High throughput screening and quantitative structure efficacy relationship models for designing displacers for antisense oligonucleotide purification in anion-exchange systems

Abstract

A high throughput screening (HTS) technique was developed for the rapid evaluation of displacers for the purification of antisense oligonucleotides using anion-exchange systems. By employing this technique, a large number of potential displacers with a variety of structural properties were evaluated in parallel, dramatically decreasing the time required for displacer discovery. A database was generated containing molecular descriptors of the screened displacer probes as well as their displacement data obtained from the HTS experiments. A subset of the probe data was used to derive a predictive quantitative structure efficacy relationship (QSER) model using a partial least squares (PLS) approach. The resulting model was well correlated with In addition, the model was shown to predict the molecules not included in the model successfully.

The results presented in this paper demonstrate the utility of the HTS technique for the rapid evaluation of displacers for the purification of antisense oligonucleotides. These results applied in concert with the QSER modeling, can aid in the a priori design of high-affinity displacers for anion-exchange systems.

Acknowledgments

The authors acknowledge Prof. Jim Moore (Department of Chemistry, Rensselaer Polytechnic Institute) for his valuable discussions related to this work. The authors acknowledge NIH Grant GM 47372-04A2 and NSF Grant BES-0079436 for funding this research. This work was also partly funded by Isis Pharmaceuticals and Amersham Pharmacia Biotech.