CDRxAbs: Antibody Small-Molecule Conjugates with Computationally Designed Target-Binding Synergy

Abstract Antibody-drug conjugates (ADCs) combine the advantages and offset the disadvantages of their constituent parts to achieve a refined spectrum of action. We combine the concept of ADCs with the full atomic simulation capability of computational protein design to define a new class of molecular recognition agents: CDR-extended antibodies, abbreviated as CDRxAbs. A CDRxAb incorporates a covalently attached small molecule into an antibody/target binding interface using computational protein design to create an antibody small-molecule conjugate that binds tighter to the target of the small molecule than the small molecule would alone. CDRxAbs are also expected to increase the target binding specificity of their associated small molecules. In a proof-of-concept study using monomeric streptavidin/biotin pairs at either a nanomolar or micromolar-level initial affinity, we designed nanobody-biotin conjugates that exhibited >20-fold affinity improvement against their protein targets with step-wise optimization of binding kinetics and overall protein stability. The workflow explored through this process promises a novel approach to optimize small-molecule based therapeutics and to explore new chemical and target space for molecular-recognition agents in general. Significance We defined a general method for optimizing molecular recognition reagents that involve small molecules and demonstrated an application of this method using a model system. Instead of using traditional approaches for modifying a small molecule to improve its binding properties, we use computational protein design to build an antibody/small molecule conjugate that allows the target-binding strength (and specificity) of the small molecule to be tuned through changes in the amino acid sequence of the antibody scaffold. This method introduces a novel approach for optimizing the binding properties of small molecules and expands the potential application scenarios for antibody-drug conjugates.