Engineering the expression of an anti-interleukin-13 antibody through rational design and mutagenesis

Popović, Bojana; Gibson, Suzanne J.; Senussi, Tarik; Carmen, Sara; Kidd, Sara; Slidel, Tim; Strickland, Ian; Xu, Jianqing; Spooner, Jennifer; Lewis, Amanda L.; Hudson, Nathan E.; Mackenzie, Lorna; Keen, J.M.; Kemp, Ben; Hardman, Colin; Hatton, Diane; Wilkinson, Trevor; Vaughan, Tristan J.; Lowe, David C.

doi:10.1093/protein/gzx001

Cited by 7 publications

(18 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For example, they will not detect sources of immunogenicity, nor more subtle mechanisms that lead to poor stability. Nevertheless, we have shown that the TAP guidelines can selectively highlight antibodies with expression or aggregation issues (11,34). The choice of 5 th /95 th percentile amber flag cut-offs proved useful in distinguishing weak aggregators from non-aggregators ( Fig.…”

Section: Discussionmentioning

confidence: 95%

“…4B), again red-flagging the candidate with prohibitive developability issues. Both AB001 and AB008, confirmed monomers in solution (11), did not flag for CDR vicinity PSH score (Fig. 4A).…”

Section: R a F Tmentioning

confidence: 92%

“…Charge. Surface patches of positive or negative charge have also been linked to negative biophysical characteristics (10,11). We calculated two metrics designed to highlight regions of dense charge: the Patches of Positive Charge (PPC) and Patches of Negative Charge (PNC) measures (see Methods).…”

Section: R a F Tmentioning

confidence: 99%

“…4A). A lead anti-IL13 candidate, AB008, had no developability issues, but the affinity-matured version, AB001, had very poor levels of expression (seven times lower than AB008) (11). The authors highlighted the role of four consecutive negatively charged residues in the L2 loop -mutation of the fourth negatively charged residue to neutral asparagine (AB001DDEN) was able to stabilize the loop backbone, mitigating the ionic repulsion of the DDE motif, and returning acceptable levels of expression.…”

Section: R a F Tmentioning

confidence: 99%

“…Asymmetry in the net charge of the heavy and light chain variable domains is also correlated with self-association and viscosity at high concentrations (4,9). Patches of positive (10) and negative (11) charge in the CDRs are linked to high rates of clearance and poor expression levels. Product heterogeneity (e.g.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

The Therapeutic Antibody Profiler (TAP): Five Computational Developability Guidelines

Raybould

Marks

Krawczyk

et al. 2018

Preprint

View full text Add to dashboard Cite

Therapeutic monoclonal antibodies (mAbs) must not only bind to their target but must also be free from 'developability issues', such as poor stability or high levels of aggregation. While small molecule drug discovery benefits from Lipinski's rule of five to guide the selection of molecules with appropriate biophysical properties, there is currently no in silico analog for antibody design. Here, we model the variable domain structures of a large set of post-Phase I clinical-stage antibody therapeutics (CSTs), and calculate an array of metrics to estimate their typical properties. In each case, we contextualize the CST distribution against a snapshot of the human antibody gene repertoire. We describe guideline values for five metrics thought to be implicated in poor developability: the total length of the Complementarity-Determining Regions (CDRs), the extent and magnitude of surface hydrophobicity, positive charge and negative charge in the CDRs, and asymmetry in the net heavy and light chain surface charges. The guideline cut-offs for each property were derived from the values seen in CSTs, and a flagging system is proposed to identify nonconforming candidates. On two mAb drug discovery sets, we were able to selectively highlight sequences with developability issues. We make available the Therapeutic Antibody Profiler (TAP), an open-source computational tool that builds downloadable homology models of variable domain sequences, tests them against our five developability guidelines, and reports potential sequence liabilities and canonical forms. TAP is freely available at http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/TAP.php therapeutic monoclonal antibodies | developability guidelines | immunoglobulin gene sequencing | surface hydrophobicity | surface charge Correspondence: deane@stats.ox.ac.uk Raybould et al. | bioRχiv | June 29, 2018 | 1-7

show abstract

Section: Discussionmentioning

confidence: 95%

“…4B), again red-flagging the candidate with prohibitive developability issues. Both AB001 and AB008, confirmed monomers in solution (11), did not flag for CDR vicinity PSH score (Fig. 4A).…”

Section: R a F Tmentioning

confidence: 92%

Section: R a F Tmentioning

confidence: 99%

Section: R a F Tmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The Therapeutic Antibody Profiler (TAP): Five Computational Developability Guidelines

Raybould

Marks

Krawczyk

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

Effect of charged mutation on aggregation of a pentapeptide: Insights from molecular dynamics simulations

et al. 2021

View full text Add to dashboard Cite

Aggregation of therapeutic monoclonal antibodies (mAbs) can negatively affect their chemistry, manufacturing, and control attributes and lead to undesirable immune responses in patients. Therefore, optimization of lead mAb drug candidates during discovery stages to mitigate aggregation is increasingly becoming an integral part of their developability assessments. The disruption of short sequence motifs called aggregation prone regions (APRs) found in amino acid sequences of mAb candidates can potentially mitigate their aggregation. In this work, we have performed molecular dynamics simulations to study the aggregation of an APR (VLVIY) found in λ light chains of human antibodies and its single point mutant KLVIY. Eighteen different multicopy peptide simulation systems of "VLVIY" and "KLVIY" were constructed by varying their concentrations, temperatures, termini capping, and flanking gate-keeper regions. Within 20 ns of the simulation, peptide "VLVIY" formed an aggregate of 100 peptides at $0.1 M concentration with a 60% reduction in solvent accessible surface area (SASA). Furthermore, analysis of the SASA change, peptide cluster distribution, and water residence time demonstrated how Val à Lys mutation resists aggregation and improves solubility. Presence of Lys slows down aggregation kinetics via charge-charge repulsions and by raising the kinetic barrier to formation of large oligomers. However, the effect of the Val à Lys mutation is dependent on sequence and structural contexts around the APR. This mutation also alters the solvation shell around the peptide by favoring solute-solvent interactions, thereby increasing its solubility. This work has provided a detailed mechanistic explanation of how APR disruption can mitigate aggregation in biotherapeutics and improve their developability.

show abstract

Non-specificity as the sticky problem in therapeutic antibody development

et al. 2022

View full text Add to dashboard Cite

Engineering the expression of an anti-interleukin-13 antibody through rational design and mutagenesis

Cited by 7 publications

References 33 publications

The Therapeutic Antibody Profiler (TAP): Five Computational Developability Guidelines

The Therapeutic Antibody Profiler (TAP): Five Computational Developability Guidelines

Effect of charged mutation on aggregation of a pentapeptide: Insights from molecular dynamics simulations

Non-specificity as the sticky problem in therapeutic antibody development

Contact Info

Product

Resources

About