Adequate stability, manufacturability, and safety are crucial to bringing an antibody-based biotherapeutic to the market. Following the concept of holistic in silico developability, we introduce a physicochemical description of 91 market-stage antibody-based biotherapeutics based on orthogonal molecular properties of variable regions (Fvs) embedded in different simulation environments, mimicking conditions experienced by antibodies during manufacturing, formulation, and in vivo. In this work, the 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 MD significantly affects certain molecular descriptors like 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 (Ahmed et al. Proc. Natl. Acad. Sci. 2021, 118 (37), e2020577118), the hydrodynamic radius and the protein strand ratio are introduced as two additional descriptors that enable a more comprehensive in silico characterization of biotherapeutic drug candidates. Test cases show how this approach can facilitate identification and optimization of intrinsically developable lead candidates. DENIS represents an advanced computational tool to progress biotherapeutic drug candidates from discovery into early development by predicting drug properties in different aqueous environments.

Bispecific T-cell engagers (TcEs) are antibody-based immunotherapeutic drugs that specifically direct lymphocyte effector functions against tumors. TcEs have one arm with affinity for an activating immunoreceptor connected through a flexible hinge to a distinct arm with affinity for a tumor antigen to achieve tumor killing by cytotoxic immune cells. Understanding the structure-function relationships between TcE architecture, immunological synapse formation and function could accelerate design of new TcE-based cancer therapies. Here, we engineer and systematically characterize TcE formats with antigen binding antibody fragments or single chain variable fragments linked together in cis through immunoglobulin G1 hinge or in trans across the antibody constant fragment. The TcEs were tested in CD8+ T-cell killing of Her2+ breast cancer cells and evaluated by high-content imaging of immunological synapse formation on a supported lipid bilayer (SLB) platform. We find that cis TcEs perform better than a trans TcE for T-cell mediated killing. Quantification of synapse formation dynamics revealed that all three cis TcEs tested, created close contacts of < 16 nm leading to rapid synapse formation and integrin activation. In contrast, the trans TcE formed close contacts averaging ≥ 16 nm and formed synapses more slowly with weaker integrin activation. We conclude that segmental flexibility is important for TcE function, but adding additional degrees of freedom through trans formats has a cost for killing efficiency that may be explained by failure of close contact formation and integrin activation.

Biotherapeutic optimization, whether to improve general properties or to engineer specific attributes, is a time-consuming process with uncertain outcomes. Conversely, Consensus Protein Design has been shown to be a viable approach to enhance protein stability while retaining function. In adapting this method for a more limited number of protein sequences, we studied 21 consensus single-point variants from eight publicly available CD3 binding sequences with high similarity but diverse biophysical and pharmacological properties. All single-point consensus variants retained CD3 binding and performed similarly in cell-based functional assays. Using Ridge regression analysis, we identified the variants and sequence positions with overall beneficial effects on developability attributes of the CD3 binders. A second round of sequence generation that combined these substitutions into a single molecule yielded a unique CD3 binder with globally optimized developability attributes. In this first application to therapeutic antibodies, adapted Consensus Protein Design was found to be highly beneficial within lead optimization, conserving resources and minimizing iterations. Future implementations of this general strategy may help accelerate drug discovery and improve success rates in bringing novel biotherapeutics to market.

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