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 Twinkle mtDNA helicase 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 Twinkle mtDNA helicase 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 Twinkle mtDNA helicase, 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 Twinkle mtDNA helicase. 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 Twinkle mtDNA helicase. 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 Twinkle mtDNA helicase 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.
Twinkle mtDNA helicase
partner:
Reaxense
upacc:
Q96RR1
UPID:
PEO1_HUMAN
Alternative names:
Progressive external ophthalmoplegia 1 protein; T7 gp4-like protein with intramitochondrial nucleoid localization; T7-like mitochondrial DNA helicase; Twinkle protein, mitochondrial
Alternative UPACC:
Q96RR1; B2CQL2; Q6MZX2; Q6PJP5; Q96RR0
Background:
Twinkle mtDNA helicase, also known as Progressive external ophthalmoplegia 1 protein, plays a pivotal role in mitochondrial DNA replication and repair. It exhibits DNA strand separation activity essential for the formation of a processive replication fork, crucial for leading strand synthesis. This activity is facilitated by forming a replisome complex with POLG and mtSDB, highlighting its significance in mitochondrial function.
Therapeutic significance:
Given its involvement in diseases such as Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant, 3, Mitochondrial DNA depletion syndrome 7, and Perrault syndrome 5, Twinkle mtDNA helicase represents a promising target for therapeutic intervention. Understanding the role of Twinkle mtDNA helicase could open doors to potential therapeutic strategies, especially in conditions linked to mitochondrial dysfunction.
