Allosteric Inhibition of a Semaphorin 4D Receptor Plexin B1 by a High-Affinity Macrocyclic Peptide

Abstract

Semaphorin axonal guidance factors are multifunctional proteins that play important roles in immune response, cancer cell proliferation, and organogenesis, making semaphorins and their signaling receptor plexins important drug targets for various diseases. However, the large and flat binding surface of the semaphorin-plexin interaction interface is difficult to target by traditional small-molecule drugs. Here, we report the discovery of a high-affinity plexin B1 (PlxnB1)-binding macrocyclic peptide, PB1m6 (K = 3.5 nM). PB1m6 specifically inhibited the binding of physiological ligand semaphorin 4D (Sema4D) in vitro and completely suppressed Sema4D-induced cell collapse. Structural studies revealed that PB1m6 binds at a groove between the fifth and sixth blades of the sema domain in PlxnB1 distant from the Sema4D-binding site, indicating the non-competitive and allosteric nature of the inhibitory activity. The discovery of this novel allosteric site can potentially be used to target plexin family proteins for the development of drugs that modulate semaphorin and plexin signaling.

Thioether Macrocyclic Peptides Selected against TET1 Compact Catalytic Domain Inhibit TET1 Catalytic Activity

“…Thus, there is strong demand to discover molecules that selectively and potently inhibit TET1 catalysis . We have utilized the random nonstandard peptide integrated discovery (RaPID) system, in which affinity‐based selection was conducted to isolate thioether macrocyclic peptide ligands against the TET1CCD from a mass library consisting of trillions of diverse members (Figure B and Figure S2 in the Supporting Information) . This unique selection campaign by means of the RaPID system has yielded a TET1 inhibitor selective over the TET2 isoform and 2OG‐dependent oxygenases tested.…”

“…RaPID selection of macrocyclic peptide binders against TET1CD or TET1CCD : The RaPID selection was carried out as described previously . In brief, an initial mRNA library was prepared by in vitro transcription of DNA library.…”

Netrins & Semaphorins: Novel regulators of the immune response

“…Recent attempts with small molecule drugs have been unsuccessful due to their difficulty interacting with the semaphorin-plexin complex. Matsanuga et al identified an alternative allosteric site between the Plexin B1 and Semaphorin 4D complex that provided deeper insight into the morphology of these proteins [73]. To circumvent this, nanoparticle-mediated blockade approaches of these neuronal targets that confer cellular specificity should be considered.…”

Multivalent Peptide–Nanoparticle Conjugates for Influenza‐Virus Inhibition

“…They can be produced and conjugated to different polymeric scaffolds by straightforward synthetic methods as opposed to often synthetically challenging routes for stereochemically defined SA building blocks. Peptide affinity towards receptors can be easily optimized by phage display, microarray screening,27, 28, 29 as well as chemical modification.…”