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Luchini A, Tidemand FG, Araya-Secchi R, Campana M, Cárdenas M, Arleth L. Structural model of tissue factor (TF) and TF-factor VIIa complex in a lipid membrane: A combined experimental and computational study. J Colloid Interface Sci 2022; 623:294-305. [PMID: 35594588 DOI: 10.1016/j.jcis.2022.04.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/11/2022] [Accepted: 04/25/2022] [Indexed: 10/18/2022]
Abstract
Tissue factor (TF) is a membrane protein involved in blood coagulation. TF initiates a cascade of proteolytic reactions, ultimately leading to the formation of a blood clot. The first reaction consists of the binding of the coagulation factor VII and its conversion to the activated form, FVIIa. Here, we combined experimental, i.e. quartz crystal microbalance with dissipation monitoring and neutron reflectometry, and computational, i.e. molecular dynamics (MD) simulation, methods to derive a complete structural model of TF and TF/FVIIa complex in a lipid bilayer. This model shows that the TF transmembrane domain (TMD), and the flexible linker connecting the TMD to the extracellular domain (ECD), define the location of the ECD on the membrane surface. The average orientation of the ECD relative to the bilayer surface is slightly tilted towards the lipid headgroups, a conformation that we suggest is promoted by phosphatidylserine lipids, and favours the binding of FVIIa. On the other hand, the formation of the TF/FVIIa complex induces minor changes in the TF structure, and reduces the conformational freedom of both TF and FVIIA. Altogether we describe the protein-protein and protein-lipid interactions favouring blood coagulation, but also instrumental to the development of new drugs.
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Affiliation(s)
- Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
| | | | - Raul Araya-Secchi
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Mario Campana
- ISIS-STFC, Rutherford Appleton Laboratory, Chilton, Oxon OX11 0QX, United Kingdom
| | - Marité Cárdenas
- Biofilms Research Center for Biointerfaces and Department of Biomedical Science, Faculty of Health and Society, Malmö University, Per Albin Hanssons Väg 35, 21432 Malmö, Sweden
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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Yang J, Su G, Ren Y, Chen Y. Synthesis and in vitro anticoagulant activity of 3-(1H-imidazo[4,5-c]pyridin-2-yl)-1,5-diarylpyridin-2(1H)-one derivatives. Res Chem Intermed 2015. [DOI: 10.1007/s11164-015-1927-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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3
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Abstract
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.
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Affiliation(s)
- Akira R Kinjo
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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4
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Shiraishi T, Kadono S, Haramura M, Kodama H, Ono Y, Iikura H, Esaki T, Koga T, Hattori K, Watanabe Y, Sakamoto A, Yoshihashi K, Kitazawa T, Esaki K, Ohta M, Sato H, Kozono T. Design and synthesis of peptidomimetic factor VIIa inhibitors. Chem Pharm Bull (Tokyo) 2010; 58:38-44. [PMID: 20045964 DOI: 10.1248/cpb.58.38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is regarded as a promising target for developing new anticoagulant drugs. In previous reports, we described a S3 subsite found in the X-ray crystal structure of compound 2 that bound to FVIIa/soluble tissue factor (sTF). Based on the X-ray crystal structure information and with the aim of improving the inhibition activity for FVIIa/TF and selectivity against other serine proteases, we synthesized derivatives by introducing substituents at position 5 of the indole ring of compound 2. Among them, compound 16 showed high selectivity against other serine proteases. Contrary to our expectations, compound 16 did not occupy the S3-subsite; X-ray structure analysis revealed that compound 16 improved selectivity by forming hydrogen bonds with Gln217, Thr99 and Asn100.
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Affiliation(s)
- Takuya Shiraishi
- Fuji Gotemba Research Laboratories, Chugai Pharmaceutical Co., Ltd., Japan.
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5
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Ayral E, Gloanec P, Bergé G, de Nanteuil G, Mennecier P, Rupin A, Verbeuren TJ, Fulcrand P, Martinez J, Hernandez J. Design, synthesis, and biological evaluation of 1,5-benzothiazepine-4-one derivatives targeting factor VIIa/tissue factor. Bioorg Med Chem Lett 2009; 19:1386-91. [DOI: 10.1016/j.bmcl.2009.01.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 01/13/2009] [Accepted: 01/14/2009] [Indexed: 11/18/2022]
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Shiraishi T, Kadono S, Haramura M, Kodama H, Ono Y, Iikura H, Esaki T, Koga T, Hattori K, Watanabe Y, Sakamoto A, Yoshihashi K, Kitazawa T, Esaki K, Ohta M, Sato H, Kozono T. Factor VIIa inhibitors: Target hopping in the serine protease family using X-ray structure determination. Bioorg Med Chem Lett 2008; 18:4533-7. [DOI: 10.1016/j.bmcl.2008.07.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 07/09/2008] [Accepted: 07/11/2008] [Indexed: 10/21/2022]
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7
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Nieman MT, Pagan-Ramos E, Warnock M, Krijanovski Y, Hasan AAK, Schmaier AH. Mapping the interaction of bradykinin 1-5 with the exodomain of human protease activated receptor 4. FEBS Lett 2005; 579:25-9. [PMID: 15620686 DOI: 10.1016/j.febslet.2004.11.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Revised: 11/01/2004] [Accepted: 11/04/2004] [Indexed: 11/29/2022]
Abstract
The angiotensin converting enzyme breakdown product of bradykinin, bradykinin 1-5 (RPPGF), inhibits thrombin-induced human or mouse platelet aggregation. RPPGF binds to the exodomain of human protease-activated receptor 1 (PAR1). Studies determined if RPPGF also binds to the exodomain of human PAR4. RPPGF binds to a peptide of the thrombin cleavage site on PAR4. Recombinant wild-type and mutated exodomain of human PAR4 was prepared. The N-terminal arginine on RPPGF binds to the P2 position or proline46 on PAR4 to block thrombin cleavage. These data indicate that RPPGF influences thrombin activity by binding to the thrombin cleavage site on both PAR4 and PAR1.
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Affiliation(s)
- Marvin T Nieman
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-0640, USA
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Kadono S, Sakamoto A, Kikuchi Y, Oh-Eda M, Yabuta N, Koga T, Hattori K, Shiraishi T, Haramura M, Kodama H, Ono Y, Esaki T, Sato H, Watanabe Y, Itoh S, Ohta M, Kozono T. Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:169-73. [PMID: 16510984 PMCID: PMC1952254 DOI: 10.1107/s1744309105000047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2004] [Accepted: 01/03/2005] [Indexed: 11/10/2022]
Abstract
The crystal structure of human factor VIIa/soluble tissue factor (FVIIa/sTF) in complex with a highly selective peptide-mimetic FVIIa inhibitor which shows 1670-fold selectivity against thrombin inhibition has been solved at 2.6 A resolution. The inhibitor is bound to FVIIa/sTF at the S1, S2 and S3 sites and at the additional S1 subsite. Two charged groups, the amidino group in P2 and the carboxylate group in P4, form ionic interactions with Asp60 and Lys192 of FVIIa, respectively. Structural comparisons between factor VIIa and thrombin show that thrombin has oppositely charged residues, Lys60F and Glu192, in the S2 site and the S1 subsites, respectively. These data suggest that the utilization of the differences of charge distribution in the S2 site and the S1 subsites between FVIIa and thrombin is critical for achieving high selectivity against thrombin inhibition. These results will provide valuable information for the structure-based drug design of specific inhibitors for FVIIa/TF.
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Affiliation(s)
- Shojiro Kadono
- Fuji Gotemba Research Laboratories, Chugai Pharmaceutical Co. Ltd, 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan.
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9
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Kadono S, Sakamoto A, Kikuchi Y, Oh-eda M, Yabuta N, Yoshihashi K, Kitazawa T, Suzuki T, Koga T, Hattori K, Shiraishi T, Haramura M, Kodama H, Ono Y, Esaki T, Sato H, Watanabe Y, Itoh S, Ohta M, Kozono T. Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor. Biochem Biophys Res Commun 2005; 327:589-96. [DOI: 10.1016/j.bbrc.2004.12.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Indexed: 10/26/2022]
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10
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Kadono S, Sakamoto A, Kikuchi Y, Oh-Eda M, Yabuta N, Yoshihashi K, Kitazawa T, Suzuki T, Koga T, Hattori K, Shiraishi T, Haramura M, Kodama H, Ono Y, Esaki T, Sato H, Watanabe Y, Itoh S, Ohta M, Kozono T. Novel interactions of large P3 moiety and small P4 moiety in the binding of the peptide mimetic factor VIIa inhibitor. Biochem Biophys Res Commun 2005; 326:859-65. [PMID: 15607748 DOI: 10.1016/j.bbrc.2004.11.108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Indexed: 11/19/2022]
Abstract
Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is seen as a promising target for developing new anticoagulant drugs. A novel peptide mimetic factor VIIa inhibitor, ethylsulfonamide-d-biphenylalanine-Gln-p-aminobenzamidine, shows 100-fold selectivity against thrombin in spite of its large P3 moiety, unlike previously reported FVIIa/TF selective inhibitors. X-ray crystal structure analysis reveals that the large P3 moiety, d-biphenylalanine, and the small P4 moiety, ethylsulfonamide, make novel interactions with the 170-loop and Lys192 of FVIIa/TF, respectively, accompanying ligand-induced conformational changes of the 170-loop, Gln217, and Lys192. Structural comparisons of FVIIa with thrombin and amino acid sequence comparisons among coagulation serine proteases suggest that these interactions play an important role in achieving selective inhibition for FVIIa/TF.
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Affiliation(s)
- Shojiro Kadono
- Fuji Gotemba Research Labs, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan.
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