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 Retinoblastoma-like 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 Retinoblastoma-like 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 Retinoblastoma-like 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 Retinoblastoma-like 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 Retinoblastoma-like 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 Retinoblastoma-like 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.
Retinoblastoma-like protein 2
partner:
Reaxense
upacc:
Q08999
UPID:
RBL2_HUMAN
Alternative names:
130 kDa retinoblastoma-associated protein; Retinoblastoma-related protein 2; pRb2
Alternative UPACC:
Q08999; B7Z913; Q15073; Q16084; Q8NE70; Q92812
Background:
Retinoblastoma-like protein 2, also known as pRb2, plays a pivotal role in cell division, chromatin structure maintenance, and transcriptional repression. It is a key regulator, ensuring the stability of histone methylation and the formation of constitutive heterochromatin. By recruiting histone methyltransferases KMT5B and KMT5C, pRb2 exerts epigenetic control over gene expression. Its interaction with E2F5 and cyclins A and E underscores its significance in cell cycle regulation and potentially in the adenovirus E1A protein's transforming capacity.
Therapeutic significance:
Linked to Brunet-Wagner neurodevelopmental syndrome, Retinoblastoma-like protein 2's genetic variants underscore its clinical relevance. Understanding its role could unveil novel therapeutic strategies for managing severe developmental and intellectual disabilities associated with this syndrome.
