AI-ACCELERATED DRUG DISCOVERY

Matrilin-3

Explore its Potential with AI-Driven Innovation
Predicted by Alphafold

Matrilin-3 - Focused Library Design

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 Matrilin-3 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 Matrilin-3 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 Matrilin-3, 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 Matrilin-3. 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 Matrilin-3. 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 Matrilin-3 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.

Matrilin-3

partner:

Reaxense

upacc:

O15232

UPID:

MATN3_HUMAN

Alternative names:

-

Alternative UPACC:

O15232; B2CPU0; Q4ZG02

Background:

Matrilin-3, encoded by the gene with accession number O15232, is a pivotal component of the extracellular matrix in cartilage. It plays a crucial role in the formation of extracellular filamentous networks, essential for maintaining the structural integrity and function of cartilage.

Therapeutic significance:

The protein is implicated in several skeletal disorders, including Multiple epiphyseal dysplasia 5, characterized by irregular ossification and early-onset osteoarthritis, and Spondyloepimetaphyseal dysplasia, Borochowitz-Cormier-Daire type, marked by disproportionate dwarfism and skeletal abnormalities. Additionally, it is associated with Osteoarthritis 2, a degenerative joint disease. Understanding the role of Matrilin-3 could open doors to potential therapeutic strategies for these conditions.

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