Structure-Based Prediction of Asparagine and Aspartate Degradation Sites in Antibody Variable Regions
Identifieur interne : 000066 ( Main/Exploration ); précédent : 000065; suivant : 000067Structure-Based Prediction of Asparagine and Aspartate Degradation Sites in Antibody Variable Regions
Auteurs : Jasmin F. Sydow [Allemagne] ; Florian Lipsmeier [Allemagne] ; Vincent Larraillet [Allemagne] ; Maximiliane Hilger [Allemagne] ; Bjoern Mautz [Allemagne] ; Michael M Lh J [Allemagne] ; Jan Kuentzer [Allemagne] ; Stefan Klostermann [Allemagne] ; Juergen Schoch [Allemagne] ; Hans R. Voelger [Allemagne] ; Joerg T. Regula [Allemagne] ; Patrick Cramer [Allemagne] ; Apollon Papadimitriou [Allemagne] ; Hubert Kettenberger [Allemagne]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Monoclonal antibodies (mAbs) and proteins containing antibody domains are the most prevalent class of biotherapeutics in diverse indication areas. Today, established techniques such as immunization or phage display allow for an efficient generation of new mAbs. Besides functional properties, the stability of future therapeutic mAbs is a key selection criterion which is essential for the development of a drug candidate into a marketed product. Therapeutic proteins may degrade via asparagine (Asn) deamidation and aspartate (Asp) isomerization, but the factors responsible for such degradation remain poorly understood. We studied the structural properties of a large, uniform dataset of Asn and Asp residues in the variable domains of antibodies. Their structural parameters were correlated with the degradation propensities measured by mass spectrometry. We show that degradation hotspots can be characterized by their conformational flexibility, the size of the C-terminally flanking amino acid residue, and secondary structural parameters. From these results we derive an accurate
Url:
DOI: 10.1371/journal.pone.0100736
PubMed: 24959685
PubMed Central: 4069079
Affiliations:
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Sydow</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Lipsmeier, Florian" sort="Lipsmeier, Florian" uniqKey="Lipsmeier F" first="Florian" last="Lipsmeier">Florian Lipsmeier</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Larraillet, Vincent" sort="Larraillet, Vincent" uniqKey="Larraillet V" first="Vincent" last="Larraillet">Vincent Larraillet</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Hilger, Maximiliane" sort="Hilger, Maximiliane" uniqKey="Hilger M" first="Maximiliane" last="Hilger">Maximiliane Hilger</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Mautz, Bjoern" sort="Mautz, Bjoern" uniqKey="Mautz B" first="Bjoern" last="Mautz">Bjoern Mautz</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="M Lh J, Michael" sort="M Lh J, Michael" uniqKey="M Lh J M" first="Michael" last="M Lh J">Michael M Lh J</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Kuentzer, Jan" sort="Kuentzer, Jan" uniqKey="Kuentzer J" first="Jan" last="Kuentzer">Jan Kuentzer</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Disease & Translational Informatics, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Disease & Translational Informatics, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Klostermann, Stefan" sort="Klostermann, Stefan" uniqKey="Klostermann S" first="Stefan" last="Klostermann">Stefan Klostermann</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Schoch, Juergen" sort="Schoch, Juergen" uniqKey="Schoch J" first="Juergen" last="Schoch">Juergen Schoch</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Voelger, Hans R" sort="Voelger, Hans R" uniqKey="Voelger H" first="Hans R." last="Voelger">Hans R. Voelger</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Regula, Joerg T" sort="Regula, Joerg T" uniqKey="Regula J" first="Joerg T." last="Regula">Joerg T. Regula</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Cramer, Patrick" sort="Cramer, Patrick" uniqKey="Cramer P" first="Patrick" last="Cramer">Patrick Cramer</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität (LMU), Munich, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität (LMU), Munich</wicri:regionArea></affiliation></author><author><name sortKey="Papadimitriou, Apollon" sort="Papadimitriou, Apollon" uniqKey="Papadimitriou A" first="Apollon" last="Papadimitriou">Apollon Papadimitriou</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Pharmaceutical Sciences, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Pharmaceutical Sciences, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author><author><name sortKey="Kettenberger, Hubert" sort="Kettenberger, Hubert" uniqKey="Kettenberger H" first="Hubert" last="Kettenberger">Hubert Kettenberger</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Monoclonal antibodies (mAbs) and proteins containing antibody domains are the most prevalent class of biotherapeutics in diverse indication areas. Today, established techniques such as immunization or phage display allow for an efficient generation of new mAbs. Besides functional properties, the stability of future therapeutic mAbs is a key selection criterion which is essential for the development of a drug candidate into a marketed product. Therapeutic proteins may degrade via asparagine (Asn) deamidation and aspartate (Asp) isomerization, but the factors responsible for such degradation remain poorly understood. We studied the structural properties of a large, uniform dataset of Asn and Asp residues in the variable domains of antibodies. Their structural parameters were correlated with the degradation propensities measured by mass spectrometry. We show that degradation hotspots can be characterized by their conformational flexibility, the size of the C-terminally flanking amino acid residue, and secondary structural parameters. From these results we derive an accurate <italic>in silico</italic> prediction method for the degradation propensity of both Asn and Asp residues in the complementarity-determining regions (CDRs) of mAbs.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Reichert, Jm" uniqKey="Reichert J">JM Reichert</name></author><author><name sortKey="Rosensweig, Cj" uniqKey="Rosensweig C">CJ Rosensweig</name></author><author><name sortKey="Faden, Lb" uniqKey="Faden L">LB Faden</name></author><author><name sortKey="Dewitz, Mc" uniqKey="Dewitz M">MC Dewitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Swann, Pg" uniqKey="Swann P">PG Swann</name></author><author><name sortKey="Tolnay, M" uniqKey="Tolnay M">M Tolnay</name></author><author><name sortKey="Muthukkumar, S" uniqKey="Muthukkumar S">S Muthukkumar</name></author><author><name sortKey="Shapiro, Ma" uniqKey="Shapiro M">MA 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Sali</name></author><author><name sortKey="Blundell, Tl" uniqKey="Blundell T">TL Blundell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Spassov, Vz" uniqKey="Spassov V">VZ Spassov</name></author><author><name sortKey="Flook, Pk" uniqKey="Flook P">PK Flook</name></author><author><name sortKey="Yan, L" uniqKey="Yan L">L Yan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chothia, C" uniqKey="Chothia C">C Chothia</name></author><author><name sortKey="Lesk, Am" uniqKey="Lesk A">AM Lesk</name></author><author><name sortKey="Tramontano, A" uniqKey="Tramontano A">A Tramontano</name></author><author><name sortKey="Levitt, M" uniqKey="Levitt M">M Levitt</name></author><author><name sortKey="Smith Gill, Sj" uniqKey="Smith Gill S">SJ Smith-Gill</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chennamsetty, N" uniqKey="Chennamsetty N">N Chennamsetty</name></author><author><name sortKey="Voynov, V" uniqKey="Voynov V">V Voynov</name></author><author><name sortKey="Kayser, V" uniqKey="Kayser V">V Kayser</name></author><author><name sortKey="Helk, B" uniqKey="Helk B">B Helk</name></author><author><name sortKey="Trout, Bl" uniqKey="Trout B">BL Trout</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Karatzoglou, A" uniqKey="Karatzoglou A">A Karatzoglou</name></author><author><name sortKey="Smola, A" uniqKey="Smola A">A Smola</name></author><author><name sortKey="Hornik, K" uniqKey="Hornik K">K Hornik</name></author><author><name sortKey="Zeileis, A" uniqKey="Zeileis A">A Zeileis</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Sydow, Jasmin F" sort="Sydow, Jasmin F" uniqKey="Sydow J" first="Jasmin F." last="Sydow">Jasmin F. Sydow</name></noRegion><name sortKey="Cramer, Patrick" sort="Cramer, Patrick" uniqKey="Cramer P" first="Patrick" last="Cramer">Patrick Cramer</name><name sortKey="Hilger, Maximiliane" sort="Hilger, Maximiliane" uniqKey="Hilger M" first="Maximiliane" last="Hilger">Maximiliane Hilger</name><name sortKey="Kettenberger, Hubert" sort="Kettenberger, Hubert" uniqKey="Kettenberger H" first="Hubert" last="Kettenberger">Hubert Kettenberger</name><name sortKey="Klostermann, Stefan" sort="Klostermann, Stefan" uniqKey="Klostermann S" first="Stefan" last="Klostermann">Stefan Klostermann</name><name sortKey="Kuentzer, Jan" sort="Kuentzer, Jan" uniqKey="Kuentzer J" first="Jan" last="Kuentzer">Jan Kuentzer</name><name sortKey="Larraillet, Vincent" sort="Larraillet, Vincent" uniqKey="Larraillet V" first="Vincent" last="Larraillet">Vincent Larraillet</name><name sortKey="Lipsmeier, Florian" sort="Lipsmeier, Florian" uniqKey="Lipsmeier F" first="Florian" last="Lipsmeier">Florian Lipsmeier</name><name sortKey="M Lh J, Michael" sort="M Lh J, Michael" uniqKey="M Lh J M" first="Michael" last="M Lh J">Michael M Lh J</name><name sortKey="Mautz, Bjoern" sort="Mautz, Bjoern" uniqKey="Mautz B" first="Bjoern" last="Mautz">Bjoern Mautz</name><name sortKey="Papadimitriou, Apollon" sort="Papadimitriou, Apollon" uniqKey="Papadimitriou A" first="Apollon" last="Papadimitriou">Apollon Papadimitriou</name><name sortKey="Regula, Joerg T" sort="Regula, Joerg T" uniqKey="Regula J" first="Joerg T." last="Regula">Joerg T. Regula</name><name sortKey="Schoch, Juergen" sort="Schoch, Juergen" uniqKey="Schoch J" first="Juergen" last="Schoch">Juergen Schoch</name><name sortKey="Voelger, Hans R" sort="Voelger, Hans R" uniqKey="Voelger H" first="Hans R." last="Voelger">Hans R. Voelger</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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