Leveraging SBDD in Protein Therapeutic Development: Antibody Engineering

Abstract

Antibodies make up the largest, growing segment of protein therapeutics in the pharmaceutical and biotechnology industries. The development or engineering of therapeutic antibodies is based to a large extent on our knowledge of antibody structure and requires sophisticated methods that continue to evolve. In this chapter, after a review of what is known about the structure and functional properties of antibodies, the current, state-of-the-art antibody engineering methods are described. These methods include antibody humanization, antigen-affinity optimization, Fc engineering for modulated effector function and extended half-life, and engineering for improved stability and biophysical properties. X-ray crystallographic structures of antibody fragments and their complexes can play a critical role in guiding and, in some cases, accelerating these processes. These approaches represent guidelines for developing antibody therapeutics with the desired affinity, effector function, and biophysical properties.

Variable Region Identical Immunoglobulins Differing in Isotype Express Different Paratopes

“…In the crystal structure of PA1 and mAb 2H1, the parts of the peptide located in the binding pocket of 2H1 correspond to two motifs involving Thr-5 and Pro-6 and Trp-8, Met-9, and Leu-10, which are comparable with two motifs in P1 that show the greatest decreases in binding when mutated to alanine. Because these studies were done with immobilized peptide, some differences in binding observed for IgG 1 and IgG 3 may reflect a loss of avidity resulting from an inability to form binding complexes given Ab isotype-related differences in hinge angles (41). However, we think this explanation is less likely to apply for all isotypes given the strong reactivity of the IgG 2a and IgG 2b subclasses, with both GXM and P1 (7).…”

“…The V region binds antigen (Ag) and is capable of enormous combinatorial diversity that can recognize a myriad of molecular conformations, whereas the C region provides such functional capacities as the ability to interact with host receptors and activate the complement system (1). In this conception, the V and C regions functioned as two virtually independent domains, with the V region being responsible for binding Ag and the C region providing other biological functions.…”

The functional repertoire of rabbit antibodies and antibody discovery via next-generation sequencing

“…These antibodies may present liabilities with regard to the development of therapeutic antibodies. 30 Twelve-residue loops of IM sample are also rich (~65%) in Cys at position 95 and 95e, probably making of disulfide bridge. The content of Cys at those positions drops to ~20% in the BM and SP samples, suggesting a positive pressure by the peptide immunization to select for loops with a disulfide bridge between position 95 and 95e.…”

Assessment of Solvated Interaction Energy Function for Ranking Antibody–Antigen Binding Affinities

“…6,7 Many of these platforms depend on antibodies obtained by animal immunization, e.g., via the hybridoma technique, 8 and often require subsequent optimization. 9,10 Humanization, required for most antibodies from animal sources, typically leads to a reduction in affinity. Other modifications may also be also introduced in order to modulate other properties such as thermal stability, water solubility, pharmacokinetics, etc., which often results in partial losses of the original antigen-binding affinity.…”