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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] [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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2
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Tkachuk VA, Hordiyenko OV, Omelchenko IV, Medviediev VV, Arrault A. Methyl esters of 2-(N-hydroxycarbamimidoyl)benzoyl-substituted α-amino acids as promising building blocks in peptidomimetic synthesis: a comparative study. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2293-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Priestley ES, Cheney DL, DeLucca I, Wei A, Luettgen JM, Rendina AR, Wong PC, Wexler RR. Structure-Based Design of Macrocyclic Coagulation Factor VIIa Inhibitors. J Med Chem 2015; 58:6225-36. [PMID: 26151189 DOI: 10.1021/acs.jmedchem.5b00788] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
On the basis of a crystal structure of a phenylpyrrolidine lead and subsequent molecular modeling results, we designed and synthesized a novel series of macrocyclic FVIIa inhibitors. The optimal 16-membered macrocycle was 60-fold more potent than an acyclic analog. Further potency optimization by incorporation of P1' alkyl sulfone and P2 methyl groups provided a macrocycle with TF/FVIIa Ki = 1.6 nM, excellent selectivity against a panel of seven serine proteases, and FVII-deficient prothrombin time EC2x = 1.2 μM. Discovery of this potent, selective macrocyclic scaffold opens new possibilities for the development of orally bioavailable FVIIa inhibitors.
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Örtqvist P, Gising J, Ehrenberg AE, Vema A, Borg A, Karlén A, Larhed M, Danielson UH, Sandström A. Discovery of achiral inhibitors of the hepatitis C virus NS3 protease based on 2(1H)-pyrazinones. Bioorg Med Chem 2010; 18:6512-25. [DOI: 10.1016/j.bmc.2010.06.101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 06/21/2010] [Accepted: 06/29/2010] [Indexed: 10/19/2022]
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5
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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] [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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6
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Kotian PL, Krishnan R, Rowland S, El-Kattan Y, Saini SK, Upshaw R, Bantia S, Arnold S, Sudhakar Babu Y, Chand P. Design, parallel synthesis, and crystal structures of biphenyl antithrombotics as selective inhibitors of tissue factor FVIIa complex. Part 1: Exploration of S2 pocket pharmacophores. Bioorg Med Chem 2009; 17:3934-58. [DOI: 10.1016/j.bmc.2009.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 04/06/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
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7
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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] [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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8
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Abstract
The formation of the proteolytic complex composed of the serine protease Factor VIIa and the cell-associated glycoprotein tissue factor (FVIIa/TF) initiates a cascade of amplified zymogen activation reactions leading to thrombus formation. The critical role of the coagulation cascade in pathological thrombosis has been the basis for significant efforts to design selective inhibitors of the protease components as new anticoagulant alternatives for the treatment of thrombotic diseases. However, for the new generation of anticoagulant drugs in development that primarily target protease complexes distal from FVIIa/TF, the differential between efficacy and safety as defined by bleeding is unresolved. Targeting the FVIIa/TF complex has several theoretical advantages that exploit the amplified nature of the coagulation cascade. However, progress on the development of clinical-stage FVIIa/TF-based anticoagulants has not been as successful to date. This review summarizes recent efforts in the discovery of synthetic inhibitors of FVIIa/TF.
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Affiliation(s)
- Rebecca A Shirk
- Department of Cardiovascular and Metabolic Diseases Research, Wyeth Research, P.O. Box 42528, Philadelphia, PA 19101-2528, USA.
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Kamoune L, De Borggraeve WM, Gielens C, Voet A, Robeyns K, De Maeyer M, Van Meervelt L, Compernolle F, Hoornaert G. Design, Synthesis and Evaluation of Serine Protease Inhibitor Analogues. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Robins LI, Dixon SM, Wilson DK, Kurth MJ. On-bead combinatorial techniques for the identification of selective aldose reductase inhibitors. Bioorg Med Chem 2006; 14:7728-35. [PMID: 16931029 DOI: 10.1016/j.bmc.2006.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Revised: 08/04/2006] [Accepted: 08/08/2006] [Indexed: 10/24/2022]
Abstract
Aldose reductase (AKR1B1; ALR2; E.C. 1.1.1.21) is an NADPH-dependent carbonyl reductase which has long been associated with complications resulting from the elevated blood glucose often found in diabetics. The development of effective inhibitors has been plagued by lack of specificity which has led to side effects in clinical trials. To address this problem, a library of bead-immobilized compounds was screened against fluorescently labeled aldose reductase in the presence of fluorescently labeled aldehyde reductase, a non-target enzyme, to identify compounds which were aldose reductase specific. Picked beads were decoded via novel bifunctional bead mass spec-based techniques and kinetic analysis of the ten inhibitors which were identified using this protocol yielded IC50 values in the micromolar range. Most importantly, all of these compounds showed a preference for aldose reductase with selectivities as high as approximately 7500-fold. The most potent of these exhibited uncompetitive inhibition versus the carbonyl-containing substrate D/L-glyceraldehyde with a Ki of 1.16 microM.
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Affiliation(s)
- Lori I Robins
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
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Kohrt JT, Filipski KJ, Cody WL, Cai C, Dudley DA, Van Huis CA, Willardsen JA, Narasimhan LS, Zhang E, Rapundalo ST, Saiya-Cork K, Leadley RJ, Edmunds JJ. The discovery of fluoropyridine-based inhibitors of the factor VIIa/TF complex—Part 2. Bioorg Med Chem Lett 2006; 16:1060-4. [PMID: 16289811 DOI: 10.1016/j.bmcl.2005.10.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 10/21/2005] [Accepted: 10/21/2005] [Indexed: 10/25/2022]
Abstract
The activated factor VII/tissue factor complex (FVIIa/TF) is known to play a key role in the formation of blood clots. Inhibition of this complex may lead to new antithrombotic drugs. A fluoropyridine-based series of FVIIa/TF inhibitors was discovered which utilized a diisopropylamino group for binding in the S2 and S3 binding pockets of the active site of the enzyme complex. In this series, an enhancement in binding affinity was observed by substitution at the 5-position of the hydroxybenzoic acid sidechain. An X-ray crystal structure indicates that amides at this position may increase inhibitor binding affinity through interactions with the S1'/S2' pocket.
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Affiliation(s)
- Jeffrey T Kohrt
- Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.
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12
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Kohrt JT, Filipski KJ, Cody WL, Cai C, Dudley DA, Van Huis CA, Willardsen JA, Rapundalo ST, Saiya-Cork K, Leadley RJ, Narasimhan L, Zhang E, Whitlow M, Adler M, McLean K, Chou YL, McKnight C, Arnaiz DO, Shaw KJ, Light DR, Edmunds JJ. The discovery of fluoropyridine-based inhibitors of the Factor VIIa/TF complex. Bioorg Med Chem Lett 2005; 15:4752-6. [PMID: 16125385 DOI: 10.1016/j.bmcl.2005.07.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 07/25/2005] [Accepted: 07/25/2005] [Indexed: 11/29/2022]
Abstract
The activated Factor VII/tissue factor complex (FVIIa/TF) plays a key role in the formation of blood clots. Inhibition of this complex may lead to new antithrombotic drugs. An X-ray crystal structure of a fluoropyridine-based FVIIa/TF inhibitor bound in the active site of the enzyme complex suggested that incorporation of substitution at the 5-position of the hydroxybenzoic acid side chain could lead to the formation of more potent inhibitors through interactions with the S1'/S2' pocket.
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Affiliation(s)
- Jeffrey T Kohrt
- Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.
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