Stability-Diversity Tradeoffs Impose Fundamental Constraints on Selection of Synthetic Human V(H)/V(L) Single-Domain Antibodies from In Vitro Display Libraries

Human autonomous V(H)/V(L) single-domain antibodies (sdAbs) are attractive therapeutic molecules, but often suffer from suboptimal stability, solubility and affinity for cognate antigens. Most commonly, human sdAbs have been isolated from in vitro display libraries constructed via synthetic randomization of rearranged V(H)/V(L) domains. Here, we describe the design and characterization of three novel human V(H)/V(L) sdAb libraries through a process of: (i) exhaustive biophysical characterization of 20 potential V(H)/V(L) sdAb library scaffolds, including assessment of expression yield, aggregation resistance, thermostability and tolerance to complementarity-determining region (CDR) substitutions; (ii) in vitro randomization of the CDRs of three V(H)/V(L) sdAb scaffolds, with tailored amino acid representation designed to promote solubility and expressibility; and (iii) systematic benchmarking of the three V(H)/V(L) libraries by panning against five model antigens. We isolated ≥1 antigen-specific human sdAb against four of five targets (13 V(H)s and 7 V(L)s in total); these were predominantly monomeric, had antigen-binding affinities ranging from 5 nM to 12 µM (average: 2–3 µM), but had highly variable expression yields (range: 0.1–19 mg/L). Despite our efforts to identify the most stable V(H)/V(L) scaffolds, selection of antigen-specific binders from these libraries was unpredictable (overall success rate for all library-target screens: ~53%) with a high attrition rate of sdAbs exhibiting false positive binding by ELISA. By analyzing V(H)/V(L) sdAb library sequence composition following selection for monomeric antibody expression (binding to protein A/L followed by amplification in bacterial cells), we found that some V(H)/V(L) sdAbs had marked growth advantages over others, and that the amino acid composition of the CDRs of this set of sdAbs was dramatically restricted (bias toward Asp and His and away from aromatic and hydrophobic residues). Thus, CDR sequence clearly dramatically impacts the stability of human autonomous V(H)/V(L) immunoglobulin domain folds, and sequence-stability tradeoffs must be taken into account during the design of such libraries.