Proteins are at the core of life, driving everything from muscle movement to cellular signaling. Yet, designing proteins that function beyond their natural roles has long been a scientific challenge—especially for G-protein-coupled receptors (GPCRs), vital proteins targeted by one-third of all pharmaceuticals. Groundbreaking research from EPFL, published in Nature Chemistry, now unveils a computational tool that uses water-mediated interactions to engineer superior synthetic GPCRs, heralding advancements in drug discovery and synthetic biology.

One notable class of proteins that depend on specialized environments is membrane receptors. These biological “antennas” sense environmental signals and initiate cellular responses. Among them, G-protein-coupled receptors (GPCRs) stand out as the critical players in how cells perceive and react to external stimuli. Their function hinges on a delicate balance of structural stability, flexibility, and ligand binding—all intricately influenced by water. These interactions allow GPCRs to reshape and transmit signals into cells.

GPCRs are essential for normal cellular operations, making them prime targets for drug development. Remarkably, about one-third of all drugs on the market are designed to influence GPCRs. Beyond medicine, these receptors are a focal point for engineering efforts aimed at enhancing drug efficacy, developing novel treatments, and repurposing them as biosensors for synthetic biology.

However, GPCRs’ reliance on water-mediated interactions has long been a barrier to rational engineering—until now.

New Computational Breakthrough

A research team led by Patrick Barth at EPFL has developed an advanced computational design tool that manipulates GPCRs' water-mediated interactions to create synthetic receptors surpassing their natural counterparts. The findings from this new study have profound implications for medicine and synthetic biology.

“Water is everywhere,” says Lucas Rudden, co-first author of the study. “It’s the unsung hero of protein function, but it’s often ignored in design, particularly when we look at membrane receptor allostery, because it’s hard to model explicitly. We wanted to develop a method that can design new sequences while thinking about the impact of water in those intricate hydrogen bonding networks that are so crucial for mediating signals into the cell.”

Designing Superior Proteins

At the core of this breakthrough is SPaDES, a computational design tool used to engineer synthetic GPCRs. Starting with the adenosine A2A receptor as a template, the researchers focused on its “communication hubs”—key interaction sites where water molecules and amino acids converge. These hubs act as switchboards, relaying critical information throughout the protein. By optimizing these water-mediated connections, the team designed 14 receptor variants.

The SPaDES software simulated how these changes would impact receptor shapes and functions in different critical states. After computational screening, the researchers synthesized the most promising receptors and tested their activity in cells.

The results were groundbreaking. The density of water-mediated interactions emerged as a key determinant of receptor activity. Variants with more of these interactions demonstrated higher stability and signaling efficiency. The standout design, Hyd_high7, even adopted an unpredicted shape, validating the computational model.

Applications in Medicine and Beyond

The 14 new receptors outperformed their natural counterparts in several ways, including increased stability at high temperatures and improved ligand binding. These attributes make them ideal for drug discovery and synthetic biology applications.

The implications are vast. By enabling precise engineering of membrane receptors, this technology could revolutionize targeted therapies for conditions like cancer and neurological disorders. Beyond medicine, synthetic receptors could power biosensors for environmental monitoring or other applications.

The study also challenges long-standing assumptions about GPCRs, revealing surprising flexibility in their water-mediated interaction networks. This discovery opens doors to exploring untapped potential in these proteins, both in nature and in the lab.