Engineered protein-small molecule conjugates empower selective enzyme inhibition

Andrew K. Lewis, Abbigael Harthorn, Sadie M. Johnson, Roy R. Lobb, Benjamin J. Hackel

Research output: Contribution to journalArticlepeer-review


Potent, specific ligands drive precision medicine and fundamental biology. Proteins, peptides, and small molecules constitute effective ligand classes. Yet greater molecular diversity would aid the pursuit of ligands to elicit precise biological activity against challenging targets. We demonstrate a platform to discover protein-small molecule (PriSM) hybrids to combine unique pharmacophore activities and shapes with constrained, efficiently engineerable proteins. In this platform, a fibronectin protein library is displayed on yeast with a single cysteine coupled to acetazolamide via a maleimide-poly(ethylene glycol) linker. Magnetic and flow cytometric sorts enrich specific binders to carbonic anhydrase isoforms. Isolated PriSMs exhibit potent, specific inhibition of carbonic anhydrase isoforms with efficacy superior to that of acetazolamide or protein alone, including an 80-fold specificity increase and 9-fold potency gain. PriSMs are engineered with multiple linker lengths, protein conjugation sites, and sequences against two different isoforms, which reveal platform flexibility and impacts of molecular designs. PriSMs advance the molecular diversity of efficiently engineerable ligands.

Original languageEnglish (US)
Pages (from-to)328-338.e4
JournalCell Chemical Biology
Issue number2
StatePublished - Feb 17 2022

Bibliographical note

Funding Information:
We thank Alex Golinski for guidance on sequence analysis and Jim Van Deventer for useful discussions. We thank the University of Minnesota Flow Cytometry Resource for cell sorting, the University of Minnesota Genomics Center for assistance with deep sequencing, and the Minnesota Supercomputing Institute for computing resources. Research was supported by the National Institutes of Health ( R01 EB023339 and R01 EB028274 ) and Itara Biotherapeutics.

Publisher Copyright:
© 2021 Elsevier Ltd


  • hybrid
  • ligand
  • pharmacophore
  • protein engineering
  • protein scaffold
  • yeast display

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't


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