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 Nucleic acid dioxygenase ALKBH1 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 Nucleic acid dioxygenase ALKBH1 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 Nucleic acid dioxygenase ALKBH1, 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 Nucleic acid dioxygenase ALKBH1. 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 Nucleic acid dioxygenase ALKBH1. 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 Nucleic acid dioxygenase ALKBH1 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.
Nucleic acid dioxygenase ALKBH1
partner:
Reaxense
upacc:
Q13686
UPID:
ALKB1_HUMAN
Alternative names:
Alkylated DNA repair protein alkB homolog 1; Alpha-ketoglutarate-dependent dioxygenase ABH1; DNA 6mA demethylase; DNA N6-methyl adenine demethylase ALKBH1; DNA lyase ABH1; DNA oxidative demethylase ALKBH1; mRNA N(3)-methylcytidine demethylase
Alternative UPACC:
Q13686; Q8TAU1; Q9ULA7
Background:
Nucleic acid dioxygenase ALKBH1, also known as DNA 6mA demethylase, plays a crucial role in nucleic acid metabolism. It acts on DNA and tRNA, requiring molecular oxygen, alpha-ketoglutarate, and iron for its activity. ALKBH1 is involved in the demethylation of tRNAs, particularly removing N(1)-methyladenine, and regulates translation in response to glucose deprivation. It also interacts with mitochondrial tRNA, contributing to mitochondrial translation by expanding codon recognition. Additionally, ALKBH1 demethylates DNA and mRNAs, and possesses DNA lyase activity, introducing double-stranded breaks at abasic sites.
Therapeutic significance:
Understanding the role of Nucleic acid dioxygenase ALKBH1 could open doors to potential therapeutic strategies.
