Imaging combinatorial libraries by mass spectrometry: from peptide to organic-supported syntheses

Bead-based screening in chemical biology and drug discovery

High-throughput screening is an important component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds requires assays amenable to miniaturisation and automization. Combinatorial chemistry holds a unique promise to deliver structurally diverse libraries for early drug discovery. Among the various library forms, the one-bead-one-compound (OBOC) library, where each bead carries many copies of a single compound, holds the greatest potential for the rapid identification of novel hits against emerging drug targets. However, this potential has not yet been fully realized due to a number of technical obstacles. In this feature article, we review the progress that has been made in bead-based library screening and its application to the discovery of bioactive compounds. We identify the key challenges of this approach and highlight key steps needed for making a greater impact in the field.

Correlated matrix-assisted laser desorption/ionization mass spectrometry and fluorescent imaging of photocleavable peptide-coded random bead-arrays

RATIONALE

Rapidly performing global proteomic screens is an important goal in the post-genomic era. Correlated matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and fluorescent imaging of photocleavable peptide-coded random bead-arrays was evaluated as a critical step in a new method for proteomic screening that combines many of the advantages of MS with fluorescence-based microarrays.

METHODS

Small peptide-coded model bead libraries containing up to 20 different bead species were constructed by attaching peptides to 30-34 µm diameter glass, agarose or TentaGel® beads using photocleavable biotin or a custom-designed photocleavable linker. The peptide-coded bead libraries were randomly arrayed into custom gold-coated micro-well plates with 45 µm diameter wells and subjected to fluorescence and MALDI mass spectrometric imaging (MALDI-MSI).

RESULTS

Photocleavable mass-tags from individual beads in these libraries were spatially localized as ~65 µm spots using MALDI-MSI with high sensitivity and mass resolution. Fluorescently tagged beads were identified and correlated with their matching photocleavable mass-tags by comparing the fluorescence and MALDI-MS images of the same bead-array. Post-translational modification of the peptide Kemptide was also detected on individual beads in a photocleavable peptide-coded bead-array by MALDI-MSI alone, after exposure of the beads to protein kinase A (PKA).

CONCLUSIONS

Correlated MALDI-MS and fluorescent imaging of photocleavable peptide-coded random bead-arrays can provide a basis for performing global proteomic screening.

Classification of spectroscopically encoded resins by Raman mapping and infrared hyperspectral imaging

Barcoded resins (BCRs) were recently introduced as a potential platform for pre-encoded multiplexed synthesis, screening, and biomedical diagnostics. A key step toward the development of this strategy is the ability to rapidly interrogate and classify the BCRs in a high-throughput, noninvasive manner. Here, we describe a one-step strategy based on Raman mapping and Fourier transform infrared imaging to classify and spatially resolve randomly distributed BCRs. To illustrate this methodology, mixtures of up to 25 different BCRs were imaged and classified with 100% confidence. This strategy can be readily extended to a larger pool of resins, provided each BCR features a unique vibrational fingerprint (spectroscopic barcode). We have also established that reliable single-bead Raman spectra can be recorded in 10 ms, thus confirming that Raman mapping, in particular, could be a very fast method to classify the BCRs.

Spectroscopically encoded resins for high throughput imaging time-of-flight secondary ion mass spectrometry

Spectroscopic barcoding was recently introduced as a new pre-encoding strategy wherein the resin beads are not just carriers for solid phase synthesis, but are, in addition, the repository of the synthetic scheme to which they were subjected. To expand the repertoire of spectroscopically barcoded resins (BCRs), here we introduce a new family of halogenated polystyrene-based polymers designed for high-throughput combinatorial analysis using not only infrared and Raman spectroscopy but also imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS). In particular, we have established that (a) the halogen content of these new resins can be used as an encoding element in quantitative imaging ToF-SIMS and (b) the number of styrene monomers used to generate unique vibrational fingerprints can be significantly reduced by using monomers in different molar ratios. The combination of quantitative imaging ToF-SIMS and vibrational spectroscopy is anticipated to dramatically increase the repertoire of possible BCRs from a few hundreds to several thousands.

MALDI-TOF MS analysis of soluble PEG based multi-step synthetic reaction mixtures with automated detection of reaction failure

Macromolecules of tunable solubility, used to mimic inert insoluble materials while maintaining solution conditions, allowed the performance of efficient supported organic chemistry and facilitated in situ reaction monitoring. To satisfy the high throughput requirements of automated synthetic processes, organic syntheses carried out on bifunctional polyethylene glycol polymers (PEG(3400)-OH) were monitored step-by-step by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). A protocol was designed to control the ionization mechanism of such polymers exhibiting high affinity for alkali metal cations. Automated, rapid, and reliable data interpretation was performed by an in-house developed visual basic application relying on the sodiated ion accurate monoisotopic mass measurement. The methodology was illustrated through the monitoring of a six-step synthetic scheme.

Molecule-Specific Imaging with Mass Spectrometry and a Buckminsterfullerene Probe: Application to Characterizing Solid-Phase Synthesized Combinatorial Libraries

We employ a newly developed buckminsterfullerene (C(60)) primary ion beam with time-of-flight secondary ion mass spectrometry to create molecule-specific images of resin particles employed in the solid-phase synthesis of peptide combinatorial libraries. This new cluster ion source, when operated at an incident energy of 20 keV, is remarkably effective at desorbing small peptides directly from a polymer surface and opens new possibilities for characterizing large arrays of diverse sets of molecules. In addition, the C(60) ion beam may be focused to a spot of 1.5 microm in diameter, enabling molecule-specific images of single 100 microm resin particles to be acquired. We report three significant aspects associated with utilizing the C(60) projectile that show how this technology can be taken to a more advanced level, especially when compared to results obtained with more conventional atomic primary ions. First, the useful yield of molecular ions is generally observed to be enhanced by at least 3 orders of magnitude over those previously possible. Second, the energy dissipation process associated with the C(60) impact is most efficient at desorbing molecules on soft substrates such as polymer surfaces rather than harder substrates such as metals or semiconductors. Third, there is a greatly reduced tendency for insulating surfaces to build up excess charge, obviating the need for charge compensation. Using a small five-member peptide library as a model, we show that by utilizing the focusing properties of the C(60) beam, it is possible to assay the surface composition of 100-microm polymer beads at a rate of up to 10 particles/s. Moreover, even at the picomole level, there are enough sequence ions in the mass spectrum to determine a unique composition. The results illustrate the ability to quickly assay large libraries without the use of tags and suggest the strategy may be applicable to a range of high-throughput experiments.

Direct Mass Spectrometric Monitoring of Solid Phase Organic Syntheses

Direct on-bead monitoring of solid-phase reactions is possible with soft laser desorption time-of-flight mass spectrometry (SLD-TOF MS) without prior cleavage from the resin if photocleavable phenacyl ester or o-nitroveratryl linker groups are employed.

Preparation, physical properties, on-bead binding assay and spectroscopic reliability of 25 barcoded polystyrene-poly(ethylene glycol) graft copolymers

Here we describe the preparation of 25 beaded polystyrene-poly(ethylene glycol) graft copolymers from six spectroscopically active styrene monomers: styrene, 2,5-dimethylstyrene, 4-methylstyrene, 2,4-dimethylstyrene, 4-tert-butylstyrene, and 3-methylstyrene. These polymers were thoroughly characterized by Raman, infrared, and (1)H/(13)C NMR spectroscopies, and differential scanning calorimetry. Determination of the swelling properties, peptide synthesis, and on-bead streptavidin-alkaline phosphatase (SAP) binding assay further established that their physical and chemical properties where not significantly altered by the diversity of their encoded polystyrene core. Each of the 25 resins displayed a unique Raman and infrared vibrational fingerprint, which was converted into a "spectroscopic barcode". The position of each bar matches the peak wavenumber in the corresponding spectrum but is independent of its intensity. From this simplified representation similarity maps comparing 35 000 resin pairs were generated to establish the spectroscopic barcoding as a reliable encoding methodology. In effect, in 99% of the cases, the highest similarity coefficients were obtained for resin pairs prepared from the same styrene derivatives even after SAP binding assay. We have also shown that a small but unique combination of a resin's vibrations (30-40%) is sufficient for its identification. However, in rare cases where a resin's vibrational signature has been severely compromised, both the Raman and infrared barcodes were synergistically and reliably utilized to unequivocally identify its chemical make up.