Machine Learning Informs RNA-Binding Chemical Space

Abstract

Small molecule targeting of RNA has emerged as a new frontier in medicinal chemistry, but compared to the protein targeting literature our understanding of chemical matter that binds to RNA is limited. In this study, we report Repository Of BInders to Nucleic acids (ROBIN), a new library of nucleic acid binders identified by small molecule microarray (SMM) screening. The complete results of 36 individual nucleic acid SMM screens against a library of 24,572 small molecules are reported (including a total of 1,627,072 interactions assayed). A set of 2,003 RNA-binding small molecules is identified, representing the largest fully public, experimentally derived library of its kind to date. Machine learning is used to develop highly predictive and interpretable models to characterize RNA-binding molecules. This work demonstrates that machine learning algorithms applied to experimentally derived sets of RNA binders are a powerful method to inform RNA-targeted chemical space.