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Komarov IV, Bugrov VA, Cherednychenko A, Grygorenko OO. Insights into Modeling Approaches in Chemistry: Assessing Ligand-Protein Binding Thermodynamics Based on Rigid-Flexible Model Molecules. CHEM REC 2024; 24:e202300276. [PMID: 37847887 DOI: 10.1002/tcr.202300276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/29/2023] [Indexed: 10/19/2023]
Abstract
In the field of chemistry, model compounds find extensive use for investigating complex objects. One prime example of such object is the protein-ligand supramolecular interaction. Prediction the enthalpic and entropic contribution to the free energy associated with this process, as well as the structural and dynamic characteristics of protein-ligand complexes poses considerable challenges. This review exemplifies modeling approaches used to study protein-ligand binding (PLB) thermodynamics by employing pairs of conformationally constrained/flexible model molecules. Strategically designing the model molecules can reduce the number of variables that influence thermodynamic parameters. This enables scientists to gain deeper insights into the enthalpy and entropy of PLB, which is relevant for medicinal chemistry and drug design. The model studies reviewed here demonstrate that rigidifying ligands may induce compensating changes in the enthalpy and entropy of binding. Some "rules of thumb" have started to emerge on how to minimize entropy-enthalpy compensation and design efficient rigidified or flexible ligands.
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Affiliation(s)
- Igor V Komarov
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
| | - Volodymyr A Bugrov
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Anton Cherednychenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
| | - Oleksandr O Grygorenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
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Zhang D, Xu ZC, Su W, Yang YH, Lv H, Yang H, Lin H. iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features. Bioinformatics 2021; 37:171-177. [PMID: 32766811 DOI: 10.1093/bioinformatics/btaa702] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/12/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Protein carbonylation is one of the most important oxidative stress-induced post-translational modifications, which is generally characterized as stability, irreversibility and relative early formation. It plays a significant role in orchestrating various biological processes and has been already demonstrated to be related to many diseases. However, the experimental technologies for carbonylation sites identification are not only costly and time consuming, but also unable of processing a large number of proteins at a time. Thus, rapidly and effectively identifying carbonylation sites by computational methods will provide key clues for the analysis of occurrence and development of diseases. RESULTS In this study, we developed a predictor called iCarPS to identify carbonylation sites based on sequence information. A novel feature encoding scheme called residues conical coordinates combined with their physicochemical properties was proposed to formulate carbonylated protein and non-carbonylated protein samples. To remove potential redundant features and improve the prediction performance, a feature selection technique was used. The accuracy and robustness of iCarPS were proved by experiments on training and independent datasets. Comparison with other published methods demonstrated that the proposed method is powerful and could provide powerful performance for carbonylation sites identification. AVAILABILITY AND IMPLEMENTATION Based on the proposed model, a user-friendly webserver and a software package were constructed, which can be freely accessed at http://lin-group.cn/server/iCarPS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dan Zhang
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhao-Chun Xu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen 333403, China
| | - Wei Su
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yu-He Yang
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lv
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Yang
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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iBLP: An XGBoost-Based Predictor for Identifying Bioluminescent Proteins. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:6664362. [PMID: 33505515 PMCID: PMC7808816 DOI: 10.1155/2021/6664362] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/13/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023]
Abstract
Bioluminescent proteins (BLPs) are a class of proteins that widely distributed in many living organisms with various mechanisms of light emission including bioluminescence and chemiluminescence from luminous organisms. Bioluminescence has been commonly used in various analytical research methods of cellular processes, such as gene expression analysis, drug discovery, cellular imaging, and toxicity determination. However, the identification of bioluminescent proteins is challenging as they share poor sequence similarities among them. In this paper, we briefly reviewed the development of the computational identification of BLPs and subsequently proposed a novel predicting framework for identifying BLPs based on eXtreme gradient boosting algorithm (XGBoost) and using sequence-derived features. To train the models, we collected BLP data from bacteria, eukaryote, and archaea. Then, for getting more effective prediction models, we examined the performances of different feature extraction methods and their combinations as well as classification algorithms. Finally, based on the optimal model, a novel predictor named iBLP was constructed to identify BLPs. The robustness of iBLP has been proved by experiments on training and independent datasets. Comparison with other published method further demonstrated that the proposed method is powerful and could provide good performance for BLP identification. The webserver and software package for BLP identification are freely available at http://lin-group.cn/server/iBLP.
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Feng C, Roy A, Post CB. Entropic allostery dominates the phosphorylation-dependent regulation of Syk tyrosine kinase release from immunoreceptor tyrosine-based activation motifs. Protein Sci 2018; 27:1780-1796. [PMID: 30051939 PMCID: PMC6225982 DOI: 10.1002/pro.3489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/05/2018] [Accepted: 07/05/2018] [Indexed: 01/15/2023]
Abstract
Spleen tyrosine kinase (Syk) is an essential player in immune signaling through its ability to couple multiple classes of membrane immunoreceptors to intracellular signaling pathways. Ligand binding leads to the recruitment of Syk to a phosphorylated cytoplasmic region of the receptors called ITAM. Syk binds to ITAM with high-affinity (nanomolar Kd ) via its tandem pair of SH2 domains. The affinity between Syk and ITAM is allosterically regulated by phosphorylation at Y130 in a linker connecting the tandem SH2 domains; when Y130 is phosphorylated, the binding affinity decreases (micromolar Kd ). Previous equilibrium binding studies attribute the increase in the binding free energy to an intra-molecular binding (isomerization) step of the tandem SH2 and ITAM, but a physical basis for the increased free energy is unknown. Here, we provide evidence that Y130 phosphorylation imposes an entropy penalty to isomerization, but surprisingly, has negligible effect on the SH2 binding interactions with ITAM and thus on the binding enthalpy. An analysis of NMR chemical shift differences characterized conformational effects of ITAM binding, and binding thermodynamics were measured from isothermal titration calorimetry. Together the data support a previously unknown mechanism for the basis of regulating protein-protein interactions through protein phosphorylation. The decreased affinity for Syk association with immune receptor ITAMs by Y130 phosphorylation is an allosteric mechanism driven by an increased entropy penalty, likely contributed by conformational disorder in the SH2-SH2 inter-domain structure, while SH2-ITAM binding contacts are not affected, and binding enthalpy is unchanged.
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Affiliation(s)
- Chao Feng
- Department of Medicinal Chemistry and Molecular PharmacologyMarkey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue UniversityWest Lafayette, Indiana, 47907
| | - Amitava Roy
- Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, NIAIDNational Institutes of HealthHamilton, Montana, 59840
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular PharmacologyMarkey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue UniversityWest Lafayette, Indiana, 47907
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Bonetti D, Troilo F, Toto A, Travaglini-Allocatelli C, Brunori M, Gianni S. Mechanism of Folding and Binding of the N-Terminal SH2 Domain from SHP2. J Phys Chem B 2018; 122:11108-11114. [DOI: 10.1021/acs.jpcb.8b05651] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Daniela Bonetti
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Francesca Troilo
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Angelo Toto
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Carlo Travaglini-Allocatelli
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Maurizio Brunori
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur, Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
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Babii O, Afonin S, Schober T, Komarov IV, Ulrich AS. Flexibility vs rigidity of amphipathic peptide conjugates when interacting with lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2505-2515. [PMID: 28958778 PMCID: PMC5667891 DOI: 10.1016/j.bbamem.2017.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/05/2017] [Accepted: 09/21/2017] [Indexed: 01/17/2023]
Abstract
For the first time, the photoisomerization of a diarylethene moiety (DAET) in peptide conjugates was used to probe the effects of molecular rigidity/flexibility on the structure and behavior of model peptides bound to lipid membranes. The DAET unit was incorporated into the backbones of linear peptide-based constructs, connecting two amphipathic sequences (derived from the β-stranded peptide (KIGAKI)3 and/or the α-helical peptide BP100). A β-strand-DAET-α-helix and an α-helix-DAET-α-helix models were synthesized and studied in phospholipid membranes. Light-induced photoisomerization of the linker allowed the generation of two forms of each conjugate, which differed in the conformational mobility of the junction between the α-helical and/or the β-stranded part of these peptidomimetic molecules. A detailed study of their structural, orientational and conformational behavior, both in isotropic solution and in phospholipid model membranes, was carried out using circular dichroism and solid-state 19F-NMR spectroscopy. The study showed that the rigid and flexible forms of the two conjugates had appreciably different structures only when embedded in an anisotropic lipid environment and only in the gel phase. The influence of the rigidity/flexibility of the studied conjugates on the lipid thermotropic phase transition was also investigated by differential scanning calorimetry. Both models were found to destabilize the lamellar gel phases. DAET building blocks can be used to study rigidity/flexibility effects in supramolecular model systems. Photoswitchable DAET linkers perturb only up to 3–4 adjacent amino acid residues. Membrane-bound amphiphilic secondary structure elements exert a negligible influence on each other when linked by DAET. The rigidity of peptide conjugates affected their structural behavior only in the lipid gel phase.
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Affiliation(s)
- Oleg Babii
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Sergii Afonin
- Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Tim Schober
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Igor V Komarov
- Taras Shevchenko National University of Kyiv, Institute of High Technologies, Volodymyrska 60, 01601 Kyiv, Ukraine.
| | - Anne S Ulrich
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Karlsruhe Institute of Technology, Institute of Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany.
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Marczynke M, Gröger K, Seitz O. Selective Binders of the Tandem Src Homology 2 Domains in Syk and Zap70 Protein Kinases by DNA-Programmed Spatial Screening. Bioconjug Chem 2017; 28:2384-2392. [PMID: 28767218 DOI: 10.1021/acs.bioconjchem.7b00382] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Members of the Syk family of tyrosine kinases arrange Src homology 2 (SH2) domains in tandem to allow the firm binding of immunoreceptor tyrosine-based interaction motifs (ITAMs). While the advantages provided by the bivalency enhanced interactions are evident, the impact on binding specificity is less-clear. For example, the spleen tyrosine kinase (Syk) and the ζ-chain-associated protein kinase (ZAP-70) recognize the consensus sequence pYXXI/L(X)6-8 pYXXI/L with near-identical nanomolar affinity. The nondiscriminatory recognition, on the one hand, poses a specificity challenge for the design of subtype selective protein binders and, on the other hand, raises the question as to how differential activation of Syk and ZAP-70 is ensured when both kinases are co-expressed. Herein, we identified the criteria for the design of binders that specifically address either the Syk or the Zap-70 tSH2 domain. Our approach is based on DNA-programmed spatial screening. Tyrosine-phosphorylated peptides containing the pYXXI/L motif were attached to oligonucleotides and aligned in tandem on a DNA template by means of nucleic acid hybridization. The distance between the pYXXI/L motifs and the orientation of strands were varied. The exploration exposed remarkably different recognition characteristics. While Syk tSH2 has a rather broad substrate scope, ZAP-70 tSH2 required a proximal arrangement of the phosphotyrosine ligands in defined strand orientation. The spatial screen led to the design of mutually selective, DNA-free binders, which discriminate Zap-70 and Syk tSH2 by 1 order of magnitude in affinity.
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Affiliation(s)
- Michaela Marczynke
- Institut für Chemie, Humboldt-Universität zu Berlin , Brook-Taylor-Straße 2, D-12489 Berlin, Germany
| | - Katharina Gröger
- Institut für Chemie, Humboldt-Universität zu Berlin , Brook-Taylor-Straße 2, D-12489 Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin , Brook-Taylor-Straße 2, D-12489 Berlin, Germany
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Kitai M, Fukuda N, Ueno T, Endo M, Maruyama T, Abe M, Okada K, Soma M, Matsumoto K. Effects of a spleen tyrosine kinase inhibitor on progression of the lupus nephritis in mice. J Pharmacol Sci 2017; 134:29-36. [PMID: 28479222 DOI: 10.1016/j.jphs.2017.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/13/2017] [Accepted: 02/22/2017] [Indexed: 01/14/2023] Open
Abstract
The Fc receptors (FcR) have pivotal roles in the pathogenesis of the autoimmune glomerulonephritis. We therefore investigated the effects of a Syk inhibitor on the progression of lupus nephritis and SH3 domain binding protein 2 and p38MAP kinase signalings in mice. NZB/W F1 mice, a model of lupus nephritis, received a Syk inhibitor R406. Western blotting and immunohistochemistry revealed that R406 treatment significantly delayed the appearance of proteinuria, histologically improved their glomerulosclerosis and inhibited the increased the expression of MCP-1 and TGF-β1 mRNAs and the nephrin and podocin proteins in the kidney. The treatment suppressed the phosphorylation of 3BP2 in white blood cells from the spleen and significantly inhibited the phosphorylation of p38MAPK in the kidney but did not affect expression of neonatal Fc receptor. These findings indicate the important roles and mechanisms of Fcγ receptors I and III in the development of autoimmune glomerulonephritis and suggest the possible application of Syk inhibitors as novel medicines for the glomerulonephritis.
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Affiliation(s)
- Maki Kitai
- Division of Nephrology Hypertension and Endocrinology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Noboru Fukuda
- Division of Nephrology Hypertension and Endocrinology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan; Research Center of Nihon University, Tokyo, Japan.
| | - Takahiro Ueno
- Division of Nephrology Hypertension and Endocrinology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Morito Endo
- Faculty of Human Health Science, Hachinohe Gakuin University, Hachinohe, Aomori, Japan
| | - Takashi Maruyama
- Division of Nephrology Hypertension and Endocrinology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Masanori Abe
- Division of Nephrology Hypertension and Endocrinology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Kazuyoshi Okada
- Division of Nephrology Hypertension and Endocrinology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Masayoshi Soma
- Division of General Medicine, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Koichi Matsumoto
- Division of Nephrology Hypertension and Endocrinology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
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Feng C, Post CB. Insights into the allosteric regulation of Syk association with receptor ITAM, a multi-state equilibrium. Phys Chem Chem Phys 2016; 18:5807-18. [PMID: 26468009 PMCID: PMC4758936 DOI: 10.1039/c5cp05417f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The phosphorylation of interdomain A (IA), a linker region between tandem SH2 domains of Syk tyrosine kinase, regulates the binding affinity for association of Syk with doubly-phosphorylated ITAM regions of the B cell receptor. The mechanism of this allosteric regulation has been suggested to be a switch from the high-affinity bifunctional binding, mediated through both SH2 domains binding two phosphotyrosine residues of ITAM, to a substantially lower-affinity binding of only one SH2 domain. IA phosphorylation triggers the switch by inducing disorder in IA and weakening the SH2-SH2 interaction. The postulated switch to a single-SH2-domain binding mode is examined using NMR to monitor site-specific binding to each SH2 domain of Syk variants engineered to have IA regions that differ in conformational flexibility. The combined analysis of titration curves and NMR line-shapes provides sufficient information to determine the energetics of inter-molecular binding at each SH2 site along with an intra-molecular binding or isomerization step. A less favorable isomerization equilibrium associated with the changes in the SH2-SH2 conformational ensemble and IA flexibility accounts for the inhibition of Syk association with membrane ITAM regions when IA is phosphorylated, and refutes the proposed switch to single-SH2-domain binding. Syk localizes in the cell through its SH2 interactions, and this basis for allosteric regulation of ITAM association proposes for the first time a phosphorylation-dependent model to regulate Syk binding to alternate receptors and other signaling proteins that differ either in the number of residues separating ITAM phosphotyrosines or by having only one phosphotyrosine, a half ITAM.
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Affiliation(s)
- Chao Feng
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA.
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Strack M, Langklotz S, Bandow JE, Metzler-Nolte N, Bauke Albada H. Synthesis of bisarylethyne–peptide conjugates. Org Chem Front 2015. [DOI: 10.1039/c4qo00357h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Convenient preparation of bisarylethyne–peptide conjugates, and a mild procedure for the H- or D-reduction of the bisarylethyne triple bond.
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Affiliation(s)
- Martin Strack
- Inorganic Chemistry I
- Bioinorganic Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- Bochum
| | - Sina Langklotz
- Applied Microbiology
- Faculty of Biology and Biotechnology
- Ruhr University Bochum
- Bochum
- Germany
| | - Julia E. Bandow
- Applied Microbiology
- Faculty of Biology and Biotechnology
- Ruhr University Bochum
- Bochum
- Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I
- Bioinorganic Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- Bochum
| | - H. Bauke Albada
- Inorganic Chemistry I
- Bioinorganic Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- Bochum
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Wang Y, Kirschner A, Fabian AK, Gopalakrishnan R, Kress C, Hoogeland B, Koch U, Kozany C, Bracher A, Hausch F. Increasing the efficiency of ligands for FK506-binding protein 51 by conformational control. J Med Chem 2013; 56:3922-35. [PMID: 23647266 DOI: 10.1021/jm400087k] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The design of efficient ligands remains a key challenge in drug discovery. In the quest for lead-like ligands for the FK506-binding protein 51 (FKBP51), we designed two new classes of bicyclic sulfonamides to probe the contribution of conformational energy in these ligands. The [4.3.1] scaffold had consistently higher affinity compared to the [3.3.1] or monocyclic scaffolds, which could be attributed to better preorganization of two key recognition motifs. Surprisingly, the binding of the rigid [4.3.1] scaffold was enthalpy-driven and entropically disfavored compared to the flexible analogues. Cocrystal structures at atomic resolution revealed that the sulfonamide nitrogen in the bicyclic scaffolds can accept an unusual hydrogen bond from Tyr(113) that mimics the putative FKBP transition state. This resulted in the first lead-like, functionally active ligand for FKBP51. Our work exemplifies how atom-efficient ligands can be achieved by careful conformational control even in very open and thus difficult binding sites such as FKBP51.
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Affiliation(s)
- Yansong Wang
- AG Chemical Genomics, Max Planck Institute of Psychiatry , Kraepelinstraße 2, 80804 Munich, Germany
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12
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de Mol NJ, Kruijtzer JA, Moret EE, Broutin I, Liskamp RM. Unusual binding of Grb2 protein to a bivalent polyproline-ligand immobilized on a SPR sensor: Intermolecular bivalent binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:524-35. [DOI: 10.1016/j.bbapap.2012.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 10/22/2012] [Accepted: 11/05/2012] [Indexed: 10/27/2022]
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13
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Kraskouskaya D, Duodu E, Arpin CC, Gunning PT. Progress towards the development of SH2 domain inhibitors. Chem Soc Rev 2013; 42:3337-70. [DOI: 10.1039/c3cs35449k] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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14
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Brock A. Fragmentation hydrogen exchange mass spectrometry: A review of methodology and applications. Protein Expr Purif 2012; 84:19-37. [DOI: 10.1016/j.pep.2012.04.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 04/13/2012] [Indexed: 01/19/2023]
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15
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Barua D, Hlavacek WS, Lipniacki T. A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. THE JOURNAL OF IMMUNOLOGY 2012; 189:646-58. [PMID: 22711887 DOI: 10.4049/jimmunol.1102003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BCR signaling regulates the activities and fates of B cells. BCR signaling encompasses two feedback loops emanating from Lyn and Fyn, which are Src family protein tyrosine kinases (SFKs). Positive feedback arises from SFK-mediated trans phosphorylation of BCR and receptor-bound Lyn and Fyn, which increases the kinase activities of Lyn and Fyn. Negative feedback arises from SFK-mediated cis phosphorylation of the transmembrane adapter protein PAG1, which recruits the cytosolic protein tyrosine kinase Csk to the plasma membrane, where it acts to decrease the kinase activities of Lyn and Fyn. To study the effects of the positive and negative feedback loops on the dynamical stability of BCR signaling and the relative contributions of Lyn and Fyn to BCR signaling, we consider in this study a rule-based model for early events in BCR signaling that encompasses membrane-proximal interactions of six proteins, as follows: BCR, Lyn, Fyn, Csk, PAG1, and Syk, a cytosolic protein tyrosine kinase that is activated as a result of SFK-mediated phosphorylation of BCR. The model is consistent with known effects of Lyn and Fyn deletions. We find that BCR signaling can generate a single pulse or oscillations of Syk activation depending on the strength of Ag signal and the relative levels of Lyn and Fyn. We also show that bistability can arise in Lyn- or Csk-deficient cells.
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Affiliation(s)
- Dipak Barua
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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16
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Kim SK, Huang L. Nanoparticle delivery of a peptide targeting EGFR signaling. J Control Release 2011; 157:279-86. [PMID: 21871507 DOI: 10.1016/j.jconrel.2011.08.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Revised: 06/23/2011] [Accepted: 08/09/2011] [Indexed: 11/15/2022]
Abstract
EGFR serves as an important therapeutic target because of its over-expression in many cancers. In this study, we investigated a peptide-based therapy aimed at blocking intracellular protein-protein interactions during EGFR signaling and evaluated a targetable lipid carrier system that can deliver peptides to intracellular targets in human cancer cells. EEEEpYFELV (EV), a nonapeptide mimicking the Y845 site of EGFR which is responsible for STAT5b phosphorylation, was designed to block EGFR downstream signaling. EV was loaded onto LPH nanoparticles that are comprised of a membrane/core structure including a surface-grafted polyethylene glycol (PEG) used to evade the reticuloendothelial system (RES) and anisamide (AA) for targeting the sigma receptor over-expressed in H460 human lung cancer cells. EV formulated with PEGylated and targeted LPH (LPH-PEG-AA) was taken up by the tumor cells and trafficked to the cytoplasm with high efficiency. Using this approach, EV acted as a dominant negative inhibitor of STAT5b phosphorylation, arrested cell proliferation, and induced massive apoptosis. Intravenous administration of EV loaded in LPH-PEG-AA led to efficient EV peptide delivery to the tumor in a xenograft mouse model, and multiple injections inhibited tumor growth in a dose-dependent manner. Our findings offer proof-of-concept for an intracellular peptide-mediated cancer therapy that is delivered by carefully designed nanoparticles.
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Affiliation(s)
- Sang Kyoon Kim
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
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17
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Eberhard H, Diezmann F, Seitz O. DNA as a molecular ruler: interrogation of a tandem SH2 domain with self-assembled, bivalent DNA-peptide complexes. Angew Chem Int Ed Engl 2011; 50:4146-50. [PMID: 21455916 DOI: 10.1002/anie.201007593] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/18/2011] [Indexed: 01/01/2023]
Affiliation(s)
- Hendrik Eberhard
- Department of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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Eberhard H, Diezmann F, Seitz O. DNA as a Molecular Ruler: Interrogation of a Tandem SH2 Domain with Self-Assembled, Bivalent DNA-Peptide Complexes. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007593] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Kuil J, Fischer MJE, de Mol NJ, Liskamp RMJ. Cell permeable ITAM constructs for the modulation of mediator release in mast cells. Org Biomol Chem 2010; 9:820-33. [PMID: 21107489 DOI: 10.1039/c0ob00441c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spleen tyrosine kinase (Syk) is essential for high affinity IgE receptor (FcεRI) mediated mast cell degranulation. Once FcεRI is stimulated, intracellular ITAM motifs of the receptor are diphosphorylated (dpITAM) and Syk is recruited to the receptor by binding of the Syk tandem SH2 domain to dpITAM, resulting in activation of Syk and, eventually, degranulation. To investigate intracellular effects of ITAM mimics, constructs were synthesized with ITAM mimics conjugated to different cell penetrating peptides, i.e. Tat, TP10, octa-Arg and K(Myr)KKK, or a lipophilic C(12)-chain. In most constructs the cargo and carrier were linked to each other through a disulfide bridge, which is convenient for combining different cargos with different carriers and has the advantage that the cargo and the carrier may be separated by reduction of the disulfide once it is intracellular. The ability of these ITAM constructs to label RBL-2H3 cells was assessed using flow cytometry. Fluorescence microscopy showed that the octa-Arg-SS-Flu-ITAM construct was present in various parts of the cells, although it was not homogeneously distributed. In addition, cell penetrating constructs without fluorescent labels were synthesized to examine degranulation in RBL-2H3 cells. Octa-Arg-SS-ITAM stimulated the mediator release up to 140%, indicating that ITAM mimics may have the ability to activate non-receptor bound Syk.
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Affiliation(s)
- Joeri Kuil
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht, The Netherlands
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20
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Huang Y, Liu Z. Smoothing molecular interactions: The “kinetic buffer” effect of intrinsically disordered proteins. Proteins 2010; 78:3251-9. [DOI: 10.1002/prot.22820] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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21
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Peng Q, Malhotra S, Torchia JA, Kerr WG, Coggeshall KM, Humphrey MB. TREM2- and DAP12-dependent activation of PI3K requires DAP10 and is inhibited by SHIP1. Sci Signal 2010; 3:ra38. [PMID: 20484116 DOI: 10.1126/scisignal.2000500] [Citation(s) in RCA: 271] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The activation and fusion of macrophages and of osteoclasts require the adaptor molecule DNAX-activating protein of 12 kD (DAP12), which contains immunoreceptor tyrosine-based activation motifs (ITAMs). TREM2 (triggering receptor expressed on myeloid cells-2) is the main DAP12-associated receptor in osteoclasts and, similar to DAP12 deficiency, loss of TREM2 in humans leads to Nasu-Hakola disease, which is characterized by bone cysts and dementia. Furthermore, in vitro experiments have shown that deficiency in DAP12 or TREM2 leads to impaired osteoclast development and the formation of mononuclear osteoclasts. Here, we demonstrate that the ligation of TREM2 activated phosphatidylinositol 3-kinase (PI3K), extracellular signal-regulated kinase 1 (ERK1) and ERK2, and the guanine nucleotide exchange factor Vav3; induced the mobilization of intracellular calcium (Ca(2+)) and the reorganization of actin; and prevented apoptosis. The signaling adaptor molecule DAP10 played a key role in the TREM2- and DAP12-dependent recruitment of PI3K to the signaling complex. Src homology 2 (SH2) domain-containing inositol phosphatase-1 (SHIP1) inhibited TREM2- and DAP12-induced signaling by binding to DAP12 in an SH2 domain-dependent manner and preventing the recruitment of PI3K to DAP12. These results demonstrate a previously uncharacterized interaction of SHIP1 with DAP12 that functionally limits TREM2- and DAP12-dependent signaling and identify a mechanism through which SHIP1 regulates key ITAM-containing receptors by directly blocking the binding and activation of PI3K.
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Affiliation(s)
- Qisheng Peng
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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22
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Abstract
Surface plasmon resonance (SPR) analysis is rather unique in that it allows assay of binding constants (affinity) and kinetic analysis of binding phenomena. This introductory chapter deals with some specific features that are relevant to many diverse applications. The role and impact of kinetics in biomolecular interactions is highlighted. A concise description of the physical principles of the SPR phenomenon is given from a practical point of view, such that some possibilities and limitations of the method can be rationalized, e.g., depth of the evanescent field. A specific condition that may come forward in kinetic analysis is mass transport limitation (MTL). A practical model is presented, which allows estimation of the extent of MTL. Based on this model it can be rationalized whether MTL can be avoided by experimental design. In this framework also rules are presented to convert SPR signals (RU or millidegree) to mass/surface unit. The chapter concludes with an overview of commercially available SPR equipment.
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Affiliation(s)
- Nico J de Mol
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands
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Extensions to amino acid description. Mol Divers 2009; 14:709-18. [DOI: 10.1007/s11030-009-9204-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 10/20/2009] [Indexed: 10/20/2022]
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Kuil J, van Wandelen LT, de Mol NJ, Liskamp RM. Switching between low and high affinity for the Syk tandem SH2 domain by irradiation of azobenzene containing ITAM peptidomimetics. J Pept Sci 2009; 15:685-91. [DOI: 10.1002/psc.1173] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Moghaddam S, Inoue Y, Gilson MK. Host-guest complexes with protein-ligand-like affinities: computational analysis and design. J Am Chem Soc 2009; 131:4012-21. [PMID: 19133781 DOI: 10.1021/ja808175m] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It has recently been discovered that guests combining a nonpolar core with cationic substituents bind cucurbit[7]uril (CB[7]) in water with ultrahigh affinities. The present study uses the Mining Minima algorithm to study the physics of these extraordinary associations and to computationally test a new series of CB[7] ligands designed to bind with similarly high affinity. The calculations reproduce key experimental observations regarding the affinities of ferrocene-based guests with CB[7] and beta-cyclodextrin and provide a coherent view of the roles of electrostatics and configurational entropy as determinants of affinity in these systems. The newly designed series of compounds is based on a bicyclo[2.2.2]octane core, which is similar in size and polarity to the ferrocene core of the existing series. Mining Minima predicts that these new compounds will, like the ferrocenes, bind CB[7] with extremely high affinities.
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Affiliation(s)
- Sarvin Moghaddam
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
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Kuil J, Branderhorst HM, Pieters RJ, de Mol NJ, Liskamp RMJ. ITAM-derived phosphopeptide-containing dendrimers as multivalent ligands for Syk tandem SH2 domain. Org Biomol Chem 2009; 7:4088-94. [DOI: 10.1039/b905938e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Kuil J, Wandelen LTMV, Mol NJD, Liskamp RMJ. Peptidomimetic Ligands for the Tandem SH2 Domain of the Syk Protein Involved in Signal Transduction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 611:81-2. [DOI: 10.1007/978-0-387-73657-0_36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Holdgate GA. Thermodynamics of binding interactions in the rational drug design process. Expert Opin Drug Discov 2007; 2:1103-14. [DOI: 10.1517/17460441.2.8.1103] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Geoff A Holdgate
- Global Compound Sciences, Lead Generation - Discovery Enabling Capabilities & Sciences, AstraZeneca Pharmaceuticals, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
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Chapter 24 Spleen Tyrosine Kinase (Syk) Biology, Inhibitors and Therapeutic Applications. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2007. [DOI: 10.1016/s0065-7743(07)42024-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Abstract
We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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