Design of novel granulopoietic proteins by topological rescaffolding

PLoS Biol. 2020 Dec 22;18(12):e3000919. doi: 10.1371/journal.pbio.3000919. eCollection 2020 Dec.

Abstract

Computational protein design is rapidly becoming more powerful, and improving the accuracy of computational methods would greatly streamline protein engineering by eliminating the need for empirical optimization in the laboratory. In this work, we set out to design novel granulopoietic agents using a rescaffolding strategy with the goal of achieving simpler and more stable proteins. All of the 4 experimentally tested designs were folded, monomeric, and stable, while the 2 determined structures agreed with the design models within less than 2.5 Å. Despite the lack of significant topological or sequence similarity to their natural granulopoietic counterpart, 2 designs bound to the granulocyte colony-stimulating factor (G-CSF) receptor and exhibited potent, but delayed, in vitro proliferative activity in a G-CSF-dependent cell line. Interestingly, the designs also induced proliferation and differentiation of primary human hematopoietic stem cells into mature granulocytes, highlighting the utility of our approach to develop highly active therapeutic leads purely based on computational design.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Differentiation
  • Cells, Cultured
  • Computational Biology / methods
  • Granulocyte Colony-Stimulating Factor / pharmacology
  • Granulocytes / cytology*
  • Granulocytes / drug effects
  • Hematopoiesis / drug effects
  • Hematopoiesis / physiology
  • Hematopoietic Stem Cells / cytology
  • Humans
  • Neutrophils
  • Protein Engineering / methods*
  • Structure-Activity Relationship

Substances

  • Granulocyte Colony-Stimulating Factor

Grants and funding

This research was funded by the Max Planck Society internal funding awarded to A.N.L, the Madeleine Schickedanz-KinderKrebs-Stiftung endowed chair 'Modeling Tumorigenesis' to P.M., and BMBF MyPrep and DFG awarded to J.S.. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.