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 Methyl-CpG-binding domain protein 4 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 Methyl-CpG-binding domain protein 4 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 Methyl-CpG-binding domain protein 4, 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 Methyl-CpG-binding domain protein 4. 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 Methyl-CpG-binding domain protein 4. 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 Methyl-CpG-binding domain protein 4 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.
Methyl-CpG-binding domain protein 4
partner:
Reaxense
upacc:
O95243
UPID:
MBD4_HUMAN
Alternative names:
Methyl-CpG-binding endonuclease 1; Methyl-CpG-binding protein MBD4; Mismatch-specific DNA N-glycosylase
Alternative UPACC:
O95243; B4DZN2; D3DNC3; D3DNC4; E9PEE4; Q2MD36; Q7Z4T3; Q96F09
Background:
Methyl-CpG-binding domain protein 4 (MBD4) plays a crucial role in DNA repair, specifically targeting G:T mismatches within methylated and unmethylated CpG sites. It exhibits thymine glycosylase activity, efficiently correcting DNA errors by removing uracil or 5-fluorouracil in G:U mismatches, without possessing lyase activity. MBD4, also known as Methyl-CpG-binding endonuclease 1 and Mismatch-specific DNA N-glycosylase, is pivotal in maintaining genomic stability.
Therapeutic significance:
MBD4's involvement in tumor predisposition syndrome 2 and uveal melanoma 1 highlights its critical role in cancer development. Understanding the function of MBD4 could pave the way for innovative cancer treatment strategies, focusing on enhancing DNA repair mechanisms to prevent tumor formation and progression.
