AI modeling transforms drug development from a numbers game of screening millions of compounds to an engineering discipline. Researchers can model molecular systems upfront, understand key parameters, and design solutions for a specific problem, turning a costly screening process into a rapid, targeted design cycle.

Non-human primate models are poor predictors of human immunogenicity. The industry has shifted to human-relevant ex vivo assays using whole blood or PBMCs. These tests can assess risks like complement activation upfront, enabling proactive protein engineering to improve a drug's safety profile.

Models designed to predict and screen out compounds toxic to human cells have a serious dual-use problem. A malicious actor could repurpose the exact same technology to search for or design novel, highly toxic molecules for which no countermeasures exist, a risk the researchers initially overlooked.

Unlike traditional methods that simulate physical interactions like a key in a lock, ProPhet's AI learns the fundamental patterns governing why certain molecules and proteins interact. This allows for prediction without needing slow, expensive, and often impossible physical or computational simulations.

Instead of building from scratch, ProPhet leverages existing transformer models to create unique mathematical 'languages' for proteins and molecules. Their core innovation is an additional model that translates between them, creating a unified space to predict interactions at scale.

Professor Collins' AI models, trained only to kill a specific pathogen, unexpectedly identified compounds that were narrow-spectrum—sparing beneficial gut bacteria. This suggests the AI is implicitly learning structural features correlated with pathogen-specificity, a highly desirable but difficult-to-design property.

To ensure their AI model wasn't just luckily finding effective drug delivery peptides, researchers intentionally tested sequences the model predicted would perform poorly (negative controls). When these predictions were experimentally confirmed, it proved the model had genuinely learned the underlying chemical principles and was not just overfitting.

Profluent CEO Ali Madani frames the history of medicine (like penicillin) as one of random discovery—finding useful molecules in nature. His company uses AI language models to move beyond this "caveman-like" approach. By designing novel proteins from scratch, they are shifting the paradigm from finding a needle in a haystack to engineering the exact needle required.

ProPhet's strategy is to focus on 'hard-to-drug' proteins, which are often avoided because they lack the structural data required for traditional discovery. Because ProPhet's AI model needs very little protein information to predict interactions, this data scarcity becomes a competitive advantage.