Dataset Information

MicroMap photoproximity labeling enables small molecule binding site mapping

ABSTRACT: Proteomics data for MicroMap enabled binding site mapping

INSTRUMENT(S): timsTOF Pro 2

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: David MacMillan

PROVIDER: MSV000092043 | MassIVE | Fri May 26 13:54:00 BST 2023

REPOSITORIES: MassIVE

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Publications

μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping.

Huth Sean W SW Oakley James V JV Seath Ciaran P CP Geri Jacob B JB Trowbridge Aaron D AD Parker Dann L DL Rodriguez-Rivera Frances P FP Schwaid Adam G AG Ramil Carlo C Ryu Keun Ah KA White Cory H CH Fadeyi Olugbeminiyi O OO Oslund Rob C RC MacMillan David W C DWC

Journal of the American Chemical Society 20230720 30

The characterization of ligand binding modes is a crucial step in the drug discovery process and is especially important in campaigns arising from phenotypic screening, where the protein target and binding mode are unknown at the outset. Elucidation of target binding regions is typically achieved by X-ray crystallography or photoaffinity labeling (PAL) approaches; yet, these methods present significant challenges. X-ray crystallography is a mainstay technique that has revolutionized drug discove ...[more]

PMID: 37471577

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Project description:PRIDE > Archive > PXD013420 Project PXD013420 Download Project Files Summary Title A binding site hotspot map of the FKBP12–rapamycin–FRB ternary complex by photo-affinity labeling and mass spectrometry-based proteomics Description Structural characterization of small molecule binding site hotspots within the global proteome is uniquely enabled by photo-affinity labeling (PAL) coupled with chemical enrichment and unbiased analysis by mass spectrometry (MS). MS-based binding site hotspot maps provide structural resolution of interaction sites in conjunction with identification of target proteins. However, binding site hotspot mapping has been confined to relatively simple small molecules to date; extension to more complex compounds would enable the structural definition of new binding modes in the proteome. Here, we extend PAL and MS methods to derive a binding site hotspot map for the immunosuppressant rapamycin, a complex macrocyclic natural product that forms a ternary complex with the proteins FKBP12 and FRB. Photo-rapamycin was developed as a diazirine-based PAL probe for rapamycin, and the FKBP12–photo-rapamycin–FRB ternary complex formed readily in vitro. Photo-irradiation, digestion, and MS analysis of the ternary complex revealed a McLafferty rearrangement product of photo-rapamycin conjugated to specific surfaces on FKBP12 and FRB. Molecular modeling of the ternary complex based on the binding site map revealed a 5.0 Å minimum distance constraint between the conjugated residues and the diazirine carbon. Molecular dynamics further predicted a 9.0 Å labeling radius for the diazirine upon photo-activation that may be useful in the interpretation of binding site measurements from PAL more broadly. Thus, in characterizing the ternary complex of photo-rapamycin by MS, we applied binding site hotspot mapping to a macrocyclic natural product and extracted a precise structural measurement for interpretation of PAL products that may enable the discovery of new ligand space in the “undruggable” proteome.

Dataset Information

MicroMap photoproximity labeling enables small molecule binding site mapping

Publications

μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping.

Similar Datasets

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