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 E3 ubiquitin-protein ligase parkin 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 E3 ubiquitin-protein ligase parkin 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 E3 ubiquitin-protein ligase parkin, 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 E3 ubiquitin-protein ligase parkin. 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 E3 ubiquitin-protein ligase parkin. 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 E3 ubiquitin-protein ligase parkin 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.
E3 ubiquitin-protein ligase parkin
partner:
Reaxense
upacc:
O60260
UPID:
PRKN_HUMAN
Alternative names:
Parkin RBR E3 ubiquitin-protein ligase; Parkinson juvenile disease protein 2
Alternative UPACC:
O60260; A3FG77; A8K975; D3JZW7; D3K2X0; Q5TFV8; Q5VVX4; Q6Q2I6; Q8NI41; Q8NI43; Q8NI44; Q8WW07
Background:
E3 ubiquitin-protein ligase parkin, also known as Parkin RBR E3 ubiquitin-protein ligase and Parkinson juvenile disease protein 2, plays a pivotal role in protein degradation pathways. It functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. This process is crucial for the removal and detoxification of abnormally folded or damaged proteins, thereby maintaining cellular homeostasis.
Therapeutic significance:
Parkin is intricately linked to neurodegenerative disorders, notably Parkinson disease and Parkinson disease 2. Its involvement in the ubiquitination of specific substrates related to these diseases highlights its potential as a target for therapeutic intervention. Understanding the role of E3 ubiquitin-protein ligase parkin could open doors to potential therapeutic strategies, especially in mitigating the progression of Parkinson's disease and related neurodegenerative conditions.
