Antibody humanization by structure-based computational protein design

Abstract

(2015) Antibody humanization by structure-based computational protein design, mAbs, 7:6, 1045-1057, DOI: 10.1080DOI: 10. /19420862.2015 To link to this article: https://doi.org/10. 1080/19420862.2015 Keywords: antibody, computational protein design, human string content, humanization, pareto optimization, protein structure analysisAbbreviations: MHC, major histocompatibility complex; HSC, Human String Content; RMSD, root mean square deviation; BLI, bio-layer interferometry; IDT, Integrated DNA Technologies; PBS, phosphate-buffered saline; PBS-T, PBS C 0.1% Tween-20; PBS-F, PBS C 0.1% Bovine serum albuminAntibodies derived from non-human sources must be modified for therapeutic use so as to mitigate undesirable immune responses. While complementarity-determining region (CDR) grafting-based humanization techniques have been successfully applied in many cases, it remains challenging to maintain the desired stability and antigen binding affinity upon grafting. We developed an alternative humanization approach called CoDAH ("Computationally-Driven Antibody Humanization") in which computational protein design methods directly select sets of amino acids to incorporate from human germline sequences to increase humanness while maintaining structural stability. Retrospective studies show that CoDAH is able to identify variants deemed beneficial according to both humanness and structural stability criteria, even for targets lacking crystal structures. Prospective application to TZ47, a murine antihuman B7H6 antibody, demonstrates the approach. Four diverse humanized variants were designed, and all possible unique VH/VL combinations were produced as full-length IgG1 antibodies. Soluble and cell surface expressed antigen binding assays showed that 75% (6 of 8) of the computationally designed VH/VL variants were successfully expressed and competed with the murine TZ47 for binding to B7H6 antigen. Furthermore, 4 of the 6 bound with an estimated K D within an order of magnitude of the original TZ47 antibody. In contrast, a traditional CDR-grafted variant could not be expressed. These results suggest that the computational protein design approach described here can be used to efficiently generate functional humanized antibodies and provide humanized templates for further affinity maturation.

Beyond CDR-grafting: Structure-guided humanization of framework and CDR regions of an anti-myostatin antibody

“…Surprisingly though, the heavy chain shows an increased humanness over the light chain, which is the opposite of what is typically observed for humanized antibodies. 60 However, in this case the antibody has a relatively short 7 amino acid long CDR-H3, (80% of murine CDRs are longer than 7 amino acids) 61 and has a CDR-H1 that already matches the human germline. The further optimized clones, RK35 VL 1.4 and RK35 VH 1.5, have HSC scores of 96 and 91, respectively.…”

VH-VL orientation prediction for antibody humanization candidate selection: A case study

“…Homology models of the humanized antibody, in turn, can help to detect problematic amino acid substitutions. By now, a number of in silico tools is available to guide the humanization process 16,17 and to provide automatically generated antibody Fv models. 18 In the following, we focus on an aspect of antibody structure that, in the context of humanization, is often overlooked: the relative orientation of VH and VL domain.…”

Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies

“…In addition, the lack of sufficient maturation outside of the germinal centers and low binding affinities of mAbs derived by hybridoma, meant that only 1.5% of screened clones typically reacted to the target antigen. Due to these problems, antibody humanization was developed as an alternative to generate human format antibodies from rodent derived antibodies (Martin and Rees, 2016;Choi et al, 2015;Olimpieri et al, 2015;Safdari et al, 2013;Tsurushita et al, 2004;Ohtomo et al, 1995). Humanized antibodies are produced by methods of genetic engineering and can potentially reduce the immune response against non-human derived antibodies.…”