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 PDZ domain-containing protein 8 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 PDZ domain-containing protein 8 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 PDZ domain-containing protein 8, 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 PDZ domain-containing protein 8. 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 PDZ domain-containing protein 8. 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 PDZ domain-containing protein 8 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.
PDZ domain-containing protein 8
partner:
Reaxense
upacc:
Q8NEN9
UPID:
PDZD8_HUMAN
Alternative names:
Sarcoma antigen NY-SAR-84/NY-SAR-104
Alternative UPACC:
Q8NEN9; Q86WE0; Q86WE5; Q9UFF1
Background:
PDZ domain-containing protein 8, also known as Sarcoma antigen NY-SAR-84/NY-SAR-104, plays a pivotal role in cellular architecture by connecting endoplasmic reticulum and mitochondria membranes. This molecular tethering is crucial for Ca(2+) transfer between these organelles, impacting neuronal dendritic Ca(2+) dynamics and mitochondrial Ca(2+) uptake. Additionally, it indirectly influences cell morphology and cytoskeletal organization and may inhibit early stages of herpes simplex virus 1 infection.
Therapeutic significance:
Understanding the role of PDZ domain-containing protein 8 could open doors to potential therapeutic strategies for Intellectual developmental disorder with autism and dysmorphic facies, a neurodevelopmental disorder linked to gene variants affecting this protein.
