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi 110 025, India
| | - Mohammad Z Ashraf
- Defence Institute of Physiology & Allied Sciences, Timarpur, New Delhi 110 054, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India.
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14
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Arantes PR, Pérez-Sánchez H, Verli H. Antithrombin conformational modulation by D-myo-inositol 3,4,5,6-tetrakisphosphate (TMI), a novel scaffold for the development of antithrombotic agents. J Biomol Struct Dyn 2017; 36:4045-4056. [DOI: 10.1080/07391102.2017.1407259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Pablo Ricardo Arantes
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Murcia, Spain
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
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15
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Moffett BS, Diaz R, Galati M, Mahoney D, Teruya J, Yee DL. Population pharmacokinetics of human antithrombin concentrate in paediatric patients. Br J Clin Pharmacol 2017; 83:2450-2457. [PMID: 28664670 DOI: 10.1111/bcp.13359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 05/08/2017] [Accepted: 06/13/2017] [Indexed: 11/29/2022] Open
Abstract
AIMS Antithrombin is increasingly used in paediatric patients, yet there are few age-specific pharmacokinetic data to guide dosing. We aimed to describe the pharmacokinetic profile of human (plasma-derived) antithrombin concentrate in paediatric patients. METHODS A 5-year retrospective review was performed of patients <19 years of age admitted to our institution who received antithrombin concentrate, were not on mechanical circulatory support and had baseline (predose) and postdose plasma antithrombin activity levels available for analysis. Demographic and laboratory variables, antithrombin dosing information and data on the use of continuous infusion unfractionated heparin were collected. Population pharmacokinetic analysis was performed with bootstrap analysis. The model developed was tested against a validation dataset from a cohort of similar patients, and a predictive value was calculated. RESULTS A total 184 patients met the study criteria {46.7% male, median age [years] 0.35 [interquartile range (IQR) 0.07-3.9]}. A median of two antithrombin doses (IQR 1-4) were given to patients (at a dose of 46.3 ± 13.6 units kg-1 ), with median of three (IQR 2-7) postdose levels per patient. Continuous infusion unfractionated heparin was administered in 87.5% of patients, at a mean dose of 34.1 ± 22.7 units kg-1 h-1 . A one-compartment exponential error model best fit the data, and significant covariates included allometrically scaled weight on clearance and volume of distribution, unfractionated heparin dose on clearance, and baseline antithrombin activity level on volume of distribution. The model resulted in a median -1.75% prediction error (IQR -11.75% to 6.5%) when applied to the validation dataset (n = 30). CONCLUSIONS Antithrombin pharmacokinetics are significantly influenced by the concurrent use of unfractionated heparin and baseline antithrombin activity.
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Affiliation(s)
- Brady S Moffett
- Texas Children's Hospital, Department of Pharmacy, Houston, TX, USA.,Baylor College of Medicine, Department of Pediatrics, Houston, TX, USA
| | - Rosa Diaz
- Baylor College of Medicine, Department of Pediatrics, Houston, TX, USA
| | | | - Donald Mahoney
- Baylor College of Medicine, Department of Pediatrics, Houston, TX, USA
| | - Jun Teruya
- Baylor College of Medicine, Department of Pathology, Houston, TX, USA
| | - Donald L Yee
- Baylor College of Medicine, Department of Pediatrics, Houston, TX, USA
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16
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Azhar A, Khan MS, Swaminathan A, Naseem A, Chatterjee S, Jairajpuri MA. Oxidized antithrombin is a dual inhibitor of coagulation and angiogenesis: Importance of low heparin affinity. Int J Biol Macromol 2016; 82:541-50. [DOI: 10.1016/j.ijbiomac.2015.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 01/09/2023]
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17
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Flengsrud R, Antonsen SG. The binding of pentapeptides to biological and synthetic high affinity heparin. Bioorg Med Chem Lett 2015. [PMID: 26216842 DOI: 10.1016/j.bmcl.2015.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Pentapeptides have been shown to bind the synthetic heparin fondaparinux (Arixtra) as well the biological heparins dalteparin (Fragmin) and salmon heparin. In contrast to heparin binding consensus sequences, the pentapeptides are acidic or neutral, with no arginine or histidine residue. The peptides showed an effect on in vitro heparin anti-factor X activity with a reduction of fondaparinux activity by 65-95%. Heparin binding was further studied by using peptide solid phase chromatography and NMR analysis.
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Affiliation(s)
- Ragnar Flengsrud
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), N-1432 Ås, Norway.
| | - Simen Gjelseth Antonsen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), N-1432 Ås, Norway
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18
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Yadav VK, Mandal RS, Puniya BL, Kumar R, Dey S, Singh S, Yadav S. Structural and binding studies of SAP-1 protein with heparin. Chem Biol Drug Des 2015; 85:404-10. [PMID: 25147059 DOI: 10.1111/cbdd.12420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 07/08/2014] [Accepted: 08/13/2014] [Indexed: 02/05/2023]
Abstract
SAP-1 is a low molecular weight cysteine protease inhibitor (CPI) which belongs to type-2 cystatins family. SAP-1 protein purified from human seminal plasma (HuSP) has been shown to inhibit cysteine and serine proteases and exhibit interesting biological properties, including high temperature and pH stability. Heparin is a naturally occurring glycosaminoglycan (with varied chain length) which interacts with a number of proteins and regulates multiple steps in different biological processes. As an anticoagulant, heparin enhances inhibition of thrombin by the serpin antithrombin III. Therefore, we have employed surface plasmon resonance (SPR) to improve our understanding of the binding interaction between heparin and SAP-1 (protease inhibitor). SPR data suggest that SAP-1 binds to heparin with a significant affinity (KD = 158 nm). SPR solution competition studies using heparin oligosaccharides showed that the binding of SAP-1 to heparin is dependent on chain length. Large oligosaccharides show strong binding affinity for SAP-1. Further to get insight into the structural aspect of interactions between SAP-1 and heparin, we used modelled structure of the SAP-1 and docked with heparin and heparin-derived polysaccharides. The results suggest that a positively charged residue lysine plays important role in these interactions. Such information should improve our understanding of how heparin, present in the reproductive tract, regulates cystatins activity.
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Affiliation(s)
- Vikash K Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
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19
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Lee TW, Yang ASP, Brittain T, Birch NP. An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: application to neuroserpin reveals regions that differentially regulate inhibitory activity. Proteins 2015; 83:135-52. [PMID: 25363759 DOI: 10.1002/prot.24711] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 10/22/2014] [Accepted: 10/27/2014] [Indexed: 01/12/2023]
Abstract
The analysis of sequence conservation is commonly used to predict functionally important sites in proteins. We have developed an approach that first identifies highly conserved sites in a set of orthologous sequences using a weighted substitution-matrix-based conservation score and then filters these conserved sites based on the pattern of conservation present in a wider alignment of sequences from the same family and structural information to identify surface-exposed sites. This allows us to detect specific functional sites in the target protein and exclude regions that are likely to be generally important for the structure or function of the wider protein family. We applied our method to two members of the serpin family of serine protease inhibitors. We first confirmed that our method successfully detected the known heparin binding site in antithrombin while excluding residues known to be generally important in the serpin family. We next applied our sequence analysis approach to neuroserpin and used our results to guide site-directed polyalanine mutagenesis experiments. The majority of the mutant neuroserpin proteins were found to fold correctly and could still form inhibitory complexes with tissue plasminogen activator (tPA). Kinetic analysis of tPA inhibition, however, revealed altered inhibitory kinetics in several of the mutant proteins, with some mutants showing decreased association with tPA and others showing more rapid dissociation of the covalent complex. Altogether, these results confirm that our sequence analysis approach is a useful tool that can be used to guide mutagenesis experiments for the detection of specific functional sites in proteins.
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Affiliation(s)
- Tet Woo Lee
- School of Biological Sciences and Centre for Brain Research, University of Auckland, Auckland, New Zealand
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20
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Tóth L, Fekete A, Balogh G, Bereczky Z, Komáromi I. Dynamic properties of the native free antithrombin from molecular dynamics simulations: computational evidence for solvent- exposed Arg393 side chain. J Biomol Struct Dyn 2014; 33:2023-36. [PMID: 25483839 DOI: 10.1080/07391102.2014.986525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
While antithrombin (AT) has small basal inhibitory activity, it reaches its full inhibitory potential against activated blood coagulation factors, FXa, FIXa, and FIIa (thrombin), via an allosteric and/or template (bridging) mechanism by the action of heparin, heparan sulfate, or heparin-mimetic pentasaccharides (PS). From the numerous X-ray structures available for different conformational states of AT, only indirect and incomplete conclusions can be drawn on the inherently dynamic properties of AT. As a typical example, the basal inhibitory activity of AT cannot be interpreted on the basis of "non-activated" free antithrombin X-ray structures since the Arg393 side chain, playing crucial role in antithrombin-proteinase interaction, is not exposed. In order to reveal the intrinsic dynamic properties and the reason of basal inhibitory activity of antithrombin, 2 μs molecular dynamics simulations were carried out on its native free-forms. It was shown from the simulation trajectories that the reactive center loop which is functioning as "bait" for proteases, even without any biasing potential can populate conformational state in which the Arg393 side chain is solvent exposed. It is revealed from the trajectory analysis that the peptide sequences correspond to the helix D extension, and new helix P formation can be featured with especially large root-mean-square fluctuations. Mutual information analyses of the trajectory showed remarkable (generalized) correlation between those regions of antithrombin which changed their conformations as the consequence of AT-PS complex formation. This suggests that allosteric information propagation pathways are present even in the non-activated native form of AT.
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Affiliation(s)
- László Tóth
- a Faculty of Medicine, Division of Clinical Laboratory Science, Department of Laboratory Medicine , University of Debrecen , Debrecen , Hungary
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21
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Rashid Q, Abid M, Jairajpuri MA. Elucidating the specificity of non-heparin-based conformational activators of antithrombin for factor Xa inhibition. J Nat Sci Biol Med 2014; 5:36-42. [PMID: 24678194 PMCID: PMC3961949 DOI: 10.4103/0976-9668.127282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Introduction: Antithrombin, the principal inhibitor of coagulation proteases, requires allosteric activation by its physiological cofactor, heparin or heparin sulfate to achieve physiologically permissible rates. This forms the basis of heparin's use as a clinical anticoagulant. However, heparin therapy is beset with severe complications, giving rise to the need to search new non-heparin activators of antithrombin, devoid of these complications and with favorable safety profiles. Materials and Methods: We chose some representative organic compounds that have been shown to be involved in coagulation modulation by affecting antithrombin and applied a blind docking protocol to find the binding energy and interactions of the modified (sulfated) versus unmodified organic scaffolds. Results and Conclusion: Increased sulfation plays a key role in shifting the specificity of organic compounds like quercetin, diosmin, rutin, mangiferin, isomangostin, Trapezifolixanthone and benzofuran towards the heparin binding site (HBS). However, in hesperetin and tetrahydroisoquinoline, sulfation shifts the specificity away from HBS. We have further tried to elucidate changes in the binding affinity of quercetin on account of gradual increase in the number of hydroxyl groups being substituted by sulfate groups. The results show gradual increase in binding energy with increase in sulfation. A theoretical screening approach is an ideal mechanism to predict lead molecules as activators of antithrombin and in determining the specificity for antithrombin.
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Affiliation(s)
- Qudsia Rashid
- Department of Bio-Sciences, Protein Conformation and Enzymology Lab, New Delhi, India
| | - Mohammad Abid
- Department of Organic Synthesis Lab, Jamia Millia Islamia, New Delhi, India
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Rashid Q, Singh P, Abid M, Jairajpuri MA. Limitations of conventional anticoagulant therapy and the promises of non-heparin based conformational activators of antithrombin. J Thromb Thrombolysis 2012; 34:251-9. [DOI: 10.1007/s11239-012-0712-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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23
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Singh P, Singh K, Jairajpuri MA. Energetics of Hydrogen Bond Switch, Residue Burial and Cavity Analysis Reveals Molecular Basis of Improved Heparin Binding to Antithrombin. J Biomol Struct Dyn 2011; 29:339-50. [DOI: 10.1080/07391102.2011.10507389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Pol-Fachin L, Franco Becker C, Almeida Guimarães J, Verli H. Effects of glycosylation on heparin binding and antithrombin activation by heparin. Proteins 2011; 79:2735-45. [PMID: 21769943 DOI: 10.1002/prot.23102] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2010] [Revised: 05/31/2011] [Accepted: 06/07/2011] [Indexed: 11/06/2022]
Abstract
Antithrombin (AT), a serine protease inhibitor, circulates in blood in two major isoforms, α and β, which differ in their amount of glycosylation and affinity for heparin. After binding to this glycosaminoglycan, the native AT conformation, relatively inactive as a protease inhibitor, is converted to an activated form. In this process, β-AT presents the higher affinity for heparin, being suggested as the major AT glycoform inhibitor in vivo. However, either the molecular basis demonstrating the differences in heparin binding to both AT isoforms or the mechanism of its conformational activation are not fully understood. Thus, the present work evaluated the effects of glycosylation and heparin binding on AT structure, function, and dynamics. Based on the obtained data, besides the native and activated forms of AT, an intermediate state, previously proposed to exist between such conformations, was also spontaneously observed in solution. Additionally, Asn135-linked oligosaccharide caused a bending in AT-bounded heparin, moving such polysaccharide away from helix D, which supports its reduced affinity for α-AT. The obtained data supported the proposal of an atomic-level, solvent and amino acid residues accounting, putative model for the transmission of the conformational signal from heparin binding exosite to β-sheet A and the reactive center loop, also supporting the identification of differences in such transmission between the serpin glycoforms involving helix D, where the Asn135-linked oligosaccharide stands. Such intramolecular rearrangements, together with heparin dynamics over AT surface, may support an atomic-level explanation for the Asn135-linked glycan influence over heparin binding and AT activation.
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Affiliation(s)
- Laercio Pol-Fachin
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
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Singh P, Khan MS, Naseem A, Jairajpuri MA. Analysis of surface cavity in serpin family reveals potential binding sites for chemical chaperone to reduce polymerization. J Mol Model 2011; 18:1143-51. [PMID: 21681443 DOI: 10.1007/s00894-011-1110-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022]
Abstract
Serpin constitute about 10% of blood protein and are associated with mutations that results in aberrant intermolecular linkages which leads to polymer formation. Studies with short peptides have shown promise in depolymerization of serpins however a reactive center loop based peptide also makes the serpin inactive. A chemical chaperone based approach is a better option in terms of maintaining activity and retarding polymerization but not much is known about its binding and mechanism. Specific target for chemical chaperones and its effectiveness across many serpin is not known. We did an analysis of serpin cavity using CASTp and show that cavities are distributed throughout the molecule where the largest cavities are generally present in areas of major conformational change like shutter region, helix D and helix F. An analysis of different conformational states of serpins showed that this large cavity undergoes increase in size in latent and cleaved states as compared to native state. We targeted serpins with a variety of carbohydrate, methylamine and amino acid based chemical chaperones and selected those that have highest binding energy across different serpins to assess their ability to bind large cavities. The results show that carbohydrate based chemical chaperone like sorbitol, sucrose, arabitol and trehalose and amino acid based chaperones like dopamine, phenylalanine, arginine and glutamic acid are the most effective in binding serpins. Most of these chemical chaperone interacted with residues in the shutter region and the helix D arm at the C-terminal which are part of the largest cavities. We selected the carbohydrate based chemical chaperone with best binding energies and did experimental study under the condition that induce polymerization and show that indeed they were able to retard polymer formation with moderate effect on inhibition rates. However a fluorometric study with native antithrombin showed that chemical chaperone may effect the conformation of the proteins. Our study shows that chemical chaperones have the best binding affinities for the cavities around shutter region and helix D and that a cavity targeting based approach seems to be a better option for retarding polymerization in serpins, but a thorough analysis of its effect on folding, inhibition and cofactor binding is required.
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Affiliation(s)
- Poonam Singh
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia University, New-Delhi 110025, India
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Sekiya A, Okano-Kosugi H, Yamazaki CM, Koide T. Pigment epithelium-derived factor (PEDF) shares binding sites in collagen with heparin/heparan sulfate proteoglycans. J Biol Chem 2011; 286:26364-74. [PMID: 21652703 DOI: 10.1074/jbc.m111.252684] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pigment epithelium-derived factor (PEDF) is a collagen-binding protein that is abundantly distributed in various tissues, including the eye. It exhibits various biological functions, such as anti-angiogenic, neurotrophic, and neuroprotective activities. PEDF also interacts with extracellular matrix components such as collagen, heparan sulfate proteoglycans (HSPGs), and hyaluronan. The collagen-binding property has been elucidated to be important for the anti-angiogenic activity in vivo (Hosomichi, J., Yasui, N., Koide, T., Soma, K., and Morita, I. (2005) Biochem. Biophys. Res. Commun. 335, 756-761). Here, we investigated the collagen recognition mechanism by PEDF. We first narrowed down candidate PEDF-binding sequences by taking advantage of previously reported structural requirements in collagen. Subsequent searches for PEDF-binding sequences employing synthetic collagen-like peptides resulted in the identification of one of the critical binding sites for PEDF, human α1(I)(929-938) (IKGHRGFSGL). Further analysis revealed that the collagen recognition by PEDF is sequence- and conformation-specific, and the high affinity binding motif is KGXRGFXGL in the triple helix. The PEDF-binding motif significantly overlapped with the heparin/HSPG-binding motif, KGHRG(F/Y). The interaction of PEDF with collagen I was specifically competed with by heparin but not by chondroitin sulfate-C or hyaluronan. The binding sequences for PEDF and heparin/HSPG also overlapped with the covalent cross-linking sites between collagen molecules. These findings imply a functional relationship between PEDF and HSPGs during angiogenesis, and the interaction of these molecules is regulated by collagen modifications.
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Affiliation(s)
- Atsushi Sekiya
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
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27
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Khan MS, Singh P, Azhar A, Naseem A, Rashid Q, Kabir MA, Jairajpuri MA. Serpin Inhibition Mechanism: A Delicate Balance between Native Metastable State and Polymerization. JOURNAL OF AMINO ACIDS 2011; 2011:606797. [PMID: 22312466 PMCID: PMC3268027 DOI: 10.4061/2011/606797] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/07/2011] [Indexed: 12/02/2022]
Abstract
The serpins (serine proteinase inhibitors) are structurally similar but functionally diverse proteins that fold into a conserved structure and employ a unique suicide substrate-like inhibitory mechanism. Serpins play absolutely critical role in the control of proteases involved in the inflammatory, complement, coagulation and fibrinolytic pathways and are associated with many conformational diseases. Serpin's native state is a metastable state which transforms to a more stable state during its inhibitory mechanism. Serpin in the native form is in the stressed (S) conformation that undergoes a transition to a relaxed (R) conformation for the protease inhibition. During this transition the region called as reactive center loop which interacts with target proteases, inserts itself into the center of β-sheet A to form an extra strand. Serpin is delicately balanced to perform its function with many critical residues involved in maintaining metastability. However due to its typical mechanism of inhibition, naturally occurring serpin variants produces conformational instability that allows insertion of RCL of one molecule into the β-sheet A of another to form a loop-sheet linkage leading to its polymerization and aggregation. Thus understanding the molecular basis and amino acid involved in serpin polymerization mechanism is critical to devising strategies for its cure.
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Affiliation(s)
- Mohammad Sazzad Khan
- Department of Biosciences, Jamia Millia Islamia University, Jamia Nagar, New Delhi 110025, India
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Abstract
Serpins (serine protease inhibitors) have traditionally been grouped together based on structural homology. They share common structural features of primary sequence, but not all serpins require binding to cofactors in order to achieve maximal protease inhibition. In order to obtain physiologically relevant rates of inhibition of target proteases, some serpins utilize the unbranched sulfated polysaccharide chains known as glycosaminoglycans (GAGs) to enhance inhibition. These GAG-binding serpins include antithrombin (AT), heparin cofactor II (HCII), and protein C inhibitor (PCI). The GAGs heparin and heparan sulfate have been shown to bind AT, HCII, and PCI, while HCII is also able to utilize dermatan sulfate as a cofactor. Other serpins such as PAI-1, kallistatin, and α(1)-antitrypsin also interact with GAGs with different endpoints, some accelerating protease inhibition while others inhibit it. There are many serpins that bind or carry ligands that are unrelated to GAGs, which are described elsewhere in this work. For most GAG-binding serpins, binding of the GAG occurs in a conserved region of the serpin near or involving helix D, with the exception of PCI, which utilizes helix H. The binding of GAG to serpin can lead to a conformational change within the serpin, which can lead to increased or tighter binding to the protease, and can accelerate the rates of inhibition up to 10,000-fold compared to the unbound native serpin. In this chapter, we will discuss three major GAG-binding serpins with known physiological roles in modulating coagulation: AT (SERPINC1), HCII (SERPIND1), and PCI (SERPINA5). We will review methodologies implemented to study the structure of these serpins and those used to study their interactions with GAG's. We discuss novel techniques to examine the serpin-GAG interaction and finally we review the biological roles of these serpins by describing the mouse models used to study them.
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Affiliation(s)
- Chantelle M Rein
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Olson ST, Richard B, Izaguirre G, Schedin-Weiss S, Gettins PGW. Molecular mechanisms of antithrombin-heparin regulation of blood clotting proteinases. A paradigm for understanding proteinase regulation by serpin family protein proteinase inhibitors. Biochimie 2010; 92:1587-96. [PMID: 20685328 PMCID: PMC2974786 DOI: 10.1016/j.biochi.2010.05.011] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 05/18/2010] [Indexed: 11/20/2022]
Abstract
Serpin family protein proteinase inhibitors regulate the activity of serine and cysteine proteinases by a novel conformational trapping mechanism that may itself be regulated by cofactors to provide a finely-tuned time and location-dependent control of proteinase activity. The serpin, antithrombin, together with its cofactors, heparin and heparan sulfate, perform a critical anticoagulant function by preventing the activation of blood clotting proteinases except when needed at the site of a vascular injury. Here, we review the detailed molecular understanding of this regulatory mechanism that has emerged from numerous X-ray crystal structures of antithrombin and its complexes with heparin and target proteinases together with mutagenesis and functional studies of heparin-antithrombin-proteinase interactions in solution. Like other serpins, antithrombin achieves specificity for its target blood clotting proteinases by presenting recognition determinants in an exposed reactive center loop as well as in exosites outside the loop. Antithrombin reactivity is repressed in the absence of its activator because of unfavorable interactions that diminish the favorable RCL and exosite interactions with proteinases. Binding of a specific heparin or heparan sulfate pentasaccharide to antithrombin induces allosteric activating changes that mitigate the unfavorable interactions and promote template bridging of the serpin and proteinase. Antithrombin has thus evolved a sophisticated means of regulating the activity of blood clotting proteinases in a time and location-dependent manner that exploits the multiple conformational states of the serpin and their differential stabilization by glycosaminoglycan cofactors.
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Affiliation(s)
- Steven T Olson
- Center for Molecular Biology of Oral Diseases, University of Illinois at Chicago, Chicago, IL 60612, USA.
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30
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Fadda E, Woods RJ. Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects. Drug Discov Today 2010; 15:596-609. [PMID: 20594934 DOI: 10.1016/j.drudis.2010.06.001] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 04/20/2010] [Accepted: 06/01/2010] [Indexed: 11/16/2022]
Abstract
The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is particularly challenging for traditional experimental methods. Molecular simulation methods provide a basis for interpreting sparse experimental data and for independently predicting conformational and dynamic properties of glycans. Here, we summarize and analyze the issues associated with modeling carbohydrates, with a detailed discussion of four of the most recently developed carbohydrate force fields, reviewed in terms of applicability to natural glycans, carbohydrate-protein complexes and the emerging area of glycomimetic drugs. In addition, we discuss prospectives and new applications of carbohydrate modeling in drug discovery.
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Affiliation(s)
- Elisa Fadda
- School of Chemistry, National University of Ireland, Galway, Ireland
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Richard B, Swanson R, Olson ST. The signature 3-O-sulfo group of the anticoagulant heparin sequence is critical for heparin binding to antithrombin but is not required for allosteric activation. J Biol Chem 2009; 284:27054-64. [PMID: 19661062 PMCID: PMC2785635 DOI: 10.1074/jbc.m109.029892] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 08/04/2009] [Indexed: 11/06/2022] Open
Abstract
Heparin and heparan sulfate glycosaminoglycans allosterically activate the serpin, antithrombin, by binding through a specific pentasaccharide sequence containing a critical 3-O-sulfo group. To elucidate the role of the 3-O-sulfo group in the activation mechanism, we compared the effects of deleting the 3-O-sulfo group or mutating the Lys(114) binding partner of this group on antithrombin-pentasaccharide interactions by equilibrium binding and rapid kinetic analyses. Binding studies over a wide range of ionic strength and pH showed that loss of the 3-O-sulfo group caused a massive approximately 60% loss in binding energy for the antithrombin-pentasaccharide interaction due to the disruption of a cooperative network of ionic and nonionic interactions. Despite this affinity loss, the 3-O-desulfonated pentasaccharide retained the ability to induce tryptophan fluorescence changes and to enhance factor Xa reactivity in antithrombin, indicative of normal conformational activation. Rapid kinetic studies showed that loss of the 3-O-sulfo group affected both the ability of the pentasaccharide to recognize native antithrombin and its ability to preferentially bind and stabilize activated antithrombin. By contrast, mutation of Lys(114) solely affected the preferential interaction of the pentasaccharide with activated antithrombin. These findings demonstrate that the 3-O-sulfo group functions as a key determinant of heparin pentasaccharide activation of antithrombin both by contributing to the Lys(114)-independent recognition of native antithrombin and by triggering a Lys(114)-dependent induced fit interaction with activated antithrombin that locks the serpin in the activated state.
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Affiliation(s)
- Benjamin Richard
- From the Center for Molecular Biology of Oral Diseases, University of Illinois at Chicago, Chicago, Illinois 60612
| | - Richard Swanson
- From the Center for Molecular Biology of Oral Diseases, University of Illinois at Chicago, Chicago, Illinois 60612
| | - Steven T. Olson
- From the Center for Molecular Biology of Oral Diseases, University of Illinois at Chicago, Chicago, Illinois 60612
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32
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Lindahl U, Li JP. Interactions between heparan sulfate and proteins-design and functional implications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 276:105-59. [PMID: 19584012 DOI: 10.1016/s1937-6448(09)76003-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Heparan sulfate (HS) proteoglycans at cell surfaces and in the extracellular matrix of most animal tissues are essential in development and homeostasis, and variously implicated in disease processes. Functions of HS polysaccharide chains depend on ionic interactions with a variety of proteins including growth factors and their receptors. Negatively charged sulfate and carboxylate groups are arranged in various types of domains, generated through strictly regulated biosynthetic reactions and with enormous potential for structural variability. The level of specificity of HS-protein interactions is assessed through binding experiments in vitro using saccharides of defined composition, signaling assays in cell culture, and targeted disruption of genes for biosynthetic enzymes followed by phenotype analysis. While some protein ligands appear to require strictly defined HS structure, others bind to variable saccharide domains without any apparent dependence on distinct saccharide sequence. These findings raise intriguing questions concerning the functional significance of regulation in HS biosynthesis.
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Affiliation(s)
- Ulf Lindahl
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Uppsala, Sweden
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Gandhi NS, Mancera RL. The Structure of Glycosaminoglycans and their Interactions with Proteins. Chem Biol Drug Des 2008; 72:455-82. [DOI: 10.1111/j.1747-0285.2008.00741.x] [Citation(s) in RCA: 703] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hjelm R, Schedin-Weiss S. High affinity interaction between a synthetic, highly negatively charged pentasaccharide and alpha- or beta-antithrombin is predominantly due to nonionic interactions. Biochemistry 2007; 46:3378-84. [PMID: 17323934 DOI: 10.1021/bi6024929] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Idraparinux is a synthetic O-sulfated, O-methylated pentasaccharide that binds tightly to antithrombin (AT) and thereby specifically and efficiently induces the inactivation of the procoagulant protease, factor Xa. In this study, the affinity and kinetics of the interaction of this high-affinity pentasaccharide with alpha- and beta-AT were compared with those of a synthetic pentasaccharide comprising the natural AT-binding sequence of heparin. Dissociation equilibrium constants, Kd, for the interactions of Idraparinux with alpha- and beta-AT were approximately 0.4 and 0.1 nM, respectively, corresponding to an over 100-fold enhancement in affinity compared with that of the normal pentasaccharide. This large enhancement was due to a approximately 400-fold tighter conformationally activated complex formed in the second binding step, whereas the encounter complex established in the first step was approximately 4-fold weaker. The high-affinity and normal pentasaccharides both made a total of four ionic interactions with AT, although the high-affinity saccharide only established one ionic interaction in the first binding step and was compensated by three in the second step, whereas the normal pentasaccharide established two ionic interactions in each step. In contrast, the affinities of the nonionic interactions (Kd approximately 450 and 90 nM for the binding to alpha- and beta-AT, respectively) were considerably higher than those for the normal pentasaccharide and the highest of all AT-saccharide interactions reported so far. The nonionic contribution to the total free energy of the high-affinity pentasaccharide binding to AT thus amounted to approximately 70%. These findings show that nonionic interactions can play a predominant role in the binding of highly charged saccharide ligands to proteins and can be successfully exploited in the design of such biologically active ligands.
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Affiliation(s)
- Rebecka Hjelm
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Center, Box 582, SE-751 23 Uppsala, Sweden
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Chung K, Kim J, Cho BK, Ko BJ, Hwang BY, Kim BG. How does dextran sulfate prevent heat induced aggregation of protein?: The mechanism and its limitation as aggregation inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:249-57. [PMID: 17223396 DOI: 10.1016/j.bbapap.2006.11.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 11/02/2006] [Accepted: 11/30/2006] [Indexed: 10/23/2022]
Abstract
The effect of dextran sulfate on protein aggregation was investigated to provide the clues of its biochemical mechanism. The interaction between dextran sulfate and BSA varied with the pH values of the solution, which led to the different extent of aggregation prevention by dextran sulfate. Light scattering data with thermal scan showed that dextran sulfate suppressed BSA aggregation at pH 5.1 and pH 6.2, while it had no effect at pH 7.5. Isothermal titration calorimetric analysis suggested that the pH dependency of the role of dextran sulfate on BSA aggregation would be related to the difference in the mode of BSA-dextran sulfate complex formation. Isothermal titration calorimetric analysis at pH 6.2 indicated that dextran sulfate did not bind to native BSA at this pH, but interacted with partially unfolded BSA. While stabilizing native form of protein by the complex formation has been suggested as the suitable mechanism of preventing aggregation, our observation of conformational changes by circular dichroism spectroscopy showed that strong electrostatic interaction between dextran sulfate and BSA rather facilitated the denaturation of BSA. Combining the data from isothermal titration calorimetry, circular dichroism, and dynamic light scattering, we found that the complex formation of the intermediate state of denatured BSA with dextran sulfate is a prerequisite to suppress the aggregation by preventing further oligomerization/aggregation process of denatured protein.
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Affiliation(s)
- Kwanghun Chung
- School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, Korea
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Cruz RGCD, Jairajpuri MA, Bock SC. Disruption of a Tight Cluster Surrounding Tyrosine 131 in the Native Conformation of Antithrombin III Activates It for Factor Xa Inhibition. J Biol Chem 2006. [DOI: 10.1016/s0021-9258(19)84080-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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dela Cruz RGC, Jairajpuri MA, Bock SC. Disruption of a tight cluster surrounding tyrosine 131 in the native conformation of antithrombin III activates it for factor Xa inhibition. J Biol Chem 2006; 281:31668-76. [PMID: 16940049 DOI: 10.1074/jbc.m604826200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The native conformation of antithrombin III (ATIII) is a poor inhibitor of its coagulation pathway target enzymes because of the partial insertion of its reactive center loop (RCL) in its central A beta-sheet. This study focused on tyrosine 131, which is located at the helix D-sheet A interface, adjacent to the ATIII pentasaccharide and heparin cofactor-binding sites and some 17A away from the RCL insertion. Crystallographic structures show that the Tyr(131) ring is buried in native ATIII and then becomes exposed when pentasaccharide binds to the inhibitor and activates it. This change suggested that Tyr(131) might serve as a switch for ATIII conformational activation. The hypothesis is supported by results from this study, which progressively removed atoms from the Tyr(131) side chain. Rates of heparin-independent Y131L and Y131A factor Xa inhibition were 25 and 29 times faster than for the control and Y131F, suggesting that Tyr(131) ring interactions with neighboring helix D and strand 2A residues shift the uncatalyzed native-to-activated conformational equilibrium toward the RCL-inserted state. Thermal denaturation experiments showed Y131A and Y131L were less stable than the control and Y131F, implying an increased tendency toward A-sheet mobility in these genetically activated molecules. Thus, the tight Tyr(131)-Asn(127)-Leu(130)-Leu(140)-Ser(142) cluster at the helix D-strand 2A interface of native antithrombin contributes significantly to the stability of the ground state conformation, and tyrosine 131 serves as a heparin-responsive molecular switch during the allosteric activation of ATIII anticoagulant activity.
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Van de Water N, Tan T, Ashton F, O'Grady A, Day T, Browett P, Ockelford P, Harper P. Mutations within the protein Z-dependent protease inhibitor gene are associated with venous thromboembolic disease: a new form of thrombophilia. Br J Haematol 2004; 127:190-4. [PMID: 15461625 DOI: 10.1111/j.1365-2141.2004.05189.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein Z-dependent protease inhibitor (ZPI) is a serpin that inhibits the activated coagulation factors X and XI. The precise physiological significance of ZPI in the control of haemostasis is unknown although a deficiency of ZPI may be predicted to alter this balance. The coding region of the ZPI gene was screened for mutations using denaturing high-performance liquid chromatography. 16 mutations/polymorphisms within the coding region of ZPI were identified including two mutations, which generated stop codons at residues R67 and W303. We observed nonsense mutations within the ZPI gene in 4.4% of thrombosis patients (n = 250) compared with 0.8% of controls (n = 250). The difference in distribution of stop codon mutations between thrombosis patients and controls was significant (P = 0.02) with an odds ratio of 5.7 (95% confidence interval, 1.25-26.0). Our results suggest an association between ZPI deficiency and venous thrombosis and we propose that ZPI deficiency is potentially a new form of thrombophilia.
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Cai S, Dufner-Beattie JL, Prestwich GD. A selective protein sensor for heparin detection. Anal Biochem 2004; 326:33-41. [PMID: 14769333 DOI: 10.1016/j.ab.2003.11.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2003] [Indexed: 11/26/2022]
Abstract
No clinical assays for the direct detection of heparin in blood exist. To create a heparin sensor, the hyaluronan (HA)-binding domain (HABD) of a protein that binds heparin and HA was engineered. GST fusion proteins containing one to three HABD modules were cloned, expressed, and purified. The affinities of each construct for heparin and for HA were determined by a competitive enzyme-linked immunosorbent assay using immobilized HA or heparin. Each of the constructs showed modest affinity for immobilized HA. However, heparin was 100-fold more potent than HA as a competing ligand. With immobilized heparin, affinity increased as the HABD copy number increased. The three-copy construct, GST-HB3, detected unfractionated free heparin (UFH) as low as 39ng/ml (equivalent to approximately 0.1U/ml) with a signal-to-noise ratio of 5.6. GST-HB3 also showed 100-fold selectivity for heparin in preference to other glycosaminoglycans. The plot of logKd vs log [Na+] showed 2.5 ionic interactions per heparin-HB3 interaction. GST-HB3 showed a linear detection of both UFH (15kDa) and low-molecular-weight heparin (LMWH; 6kDa) added to human plasma. For UFH, the range examined was 78 to over 2000ng/ml (equivalent to 0.2 to 5.0U/ml). For LMWH, the useful range was 312 to over 2000ng/ml. The coefficient of variance for the assay was < 9% for six serial heparin dilutions and <12% for three plasma samples. In clinical use, GST-HB3 could accurately measure therapeutic heparin levels in plasma (0.2 to 2U/ml).
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Affiliation(s)
- Shenshen Cai
- Department of Medicinal Chemistry and Center for Cell Signaling, The University of Utah, 419 Wakara Way, Suite 205, Salt Lake City, UT 84108-1257, USA
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Steiner M, Steiner B, Rolfs A, Wangnick M, Burstein C, Freund M, Schuff-Werner P. Antithrombin gene mutation 5356-5364*delCTT with type I deficiency and early-onset thrombophilia and a brief review of the antithrombin alpha-helix D molecular pathology. Ann Hematol 2004; 84:56-8. [PMID: 15309521 DOI: 10.1007/s00277-004-0906-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 06/02/2004] [Indexed: 10/26/2022]
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Abstract
Heparin is a major anticoagulant with activity mediated primarily through its interaction with antithrombin (AT). Heparan sulfate (HS), structurally related to heparin, binds a wide range of proteins of different functionality, taking part in various physiological and pathological processes. The heparin-AT complex, the most well understood facet of anticoagulation, serves as a prototypical example of the important role of heparin/HS in vascular biology. Extensive studies have identified common structural features in heparin/HS-binding sites of proteins. These include the elucidation of consensus sequences in proteins, patterns of clusters of basic and nonbasic residues, and common spatial arrangements of basic amino acids in the heparin-binding sites. Although these studies have provided valuable information, heparin/HS-binding proteins differ widely in structure. The prediction of heparin/HS-binding proteins from sequence information is not currently possible, and elucidation of protein-binding sites requires the individual study of each glycosaminoglycan-protein complex. Thus, x-ray crystallography and site-directed mutagenesis experiments are among the most powerful tools, providing accurate structural information, facilitating the characterization of heparin-protein complexes. Heparin and structurally related heparan sulfate bind a large number of proteins, taking part in a wide range of biological processes, particularly ones involved in vascular biology. Heparin-binding domains share certain common structural features, but there is no absolute dependency on specific sequences or protein folds.
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Affiliation(s)
- Eva M Muñoz
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Izaguirre G, Zhang W, Swanson R, Bedsted T, Olson ST. Localization of an Antithrombin Exosite That Promotes Rapid Inhibition of Factors Xa and IXa Dependent on Heparin Activation of the Serpin. J Biol Chem 2003; 278:51433-40. [PMID: 14532267 DOI: 10.1074/jbc.m309266200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We have previously shown that exosites in antithrombin outside the P6-P3' reactive loop region become available upon heparin activation to promote rapid inhibition of the target proteases, factor Xa and factor IXa. To identify these exosites, we prepared six antithrombin-alpha 1-proteinase inhibitor chimeras in which antithrombin residues 224-286 and 310-322 that circumscribe a region surrounding the reactive loop on the inhibitor surface were replaced in 10-16-residue segments with the homologous segments of alpha1-proteinase inhibitor. All chimeras bound heparin with a high affinity similar to wild-type, underwent heparin-induced fluorescence changes indicative of normal conformational activation, and were able to form SDS-stable complexes with thrombin, factor Xa, and factor IXa and inhibit these proteases with stoichiometries minimally altered from those of wild-type antithrombin. With only one exception, conformational activation of the chimeras with a heparin pentasaccharide resulted in normal approximately 100-300-fold enhancements in reactivity with factor Xa and factor IXa. The exception was the chimera in which residues 246-258 were replaced, corresponding to strand 3 of beta-sheet C, which showed little or no enhancement of its reactivity with these proteases following pentasaccharide activation. By contrast, all chimeras including the strand 3C chimera showed essentially wild-type reactivities with thrombin after pentasaccharide activation as well as normal full-length heparin enhancements in reactivity with all proteases due to heparin bridging. These findings suggest that antithrombin exosites responsible for enhancing the rates of factor Xa and factor IXa inhibition in the conformationally activated inhibitor lie in strand 3 of beta-sheet C of the serpin.
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Affiliation(s)
- Gonzalo Izaguirre
- Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois 60612, USA
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Abstract
Clinically used anticoagulants are inhibitors of enzymes involved in the coagulation pathway, primarily thrombin and factor Xa. These agents can be either direct or indirect inhibitors of clotting enzymes. Heparin-based anticoagulants are indirect inhibitors that enhance the proteinase inhibitory activity of a natural anticoagulant, antithrombin. Despite its phenomenal success, current anticoagulation therapy suffers from the risk of serious bleeding. The need for safer and more effective antithrombotic agents clearly exists. The past decade has seen enormous effort directed toward discovering and/or designing new molecules with anticoagulant activity. These new molecules can be classified into (a). antithrombin and its mutants, (b). natural polysaccharides, (c). synthetic modified heparins and heparin-mimics, (d). synthetic oligosaccharides, and (e). synthetic non-sugar antithrombin activators. This review focuses on these efforts in designing or discovering new molecules that act through the antithrombin pathway of anticoagulation.
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Affiliation(s)
- Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, USA.
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