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 Polyribonucleotide 5'-hydroxyl-kinase Clp1 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 Polyribonucleotide 5'-hydroxyl-kinase Clp1 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 Polyribonucleotide 5'-hydroxyl-kinase Clp1, 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 Polyribonucleotide 5'-hydroxyl-kinase Clp1. 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 Polyribonucleotide 5'-hydroxyl-kinase Clp1. 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 Polyribonucleotide 5'-hydroxyl-kinase Clp1 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.
Polyribonucleotide 5'-hydroxyl-kinase Clp1
partner:
Reaxense
upacc:
Q92989
UPID:
CLP1_HUMAN
Alternative names:
Polyadenylation factor Clp1; Polynucleotide kinase Clp1; Pre-mRNA cleavage complex II protein Clp1
Alternative UPACC:
Q92989; B2R7J6; B4DTI8
Background:
Polyribonucleotide 5'-hydroxyl-kinase Clp1, also known as Polyadenylation factor Clp1 and Polynucleotide kinase Clp1, is a versatile enzyme with pivotal roles in RNA and DNA processing. It efficiently phosphorylates the 5'-hydroxyl groups of RNA and DNA, playing a crucial role in tRNA splicing, mRNA 3'-end formation, and the activation of short interfering RNAs (siRNAs) for RNA-induced silencing. Its activity is essential for cerebellar development and proper brain function.
Therapeutic significance:
Given its critical role in tRNA splicing and mRNA processing, Polyribonucleotide 5'-hydroxyl-kinase Clp1's dysfunction is linked to Pontocerebellar hypoplasia 10, a severe neurodegenerative disorder. Understanding the role of this protein could open doors to potential therapeutic strategies for treating or managing this debilitating condition.
