Identifying liabilities

You can define and identify sequence-based liabilities and automatically flag motifs when anntotating sequences on PipeBio

An illustration of an IgG antibody with sequence-based liabilities and post-translational modifications shown in the CDRs, C-regions and FRs of the antibody

Liability detection

Accurately annotate, define and characterize regions and liabilities of antibody sequences to de-risk antibody development

Labeling sequences with liabilities

  • PipeBio's annotation tool can detect a wide range of liabilities in sequences that can affect the binding of the antibody with the relevant antigen, aggregation etc.
  • Validations include post-translational modifications (PTMs), quality validations and structural verifications
  • Validations are specified in the scaffold (left in image) with designated liability scores
  • The image shows deamidation and glycosylation sites in the CDR-H3 region
PipeBio sequence viewer with an antibody IgG heavy chain annotated and with liabilities such as deamidation, asp-isomerization and glycosylation sites flagged

Annotation and sequence errors

  • PipeBio’s annotation engine is able to efficiently detect and label CDRs and framework regions in antibody sequences from both the heavy and light (kappa and lambda) chains
  • The variable (V), joining (J), diversity (D) and constant C gene segments are also identified thanks to our manually-curated germline databases
  • You can create custom germline databases to identify and annotate additional regions, such as linkers, tags, loops and more
IgG scaffold configuration and flagged errors in sequences on PipeBio

Post-translational modifications (PTMs) in antibody development

The importance of accurate annotation of antibody sequences

Post-translational modifications cause additional sequence variation and alter the antibody binding properties. This might be troublesome when developing antibodies designed against a specific target.

Inaccurate annotation of sequences or detection of liabilities and identification of mutations will lead to decreased efficacy of promising lead candidates. Efficient and exact annotation tools are therfore needed to ensure the developability[1].

PTMs include the addition of functional groups in the amino acid chain, the modification of existing amino acids in the sequence or the cleavage of bonds, among others [3, 4].

Which liabilities can PipeBio detect?

Below is a list of liabilities detected by the default IgG scaffold on PipeBio:

  • Asparagine deamidation
  • Aspartate isomerization
  • N-linked glycosylation
  • Lysine glycation
  • Methionine oxidation
  • Tryptophan oxidation
  • Aspartic acid – Proline cleavage
  • Hydrolysis
IgG with sequence-based predictions of sites with risk of post translational modifications such as Met or Trp oxidation, asp isomerization, asp deamidation, asp-pro cleavage, hydrolysis, lys glycosylation

References

  • Raybould, M., & Deane, C. M. (2022). The Therapeutic Antibody Profiler for Computational Developability Assessment. Methods in molecular biology (Clifton, N.J.), 2313, 115–125. https://doi.org/10.1007/978-1-0716-1450-1_5
  • Ramazi, S. & Zahiri, J. (2021). Post-translational modifications in proteins: resources, tools and prediction methods. Database, Volume 2021, baab012. https://doi.org/10.1093/database/baab012
  • Lu, X., Nobrega, R. P., Lynaugh, H., Jain, T., Barlow, K., Boland, T., Sivasubramanian, A., Vásquez, M., & Xu, Y. (2019). Deamidation and isomerization liability analysis of 131 clinical-stage antibodies. mAbs, 11(1), 45–57. https://doi.org/10.1080/19420862.2018.1548233
  • Hattori, T., & Koide, S. (2018). Next-generation antibodies for post-translational modifications. Current opinion in structural biology, 51, 141–148. https://doi.org/10.1016/j.sbi.2018.04.006