Leveraging High-Resolution Ion Mobility-Mass Spectrometry for Cyclic Peptide Soft Spot Identification.

Cyclic peptides are an important class of molecules that gained significant attention in the field of drug discovery due to their unique pharmacological characteristics and enhanced proteolytic stability. Yet, gastrointestinal degradation remains a major hurdle in the discovery of orally bioavailable cyclic peptides. Soft spot identification (SSID) of the regions in the cyclic peptide sequence susceptible to amide hydrolysis by proteases is used in the discovery stage to guide medicinal chemistry design. SSID can be an arduous task, traditionally performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS), often resulting in complex and time-consuming manual analysis, particularly when isomeric linear peptide metabolites chromatographically coelute. Here, we present an alternative orthogonal approach that entails a high-resolution ion mobility (HRIM) system based on Structures for Lossless Ion Manipulation (SLIM) technology interfaced with quadrupole time-of-flight (QTOF) mass spectrometry to address some of the challenges associated with SSID. Two strategies were used to resolve linear isomeric peptide metabolites: labeled and label-free, both utilizing the HRIM platform. The label-free strategy leverages negative polarity to ionize the isomers which achieves better separation of the gas phase ions in the ion mobility (IM) dimension as compared to positive polarity, which is a more conventional approach when studying proteins and peptides. The second approach uses an isotope-labeled dimethyl tag on the terminal amine group, acting as a "shift reagent" to influence the mobility of isomers in the positive mode. This method resulted in baseline separation for the isomers of interest and produced unique product ions in the fragmentation spectra for unambiguous soft spot identification. Both label-free and labeled strategies demonstrated the ability to solve the challenges associated with SSID for cyclic peptides.

Ligand symmetry-equivalence on thiolate protected gold nanoclusters determined by NMR spectroscopy.

The Au(144)(SR)(60) nanocluster has been a subject of structural conjecture since its initial description over a decade ago as a 29 kDa compound, yet a decisive empirical structure is elusive. Herein we show that (1)H NMR spectroscopy can provide a detailed view of ligand-layer equivalence for thiolate protected gold nanoclusters. We show that Au(25)(SR)(18), Au(38)(SR)(24) and Au(102)(SR)(44) nanoclusters have (1)H NMR spectra where the number of distinct chemical environments for the R-groups is equivalent to the number of symmetry environments of the sulfur headgroups, which anchor each ligand. We also show that the Au(144)(SR)(60)(1)H NMR spectrum is consistent with a previously published DFT-derived structural model for Au(144)(SR)(60). We suggest that this analysis may be extended to other structurally obscure nanoclusters, such as a ∼59 kDa compound for which we observe up to four symmetry environments.