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 Histone-lysine N-methyltransferase PRDM9 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 Histone-lysine N-methyltransferase PRDM9 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 Histone-lysine N-methyltransferase PRDM9, 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 Histone-lysine N-methyltransferase PRDM9. 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 Histone-lysine N-methyltransferase PRDM9. 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 Histone-lysine N-methyltransferase PRDM9 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.
Histone-lysine N-methyltransferase PRDM9
partner:
Reaxense
upacc:
Q9NQV7
UPID:
PRDM9_HUMAN
Alternative names:
PR domain zinc finger protein 9; PR domain-containing protein 9; Protein-lysine N-methyltransferase PRDM9; [histone H3]-lysine36 N-trimethyltransferase PRDM9; [histone H3]-lysine4 N-trimethyltransferase PRDM9; [histone H3]-lysine9 N-trimethyltransferase PRDM9; [histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9; [histone H4]-lysine20 N-methyltransferase PRDM9
Alternative UPACC:
Q9NQV7; B4DX22; Q27Q50
Background:
Histone-lysine N-methyltransferase PRDM9, with alternative names such as PR domain zinc finger protein 9 and Protein-lysine N-methyltransferase PRDM9, plays a pivotal role in meiotic prophase. It is responsible for the methylation of 'Lys-4' and 'Lys-36' on histone H3, facilitating meiotic recombination by determining hotspot localization. This enzyme not only modifies histone H3 but can also methylate all four core histones, with H3 being the primary substrate. Its activity is crucial for the transcriptional activation of genes during early meiotic prophase, marking a specific tag for epigenetic transcriptional activation.
Therapeutic significance:
Understanding the role of Histone-lysine N-methyltransferase PRDM9 could open doors to potential therapeutic strategies.
