When AI weds molecular biology, miracle treatments are born

Haemoglobin carries their oxygen. Insulin regulates their metabolism. And a protein called spike allows coronaviruses to invade human cells, thereby shutting down entire economies.” Proteins are the origin of existence; the tail of a human sperm is a structure composed of many types of proteins that work together to form a complex rotary engine that propels the sperm forward to fertilize an egg and create life.

It is not surprising, therefore, that the breakthrough that made me a convert to the religion of AI had to do with proteins. AlphaFold by Google DeepMind cracked one of the hardest problems in medical science—predicting how a protein would fold. Every carbon-based life form is made of proteins, and it is how they fold that decides almost everything about our physiology and life. 

There are over 200 million known proteins today, and each of them folds in a unique three-dimensional shape. It was impossible for scientists to study each one of them, which considerably hindered efforts to tackle disease. If proteins fold wrongly, for instance, they can cause horrific harm—Alzheimer’s, Parkinson’s, Huntington’s and Lou Gehrig’s disease, and thousands of diseases we do not know yet. 

DeepMind built on an existing product AlphaGo (the one that famously defeated world champion Lee Sedol in the complex game of Go) to study the sequences and structures of 100,000 proteins, and in four years brought it to a level where it can predict the folded shape of a protein right down to the molecular level. 

In 2020, the problem was declared solved; a breakthrough as important as mapping the human genome, or the discovery of antibiotics, something that can change medical science forever.

AlphaFold is built on deep learning and neural networks, technologies that shaped AI. The next powerful AI technologies, LLMs and Generative AI, are doing even more magical stuff. GenAI-based image generators like DallE, Midjourney and now Sora and GPT4o can create wondrous images and breathtaking videos with mere word prompts. 

Researchers are using these technologies to generate blueprints for new proteins, ones that nature has not been able to do. These new proteins could revolutionize our ability to battle diseases. David Baker of the University of Washington has been building artisanal proteins for years (bit.ly/3V8ie3U), but with this new technology, he can design more sophisticated protein molecules with a higher success rate, shrinking the timeframe from “years to weeks.” 

As an example, GenAI can be used to create proteins of a uniquely distinctive shape such as the spike protein of the covid virus. “What we need are new proteins that can solve modern-day problems, like cancer and viral pandemics,” says Baker. “We can’t wait for evolution.” The amazing part is that this can happen through the right kind of text prompts to begin with. 

As former Stanford researcher Namrata Anand tells Cade Metz of NYT (bit.ly/3V8ie3U): “…protein engineers can ask for a protein that binds to another in a particular way—or some other design constraint—and the generative model can build it.”

AI’s astonishing innovation in biology and genetics has just begun. A California company Profluent released a research study (bit.ly/454t4wy) where GenAI technologies can build new gene editors to edit human DNA, using a Nobel prize winning technology called CRISPR. Profluent’s technology learns from how nature creates cellular structures. 

This gives doctors and scientists another tool to create new medicines and highly personalized treatments. DeepMind just released AlphaFold 3, which goes beyond proteins and peers into biochemical networks that make cells and organisms function. This astonishing marriage of AI and molecular biology has started having demonstrable effects. The Financial Times quotes a BCG study that indicates that drugs discovered by AI have higher early-stage trials success rates (bit.ly/3yDhT1w).

For a lot of us today, AI is a gee-whiz experience of creating stunning videos, travel itineraries and food recipes. But its real benefits to humankind will be deeper and more fundamental, and nowhere more useful than in helping humans transcend our biology.