title: Structure-based prediction of asparagine and aspartate degradation sites in antibody variable regions.
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 in silico prediction method for the degradation propensity of both Asn and Asp residues in the complementarity-determining regions (CDRs) of mAbs.
authors: Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Jasmin F
authors: JF
authors: Sydow
authors: Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Florian
authors: F
authors: Lipsmeier
authors: Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Vincent
authors: V
authors: Larraillet
authors: Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Maximiliane
authors: M
authors: Hilger
authors: Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Bjoern
authors: B
authors: Mautz
authors: Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Michael
authors: M
authors: Mølhøj
authors: Disease & Translational Informatics, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Jan
authors: J
authors: Kuentzer
authors: Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Stefan
authors: S
authors: Klostermann
authors: Therapeutics Modalities Informatics, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Juergen
authors: J
authors: Schoch
authors: Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Hans R
authors: HR
authors: Voelger
authors: Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Joerg T
authors: JT
authors: Regula
authors: Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität (LMU), Munich, Germany.
authors: Patrick
authors: P
authors: Cramer
authors: Pharmaceutical Sciences, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Apollon
authors: A
authors: Papadimitriou
authors: Large Molecule Research, Roche Pharmaceutical Research and Early Development, Penzberg, Germany.
authors: Hubert
authors: H
authors: Kettenberger
mesh_terms: D001185:Artificial Intelligence; D001216:Asparagine / Q000737:chemistry* / Q000378:metabolism; D001224:Aspartic Acid / Q000737:chemistry* / Q000378:metabolism; D007135:Immunoglobulin Variable Region / Q000737:chemistry* / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008958:Models, Molecular; D008968:Molecular Conformation; D059748:Proteolysis; D012372:ROC Curve; D013329:Structure-Activity Relationship
chemical_list: D007135:Immunoglobulin Variable Region; D001224:Aspartic Acid; D001216:Asparagine