# Probing the rules of molecular recognition through the de novo design of proteins that bind small-molecule drugs.

> **NIH NIH F32** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $67,582

## Abstract

Project Summary/Abstract:
Designing ligand-binding proteins from scratch is the ultimate test of the principles of molecular recognition by
proteins. Emerging technologies recently developed in the DeGrado lab, have enabled us, for the first time, to
design small molecules in enclosed cavities in fully synthetic, designed proteins, in a single computational step.
Here, we propose to enhance our newfound understanding of protein-small-molecule interactions through the
de novo design of a therapeutic-binding protein with high thermostability, binding affinity and specificity, as well
as controlled release capabilities. As a proof-of-concept, we will design a protein carrier that tightly and
specifically binds doxorubicin, a prototypical member of the anthracycline class of topoisomerase II inhibitors.
This intrinsically fluorescent and highly complex molecule has multiple functional groups to target, closely related
structural derivatives, and several commercially available conjugates and carriers, making it an ideal proof of
concept for both the main fundamental design aspect of this project, and the potential drug delivery application.
Protein carrier design will be done by testing and extending our newly developed COMBS (Cooperative Motifs
for Binding Sites) algorithm, in conjunction with parametric protein design which allows for the precise design of
highly stable helical bundles. We will further enhance our design capabilities by utilizing histidine residues to
facilitate drug binding at physiological pH, and enable controlled release in the acidic tumor microenvironment,
owing to the pKa of the imidazole side chain. The best computationally scored designs will be bacterially
synthesized to enable rapid screening of their folding and binding capabilities. X-ray crystallography will be
carried out to determine structure-function relations and ascertain agreement of the resulting structure with our
designs. These results will be utilized for the iterative design of the carriers. The biological activity of the carriers
will be evaluated via cell viability, proliferation, and wound healing assays as well as confocal microscopy. These
will inform on future designs of the carriers, and allow us to fine-tune the amount of histidine residues utilized in
doxorubicin binding. Importantly, the carriers will be kept small, to allow for later chemical synthesis to include
all D-amino acids, to avoid early proteolysis and associated immunogenicity (as all-D configured peptides are
not displayed by major histocompatibility complexes). This function-directed approach will allow us to obtain
atomic-level control of protein-small-molecule interactions, and while this proposal is fundamental in nature,
these design principals can ultimately contribute to the development of a new class of carriers. The utilization of
this approach for the design of drug carriers is highly compatible with my scientific background, and represents
the first of its many applications...

## Key facts

- **NIH application ID:** 10463468
- **Project number:** 1F32GM143869-01A1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Lee Schnaider
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $67,582
- **Award type:** 1
- **Project period:** 2022-12-01 → 2023-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10463468

## Citation

> US National Institutes of Health, RePORTER application 10463468, Probing the rules of molecular recognition through the de novo design of proteins that bind small-molecule drugs. (1F32GM143869-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10463468. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*