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Geerds C, Haas A, Niemann HH. Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB. Acta Crystallogr F Struct Biol Commun 2021; 77:246-253. [PMID: 34341190 PMCID: PMC8329714 DOI: 10.1107/s2053230x2100738x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/16/2021] [Indexed: 12/04/2022] Open
Abstract
Virulence-associated proteins (Vaps) contribute to the virulence of the pathogen Rhodococcus equi, but their mode of action has remained elusive. All Vaps share a conserved core of about 105 amino acids that folds into a compact eight-stranded antiparallel β-barrel with a unique topology. At the top of the barrel, four loops connect the eight β-strands. Previous Vap structures did not show concave surfaces that might serve as a ligand-binding site. Here, the structure of VapB in a new crystal form was determined at 1.71 Å resolution. The asymmetric unit contains two molecules. In one of them, the loop regions at the top of the barrel adopt a different conformation from other Vap structures. An outward movement of the loops results in the formation of a hydrophobic cavity that might act as a ligand-binding site. This lends further support to the hypothesis that the structural similarity between Vaps and avidins suggests a potential binding function for Vaps.
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Affiliation(s)
- Christina Geerds
- Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Albert Haas
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Strasse 61a, 53121 Bonn, Germany
| | - Hartmut H. Niemann
- Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
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2
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Kubitza C, Ginsel C, Bittner F, Havemeyer A, Clement B, Scheidig AJ. T4 lysozyme-facilitated crystallization of the human molybdenum cofactor-dependent enzyme mARC. Acta Crystallogr F Struct Biol Commun 2018; 74:337-344. [PMID: 29870017 PMCID: PMC5987741 DOI: 10.1107/s2053230x18006921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/04/2018] [Indexed: 12/12/2022] Open
Abstract
The human mitochondrial amidoxime reducing component (hmARC) is a molybdenum cofactor-dependent enzyme that is involved in the reduction of a diverse range of N-hydroxylated compounds of either physiological or xenobiotic origin. In this study, the use of a fusion-protein approach with T4 lysozyme (T4L) to determine the structure of this hitherto noncrystallizable enzyme by X-ray crystallography is described. A set of four different hmARC-T4L fusion proteins were designed. Two of them contained either an N-terminal or a C-terminal T4L moiety fused to hmARC, while the other two contained T4L as an internal fusion partner tethered to the hmARC enzyme between two predicted secondary-structure elements. One of these internal fusion constructs could be expressed and crystallized successfully. The hmARC-T4L crystals diffracted to 1.7 Å resolution using synchrotron radiation and belonged to space group P212121 with one molecule in the asymmetric unit. Initial attempts to solve the structure by molecular replacement using T4L did not result in electron-density distributions that were sufficient for model building and interpretation of the hmARC moiety. However, this study emphasizes the utility of the T4L fusion-protein approach, which can be used for the crystallization and structure determination of membrane-bound proteins as well as soluble proteins.
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Affiliation(s)
- Christian Kubitza
- Structural Biology, Zoological Institute, Kiel University, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Carsten Ginsel
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Florian Bittner
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Antje Havemeyer
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Bernd Clement
- Pharmaceutical Institute, Kiel University, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Axel J. Scheidig
- Structural Biology, Zoological Institute, Kiel University, Am Botanischen Garten 1–9, 24118 Kiel, Germany
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3
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Islam SMA, Sajed T, Kearney CM, Baker EJ. PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides. BMC Bioinformatics 2015; 16:210. [PMID: 26142484 PMCID: PMC4491269 DOI: 10.1186/s12859-015-0633-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 06/01/2015] [Indexed: 02/07/2023] Open
Abstract
Background Numerous organisms have evolved a wide range of toxic peptides for self-defense and predation. Their effective interstitial and macro-environmental use requires energetic and structural stability. One successful group of these peptides includes a tri-disulfide domain arrangement that offers toxicity and high stability. Sequential tri-disulfide connectivity variants create highly compact disulfide folds capable of withstanding a variety of environmental stresses. Their combination of toxicity and stability make these peptides remarkably valuable for their potential as bio-insecticides, antimicrobial peptides and peptide drug candidates. However, the wide sequence variation, sources and modalities of group members impose serious limitations on our ability to rapidly identify potential members. As a result, there is a need for automated high-throughput member classification approaches that leverage their demonstrated tertiary and functional homology. Results We developed an SVM-based model to predict sequential tri-disulfide peptide (STP) toxins from peptide sequences. One optimized model, called PredSTP, predicted STPs from training set with sensitivity, specificity, precision, accuracy and a Matthews correlation coefficient of 94.86 %, 94.11 %, 84.31 %, 94.30 % and 0.86, respectively, using 200 fold cross validation. The same model outperforms existing prediction approaches in three independent out of sample testsets derived from PDB. Conclusion PredSTP can accurately identify a wide range of cystine stabilized peptide toxins directly from sequences in a species-agnostic fashion. The ability to rapidly filter sequences for potential bioactive peptides can greatly compress the time between peptide identification and testing structural and functional properties for possible antimicrobial and insecticidal candidates. A web interface is freely available to predict STP toxins from http://crick.ecs.baylor.edu/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0633-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Tanvir Sajed
- Department of Computer Science, University of Alberta, Edmonton, AB, Canada.
| | - Christopher Michel Kearney
- Institute of Biomedical Studies, Baylor University, Waco, TX, USA. .,Department of Biology, Baylor University, Waco, TX, USA.
| | - Erich J Baker
- Institute of Biomedical Studies, Baylor University, Waco, TX, USA. .,Department of Computer Science, Baylor University, One Bear Place #97356, Waco, TX, USA.
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Kobe B, Ve T, Williams SJ. Fusion-protein-assisted protein crystallization. Acta Crystallogr F Struct Biol Commun 2015; 71:861-9. [PMID: 26144231 PMCID: PMC4498707 DOI: 10.1107/s2053230x15011061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/07/2015] [Indexed: 01/29/2023] Open
Abstract
Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.
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Affiliation(s)
- Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia
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Patil NA, Tailhades J, Hughes RA, Separovic F, Wade JD, Hossain MA. Cellular disulfide bond formation in bioactive peptides and proteins. Int J Mol Sci 2015; 16:1791-805. [PMID: 25594871 PMCID: PMC4307334 DOI: 10.3390/ijms16011791] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/02/2015] [Indexed: 11/16/2022] Open
Abstract
Bioactive peptides play important roles in metabolic regulation and modulation and many are used as therapeutics. These peptides often possess disulfide bonds, which are important for their structure, function and stability. A systematic network of enzymes--a disulfide bond generating enzyme, a disulfide bond donor enzyme and a redox cofactor--that function inside the cell dictates the formation and maintenance of disulfide bonds. The main pathways that catalyze disulfide bond formation in peptides and proteins in prokaryotes and eukaryotes are remarkably similar and share several mechanistic features. This review summarizes the formation of disulfide bonds in peptides and proteins by cellular and recombinant machinery.
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Affiliation(s)
- Nitin A Patil
- Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Victoria 3010, Australia.
| | - Julien Tailhades
- Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Victoria 3010, Australia.
| | - Richard Anthony Hughes
- Department of Pharmacology and Therapeutics, the University of Melbourne, Victoria 3010, Australia.
| | - Frances Separovic
- School of Chemistry, the University of Melbourne, Victoria 3010, Australia.
| | - John D Wade
- Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Victoria 3010, Australia.
| | - Mohammed Akhter Hossain
- Florey Institute of Neuroscience and Mental Health, the University of Melbourne, Victoria 3010, Australia.
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Abstract
RNases are enzymes that cleave RNAs, resulting in remarkably diverse biological consequences. Many RNases are cytotoxic. In some cases, they attack selectively malignant cells triggering an apoptotic response. A number of eukaryotic and bacterial RNase-based strategies are being developed for use in anticancer and antiviral therapy. However, the physiological functions of these RNases are often poorly understood. This review focuses on the properties of the extracellular RNases from Bacillus amyloliquefaciens (barnase) and Bacillus intermedius (binase), the characteristics of their biosynthesis regulation and their physiological role, with an emphasis on the similarities and differences. Barnase and binase can be regarded as molecular twins according to their highly similar structure, physical-chemical and catalytic properties. Nevertheless, the 'life paths' of these enzymes are not the same, as their expression in bacteria is controlled by diverse signals. Binase is predominantly synthesized under phosphate starvation, whereas barnase production is strictly dependent on the multifunctional Spo0A regulator controlling sporulation, biofilm formation and cannibalism. Barnase and binase also have some distinctions in practical applications. Barnase was initially suggested to be useful in research and biotechnology as a tool for studying protein-protein interactions, for RNA elimination from biological samples, for affinity purification of RNase fusion proteins, for the development of cloning vectors and for sterility acquisition by transgenic plants. Binase, as later barnase, was tested for antiviral, antitumour and immunogenic effects. Both RNases have found their own niche in cancer research as a result of success in targeted delivery and selectivity towards tumour cells.
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Affiliation(s)
- Vera Ulyanova
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan, Russia
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7
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Derewenda ZS. Application of protein engineering to enhance crystallizability and improve crystal properties. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:604-15. [PMID: 20445236 PMCID: PMC3089013 DOI: 10.1107/s090744491000644x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 02/18/2010] [Indexed: 01/05/2023]
Abstract
Until recently, protein crystallization has mostly been regarded as a stochastic event over which the investigator has little or no control. With the dramatic technological advances in synchrotron-radiation sources and detectors and the equally impressive progress in crystallographic software, including automated model building and validation, crystallization has increasingly become the rate-limiting step in X-ray diffraction studies of macromolecules. However, with the advent of recombinant methods it has also become possible to engineer target proteins and their complexes for higher propensity to form crystals with desirable X-ray diffraction qualities. As most proteins that are under investigation today are obtained by heterologous overexpression, these techniques hold the promise of becoming routine tools with the potential to transform classical crystallization screening into a more rational high-success-rate approach. This article presents an overview of protein-engineering methods designed to enhance crystallizability and discusses a number of examples of their successful application.
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Affiliation(s)
- Zygmunt S Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA.
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Sommerhoff CP, Avrutina O, Schmoldt HU, Gabrijelcic-Geiger D, Diederichsen U, Kolmar H. Engineered cystine knot miniproteins as potent inhibitors of human mast cell tryptase beta. J Mol Biol 2009; 395:167-75. [PMID: 19852971 DOI: 10.1016/j.jmb.2009.10.028] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 10/12/2009] [Accepted: 10/15/2009] [Indexed: 11/16/2022]
Abstract
Here we report the design, chemical and recombinant synthesis, and functional properties of a series of novel inhibitors of human mast cell tryptase beta, a protease of considerable interest as a therapeutic target for the treatment of allergic asthma and inflammatory disorders. These inhibitors are derived from a linear variant of the cyclic cystine knot miniprotein MCoTI-II, originally isolated from the seeds of Momordica cochinchinensis. A synthetic cyclic miniprotein that bears additional positive charge in the loop connecting the N- and C-termini inhibits all monomers of the tryptase beta tetramer with an overall equilibrium dissociation constant K(i) of 1 nM and thus is one of the most potent proteinaceous inhibitors of tryptase beta described to date. These cystine knot miniproteins may therefore become valuable scaffolds for the design of a new generation of tryptase inhibitors.
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Affiliation(s)
- Christian P Sommerhoff
- Division of Clinical Chemistry and Clinical Biochemistry, Surgical Department, Ludwig-Maximilians-University Munich, Nussbaumstrasse 20, D-80336 Munich, Germany
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9
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Thongyoo P, Bonomelli C, Leatherbarrow RJ, Tate EW. Potent Inhibitors of β-Tryptase and Human Leukocyte Elastase Based on the MCoTI-II Scaffold. J Med Chem 2009; 52:6197-200. [DOI: 10.1021/jm901233u] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panumart Thongyoo
- Department of Chemistry and Chemical Biology Centre, Imperial College London SW7 2AZ, U.K
| | | | - Robin J. Leatherbarrow
- Department of Chemistry and Chemical Biology Centre, Imperial College London SW7 2AZ, U.K
| | - Edward W. Tate
- Department of Chemistry and Chemical Biology Centre, Imperial College London SW7 2AZ, U.K
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10
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de Marco A. Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. Microb Cell Fact 2009; 8:26. [PMID: 19442264 PMCID: PMC2689190 DOI: 10.1186/1475-2859-8-26] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 05/14/2009] [Indexed: 12/22/2022] Open
Abstract
Bacteria are simple and cost effective hosts for producing recombinant proteins. However, their physiological features may limit their use for obtaining in native form proteins of some specific structural classes, such as for instance polypeptides that undergo extensive post-translational modifications. To some extent, also the production of proteins that depending on disulfide bridges for their stability has been considered difficult in E. coli. Both eukaryotic and prokaryotic organisms keep their cytoplasm reduced and, consequently, disulfide bond formation is impaired in this subcellular compartment. Disulfide bridges can stabilize protein structure and are often present in high abundance in secreted proteins. In eukaryotic cells such bonds are formed in the oxidizing environment of endoplasmic reticulum during the export process. Bacteria do not possess a similar specialized subcellular compartment, but they have both export systems and enzymatic activities aimed at the formation and at the quality control of disulfide bonds in the oxidizing periplasm. This article reviews the available strategies for exploiting the physiological mechanisms of bactera to produce properly folded disulfide-bonded proteins.
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Affiliation(s)
- Ario de Marco
- Cogentech, IFOM-IEO Campus for Oncogenomic, via Adamello, 16 - 20139, Milano, Italy.
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Thongyoo P, Roqué-Rosell N, Leatherbarrow RJ, Tate EW. Chemical and biomimetic total syntheses of natural and engineered MCoTI cyclotides. Org Biomol Chem 2008; 6:1462-70. [PMID: 18385853 DOI: 10.1039/b801667d] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2025]
Abstract
The naturally-occurring cyclic cystine-knot microprotein trypsin inhibitors MCoTI-I and MCoTI-II have been synthesised using both thia-zip native chemical ligation and a biomimetic strategy featuring chemoenzymatic cyclisation by an immobilised protease. Engineered analogues have been produced containing a range of substitutions at the P1 position that redirect specificity towards alternative protease targets whilst retaining excellent to moderate affinity. Furthermore, we report an MCoTI analogue that is a selective low-microM inhibitor of foot-and-mouth-disease virus (FMDV) 3C protease, the first reported peptide-based inhibitor of this important viral enzyme.
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Affiliation(s)
- Panumart Thongyoo
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ
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12
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Head-to-Tail Cyclized Cystine-Knot Peptides by a Combined Recombinant and Chemical Route of Synthesis. Chembiochem 2008; 9:33-7. [DOI: 10.1002/cbic.200700452] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Neophytou I, Harvey R, Lawrence J, Marsh P, Panaretou B, Barlow D. Eukaryotic integral membrane protein expression utilizing the Escherichia coli glycerol-conducting channel protein (GlpF). Appl Microbiol Biotechnol 2007; 77:375-81. [PMID: 17828601 DOI: 10.1007/s00253-007-1174-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 08/20/2007] [Accepted: 08/22/2007] [Indexed: 01/17/2023]
Abstract
A fusion protein expression system is described that allows for production of eukaryotic integral membrane proteins in Escherichia coli (E. coli). The eukaryotic membrane protein targets are fused to the C terminus of the highly expressed E. coli inner membrane protein, GlpF (the glycerol-conducting channel protein). The generic utility of this system for heterologous membrane-protein expression is demonstrated by the expression and insertion into the E. coli cell membrane of the human membrane proteins: occludin, claudin 4, duodenal ferric reductase and a J-type inwardly rectifying potassium channel. The proteins are produced with C-terminal hexahistidine tags (to permit purification of the expressed fusion proteins using immobilized metal affinity chromatography) and a peptidase cleavage site (to allow recovery of the unfused eukaryotic protein).
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Affiliation(s)
- Irene Neophytou
- Pharmaceutical Sciences Division, King's College London, Franklin Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
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Werle M, Kafedjiiski K, Kolmar H, Bernkop-Schnürch A. Evaluation and improvement of the properties of the novel cystine-knot microprotein McoEeTI for oral administration. Int J Pharm 2007; 332:72-9. [PMID: 17070661 DOI: 10.1016/j.ijpharm.2006.09.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 09/14/2006] [Accepted: 09/19/2006] [Indexed: 11/18/2022]
Abstract
Cystine-knot microproteins exhibit several properties that make them highly interesting as scaffolds for oral peptide drug delivery. It was therefore the aim of the study to evaluate the novel clinically relevant cystine-knot microprotein McoEeTI regarding its potential for oral delivery. Additionally, based on the gained results, important features of McoEeTI were improved. Enzymatic degradation was caused by chymotrypsin, trypsin and porcine small intestinal juice whereas McoEeTI was stable towards elastase, membrane bound proteases, pepsin and porcine gastric juice. Only minor McoEeTI degradation was observed during a 24h incubation period in rat plasma. In the presence of various physiological ions about 50% of McoEeTI formed di- and/or trimers. P(app) value of McoEeTI was determined to be (7.4+/-0.4)x10(-6)cm/s. Sodium caprate and polycarbophil-cysteine (PCP-Cys) had no beneficial effect on McoEeTI permeation, whereas the utilization of a chitosan-thiobutylamidine (Chito-TBA) system improved McoEeTI permeation 3-fold. Enzymatic stability could be strongly improved by the utilization of Bowman-Birk-Inhibitor (BBI) as well as PCP-Cys. In conclusion, this study indicates that McoEeTI represents a promising candidate as a novel scaffold for oral peptide drug delivery.
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Affiliation(s)
- M Werle
- ThioMatrix GmbH, Research Center Innsbruck, Mitterweg 24, 6020 Innsbruck, Austria
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