ABSTRACT
MAbTope is a docking-based method for the determination of epitopes. It has been used to successfully determine the epitopes of antibodies with known 3D structures. However, during the antibody discovery process, this structural information is rarely available. Although we already have evidence that homology models of antibodies could be used instead of their 3D structure, the choice of the template, the methodology for homology modeling and the resulting performance still have to be clarified. Here, we show that MAbTope has the same performance when working with homology models of the antibodies as compared to crystallographic structures. Moreover, we show that even low-quality models can be used. We applied MAbTope to determine the epitope of dupilumab, an anti- interleukin 4 receptor alpha subunit therapeutic antibody of unknown 3D structure, that we validated experimentally. Finally, we show how the MAbTope-determined epitopes for a series of antibodies targeting the same protein can be used to predict competitions, and demonstrate the accuracy with an experimentally validated example.3D: three-dimensionalRMSD: root mean square deviationCDR: complementary-determining regionCPU: central processing unitsVH: heavy chain variable regionVL: light chain variable regionscFv: single-chain variable fragmentsVHH: single-chain antibody variable regionIL4Rα: Interleukin 4 receptor alpha chainSPR: surface plasmon resonancePDB: protein data bankHEK293: Human embryonic kidney 293 cellsEDTA: Ethylenediaminetetraacetic acidFBS: Fetal bovine serumANOVA: Analysis of varianceEGFR: Epidermal growth factor receptorPE: PhycoerythrinAPC: AllophycocyaninFSC: forward scatterSSC: side scatterWT: wild typeKeywords: MAbTope, Epitope Mapping, Molecular docking, Antibody modeling, Antibody-antigen docking.
Subject(s)
Antibodies, Monoclonal, Humanized/immunology , Antigens/immunology , Epitope Mapping , Epitopes , Interleukin-4 Receptor alpha Subunit/immunology , Molecular Docking Simulation , Antibodies, Monoclonal, Humanized/chemistry , Antibodies, Monoclonal, Humanized/metabolism , Antigens/genetics , Antigens/metabolism , Binding Sites, Antibody , ErbB Receptors/immunology , ErbB Receptors/metabolism , HEK293 Cells , Humans , Interleukin-4 Receptor alpha Subunit/genetics , Interleukin-4 Receptor alpha Subunit/metabolism , Mutation , Protein Binding , Protein Conformation , Structure-Activity RelationshipABSTRACT
Abs are very efficient drugs, â¼70 of them are already approved for medical use, over 500 are in clinical development, and many more are in preclinical development. One important step in the characterization and protection of a therapeutic Ab is the determination of its cognate epitope. The gold standard is the three-dimensional structure of the Ab/Ag complex by crystallography or nuclear magnetic resonance spectroscopy. However, it remains a tedious task, and its outcome is uncertain. We have developed MAbTope, a docking-based prediction method of the epitope associated with straightforward experimental validation procedures. We show that MAbTope predicts the correct epitope for each of 129 tested examples of Ab/Ag complexes of known structure. We further validated this method through the successful determination, and experimental validation (using human embryonic kidney cells 293), of the epitopes recognized by two therapeutic Abs targeting TNF-α: certolizumab and golimumab.
Subject(s)
Antibodies, Monoclonal/chemistry , Epitope Mapping/methods , Molecular Docking Simulation/methods , HEK293 Cells , HumansABSTRACT
Modelling river temperature at the catchment scale is needed to understand how aquatic communities may adapt to current and projected climate change. In small and medium rivers, riparian vegetation can greatly reduce maximum water temperature by providing shade. It is thus important that river temperature models are able to correctly characterise the impact of this riparian shading. In this study, we describe the use of a spatially-explicit method using LiDAR-derived data for computing the riparian shading on direct and diffuse solar radiation. The resulting data are used in the T-NET one-dimensional stream temperature model to simulate water temperature from August 2007 to July 2014 for 270km of the Loir River, an indirect tributary of the Loire River (France). Validation is achieved with 4 temperature monitoring stations spread along the Loir River. The vegetation characterised with the LiDAR approach provides a cooling effect on maximum daily temperature (Tmax) ranging from 3.0°C (upstream) to 1.3°C (downstream) in late August 2009. Compared to two other riparian shading routines that are less computationally-intensive, the use of our LiDAR-based methodology improves the bias of Tmax simulated by the T-NET model by 0.62°C on average between April and September. However, difference between the shading routines reaches up to 2°C (monthly average) at the upstream-most station. Standard deviation of errors on Tmax is not improved. Computing the impact of riparian vegetation at the hourly timescale using reach-averaged parameters provides results close to the LiDAR-based approach, as long as it is supplied with accurate vegetation cover data. Improving the quality of riparian vegetation data should therefore be a priority to increase the accuracy of stream temperature modelling at the regional scale.
