AI-ACCELERATED DRUG DISCOVERY
Available from Reaxense
This protein is integrated into the Receptor.AI ecosystem as a prospective target with high therapeutic potential. We performed a comprehensive characterization of Heparanase including:
1. LLM-powered literature research
Our custom-tailored LLM extracted and formalized all relevant information about the protein from a large set of structured and unstructured data sources and stored it in the form of a Knowledge Graph. This comprehensive analysis allowed us to gain insight into Heparanase therapeutic significance, existing small molecule ligands, relevant off-targets, and protein-protein interactions.
Fig. 1. Preliminary target research workflow
2. AI-Driven Conformational Ensemble Generation
Starting from the initial protein structure, we employed advanced AI algorithms to predict alternative functional states of Heparanase, including large-scale conformational changes along "soft" collective coordinates. Through molecular simulations with AI-enhanced sampling and trajectory clustering, we explored the broad conformational space of the protein and identified its representative structures. Utilizing diffusion-based AI models and active learning AutoML, we generated a statistically robust ensemble of equilibrium protein conformations that capture the receptor's full dynamic behavior, providing a robust foundation for accurate structure-based drug design.
Fig. 2. AI-powered molecular dynamics simulations workflow
3. Binding pockets identification and characterization
We employed the AI-based pocket prediction module to discover orthosteric, allosteric, hidden, and cryptic binding pockets on the protein’s surface. Our technique integrates the LLM-driven literature search and structure-aware ensemble-based pocket detection algorithm that utilizes previously established protein dynamics. Tentative pockets are then subject to AI scoring and ranking with simultaneous detection of false positives. In the final step, the AI model assesses the druggability of each pocket enabling a comprehensive selection of the most promising pockets for further targeting.
Fig. 3. AI-based binding pocket detection workflow
4. AI-Powered Virtual Screening
Our ecosystem is equipped to perform AI-driven virtual screening on Heparanase. With access to a vast chemical space and cutting-edge AI docking algorithms, we can rapidly and reliably predict the most promising, novel, diverse, potent, and safe small molecule ligands of Heparanase. This approach allows us to achieve an excellent hit rate and to identify compounds ready for advanced lead discovery and optimization.
Fig. 4. The screening workflow of Receptor.AI
Receptor.AI, in partnership with Reaxense, developed a next-generation technology for on-demand focused library design to enable extensive target exploration.
The focused library for Heparanase includes a list of the most effective modulators, each annotated with 38 ADME-Tox and 32 physicochemical and drug-likeness parameters. Furthermore, each compound is shown with its optimal docking poses, affinity scores, and activity scores, offering a detailed summary.
Heparanase
partner:
Reaxense
upacc:
Q9Y251
UPID:
HPSE_HUMAN
Alternative names:
Endo-glucoronidase; Heparanase-1
Alternative UPACC:
Q9Y251; A9JIG7; C7F7I3; C7F7I4; E9PCA9; E9PGR1; Q53GE5; Q9UL39
Background:
Heparanase, also known as Endo-glucoronidase or Heparanase-1, is a pivotal enzyme in the degradation and remodeling of the extracellular matrix (ECM). It selectively cleaves heparan sulfate proteoglycans into heparan sulfate side chains and core proteoglycans, playing a crucial role in processes such as tumor invasion, wound healing, and inflammation. Its activity is enhanced under acidic conditions, facilitating cell migration, angiogenesis, and procoagulant activities.
Therapeutic significance:
Understanding the role of Heparanase could open doors to potential therapeutic strategies. Its involvement in ECM degradation, cell migration, and angiogenesis highlights its significance in cancer metastasis and inflammatory diseases, suggesting that targeting Heparanase could offer novel approaches for treatment.
