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 damage-binding protein 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 damage-binding protein 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 damage-binding protein 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 damage-binding protein 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 damage-binding protein 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 damage-binding protein 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 damage-binding protein 2
partner:
Reaxense
upacc:
Q92466
UPID:
DDB2_HUMAN
Alternative names:
DDB p48 subunit; Damage-specific DNA-binding protein 2; UV-damaged DNA-binding protein 2
Alternative UPACC:
Q92466; B2R875; Q76E54; Q76E55; Q76E56; Q76E57
Background:
DNA damage-binding protein 2, also known as DDB p48 subunit, Damage-specific DNA-binding protein 2, or UV-damaged DNA-binding protein 2, plays a crucial role in DNA repair and protein ubiquitination. It is a core component of the UV-DDB complex, recognizing UV-induced DNA damage and initiating repair via the nucleotide excision repair pathway. Additionally, it functions in the DCX (DDB2-CUL4-X-box) E3 ubiquitin-protein ligase complex, facilitating the removal of histones from nucleosomes to promote DNA repair.
Therapeutic significance:
The protein's involvement in Xeroderma pigmentosum complementation group E, a disorder characterized by heightened skin cancer risk and potential neurological abnormalities due to UV sensitivity, underscores its therapeutic significance. Understanding the role of DNA damage-binding protein 2 could open doors to potential therapeutic strategies for mitigating the effects of this condition.
