Script
Here is The Daily FM summary of the Latent Space that aired on Tuesday August 11th. This episode explored what Chai Discovery calls a “phase shift” in BioAI: moving drug discovery away from slow, brute-force experimentation and toward precision engineering with AI models.
Chai cofounder Matt McPartlon and platform leader Neil Patil described the company as a software and modeling layer for pharma rather than a company trying to build its own drug pipeline. Their pitch is that better protein-structure and protein-design models can help drugmakers find therapeutic candidates faster, with more control over where and how they bind. Chai has partnered with Eli Lilly, Pfizer, Novartis, and argenx, and argues that its success is tied directly to whether those partners make better medicines. [1]
The central technical focus was antibodies: Y-shaped immune proteins whose tips can be engineered to attach to disease targets. Traditionally, antibody discovery often means immunizing mice or screening billions of possibilities in yeast-display experiments, then hoping a few molecules stick. Chai’s models aim to generate candidates intentionally, including molecules that bind a specific site, avoid similar proteins that could cause side effects, or bind both human and animal versions of a target to support preclinical testing.
McPartlon described Chai 1 as a structure-prediction model: given a protein sequence, it predicts the 3D shape. Chai 2 made the bigger leap into design, generating both a candidate’s sequence and structure for a target. In a high-profile internal challenge, the team designed antibodies against 50 targets and got binders for roughly half. One remarkable validation result showed a predicted structure only 0.33 angstroms from cryo-EM measurement—about one-third the width of an atom. The team initially suspected the lab had accidentally sent their own prediction back.
But the guests stressed that binding is only the beginning. Good drugs also need strong affinity, selectivity, stability, safety, manufacturability, and the ability to avoid unwanted aggregation. Chai 3 and subsequent iterations focus on pushing toward therapeutic-grade molecules rather than treating hit discovery and lead optimization as separate, years-long waterfall stages. [2]
Patil argued that the product should not look like a chatbot. Instead, Chai built something closer to Figma, SolidWorks, or Photoshop for molecules: scientists can visually select an epitope—the precise target region—and ask the model to generate binders under constraints. The product must also meet pharma’s strict security and intellectual-property requirements, including isolated customer deployments. [3]
A moving moment came when Patil recalled a pharma scientist crying after Chai helped generate a binder for a target she had worked on unsuccessfully for ten years. That illustrated the broader claim: these systems are beginning to work in real campaigns, not just on benchmarks.
The biggest remaining bottleneck, McPartlon said, is rapid experimental validation. Models can generate hypotheses quickly, but wet-lab proof still takes weeks or months. Patil’s answer was talent: BioAI needs more engineers and researchers to realize that biology is becoming computationally accessible. Their final message was ambitious but clear: as models predict structures within atomic accuracy and reliably design binders, biology may become less like feeling around in the dark and more like an engineering discipline. Thank you for listening to Latent Space in 3 minutes from The Daily FM. See you next time! [4]
- Latent Space: 🔬The BioAI Phase Shift - Matthew McPartlon & Neil Patil, Chai Discovery
...nd optimization where each of these has a gate and takes a few months to a few years is this very like waterfall mod where the cost of trying things and getting things early is very expensive. But I think to what Matt's saying, if you start to get in a regime where you can have models give you really promising candidates, you can start to make that look a lot more like a loop. Right. It's akin to becoming more agile in software development. But now the next problem is agonists. How do you reliably one shot hitting a switch on a cell. Right. Or buy specifics or ADCs. Right. And I think this levels of abstraction that we're going to have to climb with the product as like the models get better. If you have like these really good primitives for structure prediction and binding and design and you can kind of compose them then you can start to just like grow into like the o...
- Latent Space: 🔬The BioAI Phase Shift - Matthew McPartlon & Neil Patil, Chai Discovery
...of load up your molecule, there's this almost like Photoshop esque like design suite. You have this equivalent of paint tool to kind of paint your epitope. You have this equivalent of a content aware fill tool to kind of get your, your binders generated from Chai. And I think to add to that, right? Yeah. This notion of target discovery and hit discovery and optimization where each of these has a gate and takes a few months to a few years is this very like waterfall mod where the cost of trying things and getting things early is very expensive. But I think to what Matt's saying, if you start to get in a regime where you can have models give you really promising candidates, you can start to make that look a lot more like a loop. Right. It's akin to becoming more agile in software development. But now the next problem is agonists. How do you reliably one shot hitting a...
- Latent Space: 🔬The BioAI Phase Shift - Matthew McPartlon & Neil Patil, Chai Discovery
...of load up your molecule, there's this almost like Photoshop esque like design suite. You have this equivalent of paint tool to kind of paint your epitope. You have this equivalent of a content aware fill tool to kind of get your, your binders generated from Chai. And I think to add to that, right? Yeah. This notion of target discovery and hit discovery and optimization where each of these has a gate and takes a few months to a few years is this very like waterfall mod where the cost of trying things and getting things early is very expensive. But I think to what Matt's saying, if you start to get in a regime where you can have models give you really promising candidates, you can start to make that look a lot more like a loop. Right. It's akin to becoming more agile in software development. But now the next problem is agonists. How do you reliably one shot hitting a...
- Latent Space: 🔬The BioAI Phase Shift - Matthew McPartlon & Neil Patil, Chai Discovery
...pitope. You have this equivalent of a content aware fill tool to kind of get your, your binders generated from Chai. And I think to add to that, right? Yeah. This notion of target discovery and hit discovery and optimization where each of these has a gate and takes a few months to a few years is this very like waterfall mod where the cost of trying things and getting things early is very expensive. But I think to what Matt's saying, if you start to get in a regime where you can have models give you really promising candidates, you can start to make that look a lot more like a loop. Right. It's akin to becoming more agile in software development. But now the next problem is agonists. How do you reliably one shot hitting a switch on a cell. Right. Or buy specifics or ADCs. Right. And I think this levels of abstraction that we're going to have to climb with the product a...
