Computational exploration of chemical space is crucial in modern cheminformatics research for accelerating the discovery of new biologically active compounds. In this study, we present a detailed analysis of the chemical library of potential glucocorticoid receptor (GR) ligands generated by the molecular generator, Molpher. To generate the targeted GR library and construct the classification models, structures from the ChEMBL database as well as from the internal IMG library, which was experimentally screened for biological activity in the primary luciferase reporter cell assay, were utilized. The composition of the targeted GR ligand library was compared with a reference library that randomly samples chemical space. A random forest model was used to determine the biological activity of ligands, incorporating its applicability domain using conformal prediction. It was demonstrated that the GR library is significantly enriched with GR ligands compared to the random library. Furthermore, a prospective analysis demonstrated that Molpher successfully designed compounds, which were subsequently experimentally confirmed to be active on the GR. A collection of 34 potential new GR ligands was also identified. Moreover, an important contribution of this study is the establishment of a comprehensive workflow for evaluating computationally generated ligands, particularly those with potential activity against targets that are challenging to dock.

Center for Bioinformatics Department of Informatics Faculty of Mathematics Informatics and Natural Sciences Universität Hamburg 20146 Hamburg Germany

CZ OPENSCREEN National Infrastructure for Chemical Biology Institute of Molecular Genetics of the Czech Academy of Sciences Prague 14220 Czech Republic

Department of Informatics and Chemistry and CZ OPENSCREEN National Infrastructure for Chemical Biology Faculty of Chemical Technology University of Chemistry and Technology Prague 16628 Czech Republic

Department of Organic Chemistry Faculty of Chemical Technology University of Chemistry and Technology Prague 16628 Czech Republic

Division of Pharmaceutical Chemistry Department of Pharmaceutical Sciences Faculty of Life Sciences University of Vienna 1090 Vienna Austria

Citace poskytuje Crossref.org