DE novo design of allosteric proteins that sense and respond to small molecules

The National Institutes of Health Office of the Director awarded Dana-Farber Cancer Institute, Inc. $845,500 on September 1, 2026, under the Trans-NIH Research Support program (CFDA 93.310) to design de novo allosteric proteins that sense and respond to small molecules.

The research aims to develop "active" proteins that undergo conformational changes upon ligand binding, enabling programmable control of signaling at the nanoscale. The work combines computational design and experimental validation to establish design principles for small-molecule-induced allosteric communication. The recipient will build designed ligand-binding helical bundles connected through frustrated linkers and bioinspired approaches mimicking G-protein coupled receptor signaling mechanisms, then test these designs for cooperative binding and characterize the sequence-structure relationships governing allostery. The ultimate goal is to establish fully synthetic, fit-for-purpose GPCR-like systems with novel programmable and small-molecule-inducible functions.

Performance takes place in Boston, Massachusetts. The period of performance runs from September 1, 2026, through August 31, 2031. The award is assistance type Project Grant and is subject to NIH audit and record retention requirements under OMB 2 CFR 200 and 45 CFR 75.

Abstract

This proposal aims to design allosteric proteins driven by binding of small molecules. The deep-learning revolution has enabled facile generation of "static" binders-proteins that passively bind to peptides, proteins, or small molecules. Static binders are useful for a variety of applications (e.g., inhibitors or antidotes), but most natural proteins have more complex functions that extend beyond passive binding. We therefore aim to design "active" proteins that change shape upon binding a ligand. Such allosteric proteins would enable novel, programmable control of signaling events at the nanoscale. Through rounds of computation and experiment, we will uncover the design principles of small-molecule-induced allosteric "communication at a distance" that underpins much of biology, especially in proteins critical for cell signaling and gene regulation. Having established a repertoire of DE novo helical bundles that bind to a variety of small-molecule drugs and metabolites, we now aim to pick apart the rules of how to design allostery from scratch. Designed ligand- binding bundles will be connected through the design of frustrated linkers, as well as a more bioinspired approach that mimics signaling mechanisms of G-protein coupled receptors (GPCRS). We will test these designs for cooperative binding and uncover the sequence-structure relationships that give a quantitative understanding of allostery-such that IT can be predicted and engineered in a rational way. By testing hypotheses gleaned from natural signaling proteins, we should learn the rules that govern their function, potentially leading to more sophisticated ways to drug them with fewer side effects. More concretely, success would establish fully synthetic, fit-for-purpose "gpcr-like" systems for novel programmable and small- molecule-inducible functions. This accomplishment could potentially revolutionize the approach to targeted therapies by enabling precise drug-delivery mechanisms based on the unique metabolic environments of specific tissues, minimizing off-target effects and improving therapeutic outcomes. By accurately programming allostery, we could also create biosensors from scratch to any small molecule of interest, illuminating this difficult-to-study yet vitally important signaling axis of biology. Thus, we aim to establish a pipeline to generate genetically encodable biosensors that respond to synthetic drugs or natural metabolites at appropriate dynamic ranges to study their mechanisms of action in cells in real time. This research is broadly impactful across disparate fields such as metabolic engineering, biosensing, drug delivery, cell signaling, and neuroscience. IT promises to deepen our understanding of protein-ligand interactions, refine the rules of allosteric communication, and pave the way for new therapeutic strategies that leverage distinct metabolic environments associated with disease.