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 DNA polymerase delta subunit 2 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 DNA polymerase delta subunit 2 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 DNA polymerase delta subunit 2, 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 DNA polymerase delta subunit 2. 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 DNA polymerase delta subunit 2. 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 DNA polymerase delta subunit 2 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.
DNA polymerase delta subunit 2
partner:
Reaxense
upacc:
P49005
UPID:
DPOD2_HUMAN
Alternative names:
DNA polymerase delta subunit p50
Alternative UPACC:
P49005; A4D2J4; B2R5S4
Background:
DNA polymerase delta subunit 2, also known as DNA polymerase delta subunit p50, plays a pivotal role in high fidelity genome replication and repair. It is a crucial component of the DNA polymerase delta complex, involved in lagging strand synthesis, and exhibits significant differences in catalytic activity depending on its assembly. This protein is essential for the repair of broken replication forks and nucleotide excision repair synthesis following UV irradiation, showcasing its versatility in maintaining genome integrity.
Therapeutic significance:
Understanding the role of DNA polymerase delta subunit 2 could open doors to potential therapeutic strategies. Its involvement in genome replication and repair mechanisms highlights its potential as a target for developing treatments aimed at enhancing DNA repair pathways, crucial for combating genetic diseases and improving responses to DNA-damaging agents.
