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Woodward E, Duggan BM. Changes in Internal Structure and Dynamics upon Binding Stabilise the Nematode Anticoagulant NAPc2. Biomolecules 2024; 14:421. [PMID: 38672438 PMCID: PMC11048057 DOI: 10.3390/biom14040421] [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: 03/14/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Abnormal blood coagulation is a major health problem and natural anticoagulants from blood-feeding organisms have been investigated as novel therapeutics. NAPc2, a potent nematode-derived inhibitor of coagulation, has an unusual mode of action that requires coagulation factor Xa but does not inhibit it. Molecular dynamics simulations of NAPc2 and factor Xa were generated to better understand NAPc2. The simulations suggest that parts of NAPc2 become more rigid upon binding factor Xa and reveal that two highly conserved residues form an internal salt bridge that stabilises the bound conformation. Clotting time assays with mutants confirmed the utility of the salt bridge and suggested that it is a conserved mechanism for stabilising the bound conformation of secondary structure-poor protease inhibitors.
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Zhang ZL, Chen C, Qu SY, Ding Q, Xu Q. Unexpected Dynamic Binding May Rescue the Binding Affinity of Rivaroxaban in a Mutant of Coagulation Factor X. Front Mol Biosci 2022; 9:877170. [PMID: 35601826 PMCID: PMC9117642 DOI: 10.3389/fmolb.2022.877170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
A novel coagulation factor X (FX) Tyr319Cys mutation (Y99C as chymotrypsin numbering) was identified in a patient with severe bleeding. Unlike the earlier reported Y99A mutant, this mutant can bind and cleave its specific chromogenetic substrate at a normal level, suggesting an intact binding pocket. Here, using molecular dynamics simulations and MM-PBSA calculations on a FX-rivaroxaban (RIV) complex, we confirmed a much stronger binding of RIV in Y99C than in Y99A on a molecular level, which is actually the average result of multiple binding poses in dynamics. Detailed structural analyses also indicated the moderate flexibility of the 99-loop and the importance of the flexible side chain of Trp215 in the different binding poses. This case again emphasizes that binding of ligands may not only be a dynamic process but also a dynamic state, which is often neglected in drug design and screening based on static X-ray structures. In addition, the computational results somewhat confirmed our hypothesis on the activated Tyr319Cys FX (Y99C FXa) with an impaired procoagulant function to bind inhibitors of FXa and to be developed into a potential reversal agent for novel oral anticoagulants (NOAC).
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Affiliation(s)
- Zhi-Li Zhang
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Si-Ying Qu
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Qiulan Ding, ; Qin Xu,
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Qiulan Ding, ; Qin Xu,
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Østerud B, Latysheva N, Schoergenhofer C, Jilma B, Hansen JB, Snir O. A rapid, sensitive, and specific assay to measure TF activity based on chromogenic determination of thrombin generation. J Thromb Haemost 2022; 20:866-876. [PMID: 34822223 DOI: 10.1111/jth.15606] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/22/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Most tissue factor (TF) activity assays are based on measurement of factor X (FX) activation by TF in the presence of factor VII (FVII)/FVIIa. This requires long incubation, which may result in TF-independent activity of FX and inaccurate measurement of TF activity. AIM To develop a sensitive and specific TF activity assay, which does not register a non-specific TF activity, using commercial coagulation factors. METHODS Tissue factor activity was measured based on the ability of TF to accelerate the activation of FX by FVIIa in the presence of factor V (FV)/Va, prothrombin, and phospholipids. Following 4 min incubation at 37°C, TF activity was quantified in test samples of different nature by thrombin generation using a chromogenic substrate. RESULTS The TF activity assay proved high sensitivity (low fM range) and specificity, assessed by neutralization of TF activity by anti-TF antibody and the use of FVIIai. TF activity was detected in extracellular vesicles (EVs) derived from HAP1-TF+cells, while no activity was measured in EVs from HAP1-TF/KO cells. The assay was applicable for measurement of TF activity on the surface of live endothelial cells and monocytes activated in vitro, and cell lysates. Infusion of low dose lipopolysaccharide (2 ng/kg bodyweight endotoxin) caused a transient 8-fold increase (peaked at 4 h) in TF activity in EVs isolated from plasma of healthy volunteers. CONCLUSION Our assay provides a fast, sensitive, and specific measurement of TF activity. It reliably quantifies TF activity on cell surface, cell lysate, and isolated EVs. The assay can be used for laboratory and clinical research.
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Affiliation(s)
- Bjarne Østerud
- Thrombosis Research Center (TREC), Department of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Nadezhda Latysheva
- Thrombosis Research Center (TREC), Department of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | | | - Bernd Jilma
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - John-Bjarne Hansen
- Thrombosis Research Center (TREC), Department of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Omri Snir
- Thrombosis Research Center (TREC), Department of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
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Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles. Microorganisms 2019; 8:microorganisms8010059. [PMID: 31905784 PMCID: PMC7023208 DOI: 10.3390/microorganisms8010059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 11/25/2022] Open
Abstract
SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria.
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Kapoor K, McGill N, Peterson CB, Meyers HV, Blackburn MN, Baudry J. Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex. J Chem Inf Model 2016; 56:535-47. [PMID: 26848511 DOI: 10.1021/acs.jcim.5b00596] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The risk of serious bleeding is a major liability of anticoagulant drugs that are active-site competitive inhibitors targeting the Factor Xa (FXa) prothrombin (PT) binding site. The present work identifies several new classes of small molecule anticoagulants that can act as nonactive site inhibitors of the prothrombinase (PTase) complex composed of FXa and Factor Va (FVa). These new classes of anticoagulants were identified, using a novel agnostic computational approach to identify previously unrecognized binding pockets at the FXa-FVa interface. From about three million docking calculations of 281,128 compounds in a conformational ensemble of FXa heavy chains identified by molecular dynamics (MD) simulations, 97 compounds and their structural analogues were selected for experimental validation, through a series of inhibition assays. The compound selection was based on their predicted binding affinities to FXa and their ability to successfully bind to multiple protein conformations while showing selectivity for particular binding sites at the FXa/FVa interface. From these, thirty-one (31) compounds were experimentally identified as nonactive site inhibitors. Concentration-based assays further identified 10 compounds represented by four small-molecule families of inhibitors that achieve dose-independent partial inhibition of PTase activity in a nonactive site-dependent and self-limiting mechanism. Several compounds were identified for their ability to bind to protein conformations only seen during MD, highlighting the importance of accounting for protein flexibility in structure-based drug discovery approaches.
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Affiliation(s)
- Karan Kapoor
- UT/ORNL Program in Genome Science and Technology, Knoxville, Tennessee 37830, United States.,UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee 37830, United States
| | - Nicole McGill
- Shifa Biomedical, One Great Valley Parkway, Suite 8, Malvern, Pennsylvania 19355, United States
| | - Cynthia B Peterson
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Harold V Meyers
- Shifa Biomedical, One Great Valley Parkway, Suite 8, Malvern, Pennsylvania 19355, United States
| | - Michael N Blackburn
- Shifa Biomedical, One Great Valley Parkway, Suite 8, Malvern, Pennsylvania 19355, United States
| | - Jerome Baudry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee 37830, United States
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Abdel-Azeim S, Oliva R, Chermak E, De Cristofaro R, Cavallo L. Molecular Dynamics Characterization of Five Pathogenic Factor X Mutants Associated with Decreased Catalytic Activity. Biochemistry 2014; 53:6992-7001. [DOI: 10.1021/bi500770p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Safwat Abdel-Azeim
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department
of Sciences and Technologies, University “Parthenope” of Naples, Centro Direzionale Isola C4, 80133 Naples, Italy
| | - Edrisse Chermak
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Raimondo De Cristofaro
- Hemostasis
Research Centre, Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Rome, Italy
| | - Luigi Cavallo
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Dipartimento
di Chimica e Biologia, University of Salerno, Via Papa Giovanni Paolo II, I-84084 Fisciano, Italy
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Wang JF, Hao P, Li YX, Dai JL, Li X. Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model 2011; 18:2717-25. [PMID: 22116613 DOI: 10.1007/s00894-011-1295-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 10/24/2011] [Indexed: 11/25/2022]
Abstract
Human coagulation Factor X (FX), a member of the vitamin K-dependent serine protease family, is a crucial component of the human coagulation cascade. Activated FX (FXa) participates in forming the prothrombinase complex on activated platelets to convert prothrombin to thrombin in coagulation reactions. In the current study, 30-ns MD simulations were performed on both the open and closed states of human FXa. Root mean squares (RMS) fluctuations showed that structural fluctuations concentrated on the loop regions of FXa, and the presence of a ligand in the closed system resulted in larger fluctuations of the gating residues. The open system had a gating distance from 9.23 to 11.33 Å, i.e., significantly larger than that of the closed system (4.69-6.35 Å), which allows diversified substrates of variable size to enter. Although the solvent accessible surface areas (SASA) of FXa remained the same in both systems, the open system generally had a larger total SASA or hydrophobic SASA (or both) for residues surrounding the S4 pocket. Additionally, more hydrogen bonds were formed in the closed state than in the open state of FXa, which is believed to play a significant role in maintaining the closed confirmation of the aryl-binding site. Based on the results of MD simulations, we propose that an induced-fit mechanism governs the functioning of human coagulation FX, which helps provide a better understanding of the interactions between FXa and its substrate, and the mechanism of the conformational changes involved in human coagulation.
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Affiliation(s)
- Jing-Fang Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China.
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Wallnoefer HG, Liedl KR, Fox T. A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease. J Chem Inf Model 2011; 51:2860-7. [DOI: 10.1021/ci200138u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hannes G. Wallnoefer
- Computational Chemistry, Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co., KG, 88397 Biberach, Germany
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
| | - Thomas Fox
- Computational Chemistry, Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co., KG, 88397 Biberach, Germany
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Wallnoefer HG, Handschuh S, Liedl KR, Fox T. Stabilizing of a globular protein by a highly complex water network: a molecular dynamics simulation study on factor Xa. J Phys Chem B 2010; 114:7405-12. [PMID: 20446703 DOI: 10.1021/jp101654g] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of water molecules is increasingly attracting attention in structural biology, and many studies have demonstrated their crucial contribution to the stability and function of proteins. Here, we present molecular dynamics studies on factor Xa (fXa) to investigate the effect of water molecules in this serine protease. fXa is a key enzyme in the blood coagulation cascade, and thus, an important target for antithrombotic drugs. A reasonable representation of the structure is crucial for an investigation at the molecular level and, thus, a prerequisite for structure-based drug design. Simulations of well-resolved fXa X-ray structures with different sets of water molecules show the importance of a well-determined water set for the simulation. We discuss implications of different water sets on the structure and dynamics of fXa.
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Affiliation(s)
- Hannes G Wallnoefer
- Computational Chemistry, Department of Lead Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach, Germany
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Fatmi MQ, Ai R, Chang CEA. Synergistic Regulation and Ligand-Induced Conformational Changes of Tryptophan Synthase. Biochemistry 2009; 48:9921-31. [DOI: 10.1021/bi901358j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Qaiser Fatmi
- Department of Chemistry, University of California, Riverside, California 92521
| | - Rizi Ai
- Department of Chemistry, University of California, Riverside, California 92521
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, California 92521
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