Effects of thermal-stress and glycan-removal on structural integrity of a human IgG1 antibody: Insights from extended molecular dynamics simulations
Dheeraj Singh Tomar
Dheeraj Singh Tomar1, Sandeep Kumar1, Satish K. Singh2
Biopharmaceutical drugs are a successful class of medicines for the treatment and management of several diseases. Many challenges must be overcome at each stage in the drug discovery and development cycle for successful translation of drug discoveries into medicines available in clinic. Biopharmaceutical Informatics is a novel concept that can assist in the product development of biopharmaceutical drugs such as monoclonal antibodies by innovative applications of computational chemistry and data analyses. In an effort to advance this concept, advanced understanding of antibody structural and dynamic properties was sought to understand molecular origins of physicochemical degradation in biotherapeutics. Fully atomistic explicit water molecular dynamics simulations on human b12 monoclonal antibody molecule were performed to understand effects of thermal-stress and glycan-removal on its structural integrity. These simulations are performed at 300 K and 500 K (to mimic accelerated stability studies) and with the glycans attached and removed, thereby resulting in four separate conditions. At room temperature, variable regions of the antibody molecule fluctuate more than the constant regions. At the elevated temperature, solvent exposed surface area and Cα contact maps suggest that the entire antibody molecule collapses onto itself. Furthermore, hydrodynamic radius and radius of gyration of the Fc portion of the antibody molecule decrease suggesting that this collapse is being driven by the Fc portion. Visual examination of the elevated temperature simulation trajectories shows that quaternary structure of the CH2 region is disrupted and one of the CH2 domains contacts the CL domain in the different heavy chain-light chain pair. The above trend is further enhanced when glycans are removed. Moreover, analysis of Root Mean Square Deviations (RMSDs) reveals that thermal-stress affects the structure globally and more strongly than the glycan-removal. The RMSDs for the antibody molecule as well as the individual regions (two Fabs and Fc) are greater in the case of the thermal stress. The glycan-removal, on the other hand, leads to perturbation of the CH2 domain quaternary structure. These simulations have led to an improved understanding of the effect of inherent conformational dynamics on physicochemical degradation (for example, aggregation, oxidation, deamidation) of an antibody molecule.