A Descriptor Set for Quantitative Structure‐property Relationship Prediction in Biologics
Kannan Sankar, Kyle Trainor, Levi L. Blazer, Jarrett Adams, Sachdev S. Sidhu, Tyler Day, Elizabeth M. Meiering, Johannes Maier
Abstract
There has been a remarkable increase in the number of biologics, especially monoclonal antibodies, in the market over the last decade. In addition to attaining the desired binding to their targets, a crucial aspect is the 'developability' of these drugs, which includes several desirable properties such as high solubility, low viscosity and aggregation, physico-chemical stability, low immunogenicity and low poly-specificity. The lack of any of these desirable properties can lead to significant hurdles in advancing them to the clinic and are often discovered only during late stages of drug development. Hence, in silico methods for early detection of these properties, particularly the ones that affect aggregation and solubility in the earlier stages can be highly beneficial. We have developed a computational framework based on a large and diverse set of protein specific descriptors that is ideal for making liability predictions using a QSPR (quantitative structure-property relationship) approach. This set offers a high degree of feature diversity that may coarsely be classified based on (1) sequence (2) structure and (3) surface patches. We assess the sensitivity and applicability of these descriptors in four dedicated case studies that are believed to be representative of biophysical characterizations commonly employed during the development process of a biologics drug candidate. In addition to data sets obtained from public sources, we have validated the descriptors on novel experimental data sets in order to address antibody developability and to generate prospective predictions on Adnectins. The results show that the descriptors are well suited to assist in the improvement of protein properties of systems that exhibit poor solubility or aggregation.