Lead optimization and mode-of-action elucidation for novel antifibrotics

Idiopathic Pulmonary Fibrosis (IPF) is characterized by progressive fibrosis and chronic lung tissue remodeling with a 3-5-year median patient survival, post-diagnosis. Overproduction of extracellular matrix (ECM) by activated myofibroblasts as a result of cytokines like transforming growth factor β (TGFβ) is a key feature of IPF. Novel antifibrotics are urgently needed since the approved therapies only slow down disease progression. We took a top-down approach to drug discovery, conducting high-content drug screenings & structure-activity relationship (SAR) studies leading to the discovery of a new class of potent antifibrotics N-(2-butoxyphenyl)-3-phenyl)acrylamides (N23Ps). For lead development, we conducted a comprehensive SAR analysis on N23P-derivatives using high-content ECM deposition assays with primary IPF-derived lung fibroblasts. Here, collagen V & fibulin-1 deposition by these fibroblasts were measured against varying concentrations of N23Ps. Biological and technical replicates across 115 experiments with 142 compounds and varying degrees of structural alterations led to a complex set of dose-response data. To address the complexity and to automate the analysis, we developed metaSAR, a computational pipeline to estimate compound activities and characteristics from dose-response curves while considering outliers, edge effects, and plate & curve quality. Using cheminformatic tools and regression models, we could successfully identify chemical groups and locations associated with potency which ultimately led to highly potent & stable N23P derivates. To elucidate their effects on the lung microenvironment, we are now conducting single-cell RNA sequencing on perturbed human precision-cut lung slices.