Protein asparagine deamidation prediction based on structures with machine learning methods

Abstract

Chemical stability is a major concern in the development of protein therapeutics due to its impact on both efficacy and safety. Protein “hotspots” are amino acid residues that are subject to various chemical modifications, including deamidation, isomerization, glycosylation, oxidation etc. A more accurate prediction method for potential hotspot residues would allow their elimination or reduction as early as possible in the drug discovery process. In this work, we focus on prediction models for asparagine (Asn) deamidation. Sequence-based prediction method simply identifies the NG motif (amino acid asparagine followed by a glycine) to be liable to deamidation. It still dominates deamidation evaluation process in most pharmaceutical setup due to its convenience. However, the simple sequence-based method is less accurate and often causes over-engineering a protein. We introduce structure-based prediction models by mining available experimental and structural data of deamidated proteins. Our training set contains 194 Asn residues from 25 proteins that all have available high-resolution crystal structures. Experimentally measured deamidation half-life of Asn in penta-peptides as well as 3D structure-based properties, such as solvent exposure, crystallographic B-factors, local secondary structure and dihedral angles etc., were used to train prediction models with several machine learning algorithms. The prediction tools were cross-validated as well as tested with an external test data set. The random forest model had high enrichment in ranking deamidated residues higher than non-deamidated residues while effectively eliminated false positive predictions. It is possible that such quantitative protein structure–function relationship tools can also be applied to other protein hotspot predictions. In addition, we extensively discussed metrics being used to evaluate the performance of predicting unbalanced data sets such as the deamidation case.

Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design

“…Therefore, several computational methods have been proposed to rapidly assess the chemical stability of therapeutic proteins. 25,[101][102][103][104][105][106][107][108][109][110][111] One of the most common degradation events is the chemical modification of Asn and Asp residues, which share a degradation pathway. 25 Many of the methods to predict such degradation are statisticalbased methods, and experimental data to derive such prediction models are either from in-house experiments 101,103,107,108,110 or from literature.…”

“…25 Many of the methods to predict such degradation are statisticalbased methods, and experimental data to derive such prediction models are either from in-house experiments 101,103,107,108,110 or from literature. 104,106,111 For example, to understand origins of Asn deamidation and Asp isomerization, Sydow et al 101 used mass spectrometry to experimentally characterize 37 antibodies that were subjected to forced degradation. These experimental data, together with homology modeling of the antibodies, suggested that degradation hotspots could be characterized by their conformational flexibility, the size of the C-terminal franking residue, and secondary structures.…”

Predicting Antibody Developability Profiles Through Early Stage Discovery Screening

“…While the HT biophysical analyses presented here show meaningful correlations between properties, a larger and more diverse dataset than what is presented here will be needed to make solid correlation estimates between these assays and downstream process parameters and endpoints. [58][59][60][61][62][63][64]…”

Online control of cell culture redox potential prevents antibody interchain disulfide bond reduction

“…Deamidation can affect antibody-antigen binding if the site of deamidation is in or near the antigen binding domain of a mAb (Jia & Sun, 2017). Additionally, glycation can potentially impact the bioactivity and stability of a mAb (Wei, Berning, Quan, & Zhang, 2017).…”