Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-based Biotherapeutics

Adequate stability, manufacturability and safety is crucial to bring an antibody-based biotherapeutic to the market. Following the concept of holistic in silico developability, we introduce physicochemical description of 91 market-stage antibody-based biotherapeutics based on orthogonal molecular properties of the variable regions (Fvs) embedded in different simulation environments, mimicking conditions experienced by antibodies during manufacturing, formulation, and in vivo. In this work, evaluation of molecular properties includes conformational flexibility of the Fvs using molecular dynamics (MD) simulations. The comparison between static homology models and simulations shows that molecular dynamics significantly affects certain molecular descriptors like the surface molecular patches. Moreover, the structural stability of a subset of Fv regions is linked to changes in their specific molecular interactions with ions in different experimental conditions. This is supported by the observation of differences in protein melting temperatures upon addition of NaCl. A DEvelopability Navigator In Silico (DENIS) is proposed to compare mAb candidates for their similarity with market-stage biotherapeutics in terms of physicochemical properties and conformational stability. Expanding on our previous developability guidelines, the hydrodynamic radius and the protein strand ratio are introduced as two additional descriptors that enable more comprehensive in silico characterization of biotherapeutic drug candidates. Testcases show how this approach can facilitate identification and optimization of intrinsically developable lead candidates. DENIS represents an advanced computational tool available to progress biotherapeutic drug candidates from discovery into early development and that can have a significant impact on the prediction of drug product stability in different aqueous environments.