How AI helps scientists design the next generation of medicines

Designing and developing a new medicine is an expensive, failure-prone scientific challenge. A new drug can take many years to develop, at the cost of a significant investment. And even then, most possible candidates never reach the patient. For biologic medicines, therapies made from engineered proteins rather than synthetic chemistry (which are often used to treat conditions across most major acute and chronic diseases), the complexity is even greater.

Scientists explore vast quantities of possible molecules, looking for the rare few that will bind to the right target, remain stable in the human body, and be manufacturable at scale. Today, AI is speeding up these processes and has quickly become a core part of the infrastructure in pharmaceutical R&D.

AI-assisted design is a growing part of how biologic drug candidates are developed, and companies like AstraZeneca are actively building its engineering teams to push this further. “Everything we do, whether it’s design, make, test, or analyze, is now computationally enhanced,” says Puja Sapra, senior vice president and head of R&D biologics engineering and oncology targeted discovery at AstraZeneca. “The cycle times are getting shorter while productivity and innovation increase.”

Sapra explains that AstraZeneca’s approach follows a build-measure-learn loop. AI generates or prioritizes candidate molecules computationally, predicting which designs are most likely to succeed. Scientists then focus lab resources only on the top-ranked candidates. This leads to a tighter feedback cycle with fewer dead ends, faster iteration, and the ability to go after disease targets that were previously considered untreatable by medicine. Because the number of possible molecular combinations far exceeds what any human team can systematically explore, using AI to narrow and refine the options for testing has become a major focus in biologics drug design.

Navigating complex drug design problems

Beyond accelerating timelines, AI is also being applied to the discovery of entirely new classes of medicines. Traditional biologics typically target one disease pathway. The next generation of drugs can hit multiple targets simultaneously or precisely deliver therapeutic payloads to specific cells. Achieving this requires optimization across many variables at once. Looking ahead AI-driven models could help design these increasingly complex, multi-specific biologics, explains Puja Sapra. “For example,” she continues, “such models could help identify which two or three targets to prioritize based on the underlying biology, then optimize across multiple parameters to balance a molecule’s potency, stability, manufacturability, and safety.” “Drugging the undruggable is becoming a reality,” Sapra says. “These technologies will eventually enable us to develop medicines against targets once thought impossible to reach. The potential for benefit to patients is remarkable.”

The data moat

McKinsey estimates that generative AI, combined with other computational tools, could cut drug discovery timelines by as much as 50%. But every AI model is only as good as its training data. In drug discovery, that means ample quantities of high-quality biological data. Experiments can provide a rich source of such data. Whether they succeed or fail, each experiment generates a signal about what does and does not work.

“Data is our differentiator,” says Sapra, explaining how the company’s datasets are proprietary and multimodal and include molecular structures, binding measurements, safety profiles, and manufacturing outcomes. “We’ve built an intentionally diverse portfolio across multiple disease areas and drug types. All of that data empowers us to fine-tune frontier AI models with richer, more representative training sets.” She continues, “Further, we have invested in deep screening technologies to generate additional datasets required in volume to constantly refine and validate our models.”

Building an autonomous discovery engine

To bring all of that data together in one place, AstraZeneca is building what it calls a “lab of the future” facility in Kendall Square, Cambridge, Massachusetts where AI and robotic automation will be able to form a continuous, closed-loop discovery system. “Where a self-driving car uses sensors and models to navigate its environment, this system uses AI to make predictions, robotic systems to execute experiments, and instruments to generate data,” explains Sapra. That data feeds directly back into the models, accelerating each subsequent cycle.

“Throughout, scientists will remain central to the process, providing the oversight, judgement, and strategic direction that ensure outputs are explainable, tolerable, and directed toward potential patient benefit,” she adds.

Eventually, automated high-throughput systems will be able to make and evaluate thousands of molecular interactions on a weekly basis. “This will generate AI-ready data at a scale that traditional workflows cannot match,” Sapra says. “Robotic sample handling, automated quality checks, and integrated data pipelines also have the potential to help accelerate early drug development timelines significantly.”

The next frontier: Generating medicines from scratch

Ultimately, Sapra says, the end-state vision for AI in biologic drug discovery is what the field calls “de novo” design. For this, the goal is for AI to generate entirely new protein sequences that precisely fit the desired drug properties. This includes designing the structure, predicting safety, how it will behave in the body and how to make it manufacturable.

“The field is making great progress toward a completely AI-generated biologic, designed from scratch all the way to a clinical candidate,” Sapra says. “As we continue to leverage frontier models and fine-tune them with the right datasets, we bring ourselves closer to this reality. I believe it will come. It’s a matter of time.”

Several key elements are needed to reach this point, however. First is richer and more standardized training data across the industry. Second, robust evaluation benchmarks for AI-generated candidates. And third, teams that know how to work at the intersection of machine learning and biology. Of all the prerequisites, however, safety prediction may be the most consequential, and perhaps the least discussed, Sapra says.

“One of the hardest problems in de novo design is predicting whether a computationally generated molecule will be safe in the human body,” Sapra explains. AstraZeneca is tackling this with what amounts to virtual clinical trials. These are advanced cell systems and micro-scale organ models that function as physical testbeds, paired with AI that learns from their outputs.

“These systems have the potential to generate enhanced biological signals without traditional testing bottlenecks, and they're a critical missing piece in closing the loop between AI-generated designs and clinical-ready candidates,” Sapra adds.

A shift currently underway is the move toward agentic AI systems that can simultaneously generate molecule candidates and predict how efficacious and safe they are likely to be. These autonomous workflows can connect disease-level insights directly to molecule design, bridging what were previously separate data silos. “The complexity of the biology goes hand-in-hand with the design of the molecule,” summarizes Sapra.

Human talent unlocks AI potential

The transformation underway in biologics is not just about technology. “With more autonomous systems, human oversight remains at the heart of this approach—ensuring explainable and ethical AI for the benefit of patients,” says Sapra.

For scientists, working with AI is a collaborative process. “Scientists will work hand-in-hand with these model systems,” she says.