Mirror-image ligand discovery enabled by single-shot fast-flow synthesis of D-proteins

Alex J Callahan; Satish Gandhesiri; Tara L Travaline; Rahi M Reja; Lia Lozano Salazar; Stephanie Hanna; Yen-Chun Lee; Kunhua Li; Olena S Tokareva; Jean-Marie Swiecicki; Andrei Loas; Gregory L Verdine; John H McGee; Bradley L Pentelute

doi:10.1038/s41467-024-45634-z

Mirror-image ligand discovery enabled by single-shot fast-flow synthesis of D-proteins

Nat Commun. 2024 Feb 28;15(1):1813. doi: 10.1038/s41467-024-45634-z.

Authors

Alex J Callahan^#¹, Satish Gandhesiri^#¹, Tara L Travaline², Rahi M Reja¹, Lia Lozano Salazar¹, Stephanie Hanna¹, Yen-Chun Lee^{1

3}, Kunhua Li², Olena S Tokareva², Jean-Marie Swiecicki^{2

4}, Andrei Loas¹, Gregory L Verdine^{2

5

6

7}, John H McGee⁸, Bradley L Pentelute^{9

10

11

12}

Affiliations

¹ Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
² FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA.
³ Department of Chemistry, National Cheng Kung University, No.1, University Road, Tainan City, 701, Taiwan.
⁴ Relay Therapeutics, Inc., 399 Binney Street, 2nd Floor, Cambridge, MA, 02139, USA.
⁵ Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA.
⁶ Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.
⁷ Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA.
⁸ FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA. jmcgee@fogpharma.com.
⁹ Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA. blp@mit.edu.
¹⁰ The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02142, USA. blp@mit.edu.
¹¹ Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA. blp@mit.edu.
¹² Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA. blp@mit.edu.

^# Contributed equally.

Abstract

Widespread adoption of mirror-image biological systems presents difficulties in accessing the requisite D-protein substrates. In particular, mirror-image phage display has the potential for high-throughput generation of biologically stable macrocyclic D-peptide binders with potentially unique recognition modes but is hindered by the individualized optimization required for D-protein chemical synthesis. We demonstrate a general mirror-image phage display pipeline that utilizes automated flow peptide synthesis to prepare D-proteins in a single run. With this approach, we prepare and characterize 12 D-proteins - almost one third of all reported D-proteins to date. With access to mirror-image protein targets, we describe the successful discovery of six macrocyclic D-peptide binders: three to the oncoprotein MDM2, and three to the E3 ubiquitin ligase CHIP. Reliable production of mirror-image proteins can unlock the full potential of D-peptide drug discovery and streamline the study of mirror-image biology more broadly.

MeSH terms

Drug Discovery
Ligands
Peptides*
Proteins*

Substances

Ligands
Proteins
Peptides