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 DNA dC->dU-editing enzyme APOBEC-3D 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 DNA dC->dU-editing enzyme APOBEC-3D 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 DNA dC->dU-editing enzyme APOBEC-3D, 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 DNA dC->dU-editing enzyme APOBEC-3D. 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 DNA dC->dU-editing enzyme APOBEC-3D. 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 DNA dC->dU-editing enzyme APOBEC-3D 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.
DNA dC->dU-editing enzyme APOBEC-3D
partner:
Reaxense
upacc:
Q96AK3
UPID:
ABC3D_HUMAN
Alternative names:
-
Alternative UPACC:
Q96AK3; Q5JZ91; Q7Z2N2; Q7Z2N5; Q7Z2N6
Background:
The DNA dC->dU-editing enzyme APOBEC-3D is a pivotal protein in the human immune response, acting as a formidable barrier against retrovirus replication and retrotransposon mobility. It achieves this through both deaminase-dependent and -independent mechanisms, effectively inhibiting HIV-1 by inducing G-to-A hypermutations in viral DNA. This selective targeting of single-stranded DNA, without affecting double-stranded DNA or RNA, underscores its specificity and critical role in antiviral defense.
Therapeutic significance:
Understanding the role of DNA dC->dU-editing enzyme APOBEC-3D could open doors to potential therapeutic strategies. Its unique ability to induce hypermutations in viral DNA presents a novel avenue for the development of antiretroviral therapies, particularly against HIV-1. The enzyme's selective targeting mechanism also offers insights into designing drugs that could mimic or enhance its antiviral effects.
