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Quantifying the Risks of Asparagine Deamidation and Aspartate Isomerization in Biopharmaceuticals by Computing Reaction Free-Energy Surfaces
journal contribution
posted on 2017-01-04, 00:00 authored by Nikolay
V. Plotnikov, Satish Kumar Singh, Jason C. Rouse, Sandeep KumarEarly
identification of asparagine deamidation and aspartate isomerization
degradation sites can facilitate the successful development of biopharmaceuticals.
Several knowledge-based models have been proposed to assess these
degradation risks. In this study, we propose a physics-based approach
to identify the degradation sites on the basis of the free-energy
barriers along the prechemical conformational step and the chemical
reaction pathway. These contributions are estimated from classical
and quantum mechanics/molecular mechanics molecular dynamics simulations.
The computed barriers are compared to those for reference reactions
in water within GNG and GDG sequence motifs in peptides (which demonstrate
the highest degradation rates). Two major factors decreasing the degradation
rates relative to the reference reactions are steric hindrance toward
accessing reactive conformations and replacement of water by less
polar side chains in the solvation shell of transition states. Among
the potential degradation sites in the complementarity-determining
region of trastuzumab and between two DK sites in glial cell-derived
neurotropic factor, this method identified N30T, N55G, D102G, and D95K, respectively, in
agreement with experiments. This approach can be incorporated in early
computational screening of chemical degradation sites in biopharmaceuticals.
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degradation sitesGDG sequence motifsN 55 GSeveral knowledge-based modelsD 102 GN 30 Taccessing reactive conformationsReaction Free-Energy Surfacesreference reactionschemical reaction pathwayD 95 Kdegradation rateschemical degradation sitesDKGNGglial cell-derived neurotropic factoraspartate isomerization degradation sites
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