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Smith LJ, van Gunsteren WF, Hansen N. Using Complementary NMR Data Sets To Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4. J Phys Chem B 2017. [PMID: 28640620 DOI: 10.1021/acs.jpcb.7b03647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The derivation of protein structure from values of observable quantities measured in NMR experiments is a rather nontrivial task due to (i) the limited number of data compared to degrees of freedom of a protein, (ii) the uncertainty inherent to the function connecting an observable quantity to molecular structure, (iii) the finite quality of biomolecular models and force fields used in structure refinement, and (iv) the conformational freedom of a protein in aqueous solution, which requires extensive conformational sampling and appropriate conformational averaging when calculating or restraining to sets of NMR data. The protein interleukin-4 (IL-4) has been taken as a test case using NOE distances, S2 order parameters, and 3J-couplings as test data and the former two types of data as restraints. It is shown that, by combining sets of different, complementary NMR data as restraints in MD simulations, inconsistencies in the data or flaws in the model and procedures used to derive protein structure from NMR data can be detected. This leads to an improved structural interpretation of such data particularly in more mobile loop regions.
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Affiliation(s)
- Lorna J Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory , South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , CH-8093 Zürich, Switzerland
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany
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2
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Tsujimura Y, Yasutomi Y. Allergy Vaccines Using a Mycobacterium-Secreted Antigen, Ag85B, and an IL-4 Antagonist. Methods Mol Biol 2016; 1403:723-38. [PMID: 27076163 DOI: 10.1007/978-1-4939-3387-7_41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In recent decades, the prevalence of allergic diseases, including bronchial asthma, airway hypersensitivity, hay fever, and atopic dermatitis, has been increasing in the industrialized world, and effective treatments probably require manipulating the inflammatory response to pathogenic allergens. T helper (Th) 2 cells are thought to play a crucial role in the initiation, progression, and persistence of allergic responses in association with production of interleukin (IL)-4, IL-5, and IL-13. Therefore, a strategy of a shift from Th2- to Th1-type immune response may be valuable in the prophylaxis and management of allergic diseases. It is also necessary to develop prophylactic and therapeutic treatment that induces homeostatic functions in the multifaceted allergic environment, because various factors including innate and adaptive immunity, mucosal immune response, and functional and structural maintenance of local tissue might be involved in the pathogenesis of allergic disorders. We review herein recent findings related to the curative effect for mouse models of asthma and atopic dermatitis using DNA-, virus-, and protein-based vaccines of a Mycobacterium secretion antigen, Ag85B, and a plasmid encoding cDNA of antagonistic IL-4 mutant.
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Affiliation(s)
- Yusuke Tsujimura
- Laboratory of Immunoregulation and Vaccine Research, Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Health and Nutrition, 1-1 Hachimandai, Tsukuba, Ibaraki, 305-0843, Japan
| | - Yasuhiro Yasutomi
- Laboratory of Immunoregulation and Vaccine Research, Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Health and Nutrition, 1-1 Hachimandai, Tsukuba, Ibaraki, 305-0843, Japan. .,Department of Immunoregulation, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan.
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Lin Y, Chen Z, Kato S. Receptor-selective IL-4 mutein modulates inflammatory vascular cell phenotypes and attenuates atherogenesis in apolipoprotein E-knockout mice. Exp Mol Pathol 2015; 99:116-27. [DOI: 10.1016/j.yexmp.2015.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/15/2015] [Indexed: 01/25/2023]
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Sahoo A, Im SH. Molecular Mechanisms Governing IL-24 Gene Expression. Immune Netw 2012; 12:1-7. [PMID: 22536164 PMCID: PMC3329598 DOI: 10.4110/in.2012.12.1.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/05/2012] [Accepted: 01/10/2012] [Indexed: 12/23/2022] Open
Abstract
Interleukin-24 (IL-24) belongs to the IL-10 family of cytokines and is well known for its tumor suppressor activity. This cytokine is released by both immune and nonimmune cells and acts on non-hematopoietic tissues such as skin, lung and reproductive tissues. Apart from its ubiquitous tumor suppressor function, IL-24 is also known to be involved in the immunopathology of autoimmune diseases like psoriasis and rheumatoid arthritis. Although the cellular sources and functions of IL-24 are being increasingly investigated, the molecular mechanisms of IL-24 gene expression at the levels of signal transduction, epigenetics and transcription factor binding are still unclear. Understanding the specific molecular events that regulate the production of IL-24 will help to answer the remaining questions that are important for the design of new strategies of immune intervention involving IL-24. Herein, we briefly review the signaling pathways and transcription factors that facilitate, induce, or repress production of this cytokine along with the cellular sources and functions of IL-24.
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Affiliation(s)
- Anupama Sahoo
- School of Life Sciences and Immune Synapse Research Center, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, Korea
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Walsh STR. A biosensor study indicating that entropy, electrostatics, and receptor glycosylation drive the binding interaction between interleukin-7 and its receptor. Biochemistry 2010; 49:8766-78. [PMID: 20815339 DOI: 10.1021/bi101050h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interaction between interleukin-7 (IL-7) and its α-receptor, IL-7Rα, plays fundamental roles in the development, survival, and homeostasis of B- and T-cells. N-Linked glycosylation of human IL-7Rα enhances its binding affinity for human IL-7 300-fold versus that of the nonglycosylated receptor through an allosteric mechanism. The N-glycans of IL-7Rα do not participate directly in the binding interface with IL-7. This biophysical study involves dissection of the properties of binding of IL-7 to both nonglycosylated and glycosylated forms of the IL-7Rα extracellular domain (ECD) as functions of salt, pH, and temperature using surface plasmon resonance (SPR) spectroscopy. Interactions of IL-7 with both IL-7Rα variants display weaker binding affinities with increasing salt concentrations primarily reflected by changes in the first on rates of a two-step reaction pathway. The electrostatic parameter of the IL-7-IL-7Rα interaction is not driven by complementary charge interactions through residues at the binding interface or N-glycan composition of IL-7Rα, but presumably by favorable global charges of the two proteins. van't Hoff analysis indicates both IL-7-IL-7Rα interactions are driven by large favorable entropy changes and smaller unfavorable (nonglycosylated complex) and favorable (glycosylated complex) enthalpy changes. Eyring analysis of the IL-7-IL-7Rα interactions reveals different reaction pathways and barriers for the transition-state thermodynamics with the enthalpy and entropy changes of IL-7 binding to nonglycosylated and glycosylated IL-7Rα. There were no discernible heat capacity changes for the equilibrium or transition-state binding thermodynamics of the IL-7-IL-7Rα interactions. The results suggest that the unbound nonglycosylated IL-7Rα samples an extensive conformational landscape relative to the unbound glycosylated IL-7Rα, potentially explaining the switch from a "conformationally controlled" reaction (k(1) ∼ 10(2) M(-1) s(-1)) for the nonglycosylated interaction to a "diffusion-controlled" reaction (k(1) ∼ 10(6) M(-1) s(-1)) for the glycosylated interaction. Thus, a large favorable entropy change, a global favorable electrostatic component, and glycosylation of the receptor, albeit not at the interface, contribute significantly to the interaction between IL-7 and the IL-7Rα ECD.
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Affiliation(s)
- Scott T R Walsh
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.
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Sebald W, Nickel J, Zhang JL, Mueller TD. Molecular basis of cytokine signalling - theme and variations. FEBS J 2009; 277:106-18. [DOI: 10.1111/j.1742-4658.2009.07480.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Winger M, Yu H, Redfield C, van Gunsteren WF. Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020701613623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Nishikubo K, Imanaka-Yoshida K, Tamaki S, Hiroe M, Yoshida T, Adachi Y, Yasutomi Y. Th1-type immune responses by Toll-like receptor 4 signaling are required for the development of myocarditis in mice with BCG-induced myocarditis. J Autoimmun 2007; 29:146-53. [PMID: 17698322 DOI: 10.1016/j.jaut.2007.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2007] [Revised: 07/01/2007] [Accepted: 07/01/2007] [Indexed: 11/16/2022]
Abstract
The immunological aspects of autoimmune myocarditis are difficult to understand because of the existence of many infectious agents and animal models suggesting different mechanisms in autoimmune myocarditis. To overcome these difficulties, two strains of mice, C3H/HeN and C3H/HeJ, showing different immune responses to mycobacteria, were immunized with myosin mixed with BCG. The C3H/HeN mice with a wild-type Toll-like receptor 4 (TLR4) showed severe myocarditis, whereas the C3H/HeJ mice with nonfunctional mutated TLR4 did not. CD4(+) cells from both strains of mice exhibited appreciable proliferative responses following myosin stimulation; however, the cytokines from these cells differed between these two strains. The C3H/HeN mice showed T helper (Th)1-type cytokine responses, whereas the expressions of mRNA in C3H/HeJ mice were Th2-type cytokine. When both of these strains of immunized mice were inoculated with a plasmid encoding cDNA of interleukin (IL)-4 or agonistic IL-4, the development of myocarditis was inhibited in C3H/HeN mice. Moreover, C3H/HeJ mice, in which development of myocarditis was not induced by immunization of myosin mixed with BCG, showed myocarditis after injection of IL-4 antagonistic mutant DNA for the induction of Th1-type immune responses. The results suggested that the induction of autoimmune myocarditis by myosin is affected by Th1-type immune responses.
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Affiliation(s)
- Kimiaki Nishikubo
- Department of Rheumatology, National Hospital Organization, Mie Chuo Medical Center, Mie 514-1101, Japan
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Kozma N, Halasz M, Polgar B, Poehlmann TG, Markert UR, Palkovics T, Keszei M, Par G, Kiss K, Szeberenyi J, Grama L, Szekeres-Bartho J. Progesterone-induced blocking factor activates STAT6 via binding to a novel IL-4 receptor. THE JOURNAL OF IMMUNOLOGY 2006; 176:819-26. [PMID: 16393965 DOI: 10.4049/jimmunol.176.2.819] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Progesterone-induced blocking factor (PIBF) induces Th2-dominant cytokine production. Western blotting and EMSA revealed phosphorylation as well as nuclear translocation of STAT6 and inhibition of STAT4 phosphorylation in PIBF-treated cells. The silencing of STAT6 by small interfering RNA reduced the cytokine effects. Because the activation of the STAT6 pathway depends on the ligation of IL-4R, we tested the involvement of IL-4R in PIBF-induced STAT6 activation. Although PIBF does not bind to IL-4R, the blocking of the latter with an Ab abolished PIBF-induced STAT6 activation, whereas the blocking of the IL-13R had no effect. PIBF activated suppressor of cytokine signaling-3 and inhibited IL-12-induced suppressor of cytokine signaling-1 activation. The blocking of IL-4R counteracted all the described effects, suggesting that the PIBF receptor interacts with IL-4R alpha-chain, allowing PIBF to activate the STAT6 pathway. PIBF did not phosphorylate Jak3, suggesting that the gamma-chain is not needed for PIBF signaling. Confocal microscopic analysis revealed a colocalization and at 37 degrees C a cocapping of the FITC PIBF-activated PIBF receptor and PE anti-IL-4R-labeled IL-4R. After the digestion of the cells with phosphatidylinositol-specific phospholipase C, the STAT6-activating effect of PIBF was lost, whereas that of IL-4 remained unaltered. These data suggest the existence of a novel type of IL-4R composed of the IL-4R alpha-chain and the GPI-anchored PIBF receptor.
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Affiliation(s)
- Noemi Kozma
- Department of Medical Microbiology and Immunology, Pecs University, Pecs, Hungary
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Nishikubo K, Murata Y, Tamaki S, Sugama K, Imanaka-Yoshida K, Yuda N, Kai M, Takamura S, Sebald W, Adachi Y, Yasutomi Y. A single administration of interleukin-4 antagonistic mutant DNA inhibits allergic airway inflammation in a mouse model of asthma. Gene Ther 2004; 10:2119-25. [PMID: 14625566 DOI: 10.1038/sj.gt.3302131] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interleukin 4 (IL-4) is essential for the switching of B cells to IgE antibody production and for the maturation of T helper (Th) cells toward the Th2 phenotype. These mechanisms are thought to play a crucial role in the pathogenesis of the allergic airway inflammation observed in asthma. In the present study, we examined the anti-inflammatory effects of DNA administration of murine IL-4 mutant Q116D/Y119D (IL-4 double mutant, IL-4DM), which binds to the IL-4 receptor alpha and is an antagonist for IL-4. Immunization of BALB/c mice with alum-adsorbed ovalbumin (OVA) followed by aspiration with aerosolized OVA resulted in the development of allergic airway inflammation. A single administration of IL-4DM DNA before the aerosolized OVA challenge protected the mice from the subsequent induction of allergic airway inflammation. Serum IgE level and extent of eosinophil infiltration in bronchoalveolar lavage (BAL) from IL-4DM DNA-administered mice were significantly lower than those in BAL from control plasmid-immunized mice. In our study, IL-4 or IL-4 mutants were not detected in sera from mice that had received a single administration of IL-4DM DNA. The results of this study provide evidence for the potential utility of IL-4 mutant antagonist DNA inoculation as an approach to gene therapy for asthma.
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Affiliation(s)
- K Nishikubo
- Third Department of Internal Medicine, Mie University School of Medicine, Tsu, Mie, Japan
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Li-Weber M, Krammer PH. Regulation of IL4 gene expression by T cells and therapeutic perspectives. Nat Rev Immunol 2003; 3:534-43. [PMID: 12876556 DOI: 10.1038/nri1128] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Interleukin-4 (IL-4) is crucial for the differentiation of naive T helper (T(H)) cells into the T(H)2 effector cells that promote humoral (antibody) immunity and provide protection against intestinal helminths. IL-4 also has a central role in the pathogenesis of allergic inflammation. Many transcription factors are involved in the regulation of expression of the gene encoding IL-4. Initiation of transcription of the gene encoding IL-4 in naive T(H) cells is regulated by the T(H)2-specific transcription factor GATA3, whereas acute expression of the gene encoding IL-4 in T(H)2 cells is mediated by inducible, ubiquitous transcription factors after antigen encounter. This review focuses on acute activation of the gene encoding IL-4 in T cells and discusses therapeutic perspectives at the transcriptional level.
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Affiliation(s)
- Min Li-Weber
- Tumour Immunology Programme D030, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
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Mueller TD, Zhang JL, Sebald W, Duschl A. Structure, binding, and antagonists in the IL-4/IL-13 receptor system. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1592:237-50. [PMID: 12421669 DOI: 10.1016/s0167-4889(02)00318-x] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interleukin-4 (IL-4) and IL-13 are the only cytokines known to bind to the receptor chain IL-4Ralpha. Receptor sharing by these two cytokines is the molecular basis for their overlapping biological functions. Both are key factors in the development of allergic hypersensitivity, and they also play a major role in exacerbating allergic and asthmatic symptoms. Knowledge of structure and function of this system has allowed the development of inhibitors that block the interaction between the cytokines and their shared receptor. Mutational analysis of IL-4 has revealed variants with high-affinity binding to IL-4Ralpha but no detectable affinity for the second receptor subunit, which is either (gamma)c or IL-13Ralpha1. These IL-4 antagonists fail to induce signal transduction and block IL-4 and IL-13 effects in vitro. IL-4 antagonists prevent the development of allergic disease in vivo and an antagonistic variant of human IL-4 is now in clinical trials for asthma. Detailed knowledge of the site of interaction of IL-4 and IL-4Ralpha has been gained by structure analysis of the complex of these two proteins and through functional studies employing mutants of IL-4 and its receptor subunits. Based on these new data, the hitherto elusive goal of designing small molecular mimetics may be feasible.
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Affiliation(s)
- Thomas D Mueller
- Physiological Chemistry II, Biocenter, University of Wuerzburg, Am Hubland, Germany
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Zhang JL, Simeonowa I, Wang Y, Sebald W. The high-affinity interaction of human IL-4 and the receptor alpha chain is constituted by two independent binding clusters. J Mol Biol 2002; 315:399-407. [PMID: 11786020 DOI: 10.1006/jmbi.2001.5243] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
IL4-BP, the extracellular binding domain of the IL-4 receptor alpha chain, contains a high-affinity binding epitope for IL-4 (K(D) 150 pM). Previous results on the crystal structure of the IL-4/IL4-BP complex and on the functional epitope of IL-4 suggested that this contact comprises a mosaic of two binding clusters. The present mutational analysis of IL4-BP supports this view and demonstrates that the energetically most important group is the receptor carboxylate group of D72 forming an ion pair with IL-4 R88 in cluster II. The second main receptor determinant is the hydroxyl group of Y183 forming a hydrogen bond with IL-4 E9 in cluster I. The latter is engaged in additional hydrogen bonds with Y13 and also in van der Waals contacts with Y127. Receptor residue D72 as well as Y183 are each surrounded by a shell of hydrophobic groups from residues that upon mutation lead to smaller decreases in binding affinity. Analysis of IL4-BP double mutants showed that receptor side-chains within one cluster but not those of different clusters cooperate. Interaction analysis of IL-4 and IL4-BP single mutants also revealed additivity in binding of side-chains between clusters and cooperativity within each cluster I or II.These results show that the high-affinity IL-4/IL4-BP contact is constituted by two independent binding units, each containing a central polar or charged side-chain surrounded by hydrophobic groups (avocado cluster).
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Affiliation(s)
- Jin-Li Zhang
- Department of Physiological Chemistry II, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
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Baell JB, Forsyth SA, Gable RW, Norton RS, Mulder RJ. Design and synthesis of type-III mimetics of omega-conotoxin GVIA. J Comput Aided Mol Des 2001; 15:1119-36. [PMID: 12160094 DOI: 10.1023/a:1015930031890] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Our interest lies in the rational design and synthesis of type-III mimetics of protein and polypeptide structure and function. Our approach involves interactive design of conformationally defined molecular scaffolds that project certain functional groups in a way that mimics the projection of important binding residues as determined in the parent structure. These design principles are discussed and applied to the structurally defined polypeptide, omega-conotoxin GVIA, which blocks voltage-gated, neuronal N-type calcium channels. These ion channels represent therapeutic targets for the development of new analgesics that can treat chronic pain. It is shown how a discontinuous, 3-residue pharmacophore of GVIA can be mimicked by different molecular scaffolds. It is illustrated how such 1st generation leads must necessarily be weak and that optimisability must therefore be built-in during the design process.
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Affiliation(s)
- J B Baell
- Biomolecular Research Institute, Parkville, Victoria, Australia.
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