In the fast-evolving world of targeted protein degrader discovery and development, meaningful insights often emerge not from isolated compounds but from patterns that repeat across chemical series—shared scaffolds that link molecular design to biological activity. To help medicinal and computational chemists, drug discovery program managers, and portfolio strategists make sense of this complexity, the GOSTAR TPD platform now includes a Scaffold Landscape Analysis module. This feature transforms thousands of patented as well as published degraders into a clustered map of core scaffolds, organized by structural similarity and enriched with contextual links to targets, companies, and assay data. Whether you are looking for new ligase ligands, evaluating SAR diversity, or analyzing the competitive scaffold landscape for freedom to operate (FTO), this tool offers an efficient method to navigate the degrader chemical space and reveal structure-driven trends at scale.
Driving Design and Strategy Through Scaffold Clustering
Scaffold-level analysis makes it easier to interpret large SAR datasets and uncover patterns that guide decision-making. This analysis supports:
- Designing next-generation degraders
- Uncovering IP white space and over-crowded chemotypes
- Prioritizing lead series with meaningful SAR depth
Key Features of the GOSTAR TPD Scaffold Landscape Analysis
Cluster-by-similarity treemap
Group thousands of scaffolds into intuitive clusters based on molecular similarity.
Target-specific analysis – Filter by any TPD-relevant target and view the scaffold space shaped by published degraders.
Company mapping
Quickly identify which companies are contributing scaffolds to which parts of the landscape.
Substructure mapping
Zoom into regions of interest based on scaffold structure, and assess how extensively a scaffold has been explored across targets and companies. This feature helps identify underexploited chemotypes and flag crowded IP spaces.
Exportable for downstream analysis
Export cluster-level compounds with metadata for offline exploration, modelling, or IP landscaping.
Figure 1. A representative workflow showing scaffold diversity for the androgen receptor target
Try It Yourself
The Scaffold Landscape Analysis is available now for all GOSTAR TPD users. Navigate to the “Scaffold Landscape Analysis” tab, select your target or company of interest, and explore the chemotypes shaping the future of protein degradation.
