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 Porphobilinogen deaminase 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 Porphobilinogen deaminase 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 Porphobilinogen deaminase, 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 Porphobilinogen deaminase. 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 Porphobilinogen deaminase. 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 Porphobilinogen deaminase 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.
Porphobilinogen deaminase
partner:
Reaxense
upacc:
P08397
UPID:
HEM3_HUMAN
Alternative names:
Hydroxymethylbilane synthase; Pre-uroporphyrinogen synthase
Alternative UPACC:
P08397; A8K2L0; G3V1P4; G5EA58; P08396; Q16012
Background:
Porphobilinogen deaminase, also known as Hydroxymethylbilane synthase or Pre-uroporphyrinogen synthase, plays a crucial role in the heme biosynthetic pathway. It catalyzes the polymerization of porphobilinogen to form hydroxymethylbilane, a key precursor in the synthesis of heme, an essential component of hemoglobin, myoglobin, and various cytochromes.
Therapeutic significance:
Mutations in Porphobilinogen deaminase are linked to Acute Intermittent Porphyria (AIP), a condition characterized by gastrointestinal disturbances, neurological dysfunctions, and cardiovascular issues. Understanding the enzyme's function and its genetic variants opens avenues for targeted therapies, potentially offering relief to those affected by AIP.
