High-throughput one-bead-one-compound approach to peptide-encoded combinatorial libraries: MALDI-MS analysis of single TentaGel beads

The identification of pharmacologically promising compounds (lead compounds) from combinatorial libraries is frequently limited by the throughput of the analytical technique employed. Fourier transform mass spectrometry (FTMS) offers high sensitivity, mass accuracy (m/Deltam > 500 000), and sequencing capabilities. A rapid and efficient method for high-throughput analysis of single beads from peptide-encoded combinatorial libraries with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. Encoding peptides on single beads are identified and structurally characterized by MALDI time-of-flight (TOF) and ultrahigh-resolution MALDI Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. A strategy of on-probe sample preparation is developed to minimize handling of the beads.     

Gas-phase hydrogen/deuterium exchange as a molecular probe for the interaction of methanol and protonated peptides

The gas-phase hydrogen/deuterium (HID) exchange kinetics of several protonated amino acids and dipeptides under a background pressure of CH₃OD were determined in an external source Fourier transform mass spectrometer. H/D exchange reactions occur even when the gas-phase basicity of the compound is significantly larger (> 20 kcal/mol) than methanol. In addition; greater deuterium incorporation is observed for compounds that have multiple sites of similar basicities. A mechanism is proposed that involves a structurally specific intermediate with extensive interaction between the protonated compound and methanol.     

Chiral recognition in gas-phase cyclodextrin: Amino acid complexes—Is the three point interaction still valid in the gas phase?

The validity of the "three-point interaction" model is examined in the guest exchange reaction involving complexes of cyclodextrins and amino acids. The amino acid guest is exchanged in the gas phase in the presence of a gaseous alkyl amine. The net reaction is proton transfer between the protonated amino acid and the alkyl amine. The amino acid is lost as a neutral species. This reaction is sensitive to the chirality of the amino acid. Several amino acids are examined as well as the respective methyl esters to determine the role of the three interacting groups (ammonium, carboxylic acid, and side chain) in enantioselectivity. We find that the three-point interaction model is indeed valid in the gas phase. Enantioselectivity is optimal when two points of attraction and one repulsion is present in the gas-phase complex. The results are supported by molecular modeling calculations. A mechanism for the exchange is proposed.     

Site specificity in the H–D exchange reactions of gas-phase protonated amino acids with CH3OD

H–D exchange reactions of methanol-d₁ with protonated amino acids were performed in an external-source Fourier transform mass spectrometer. Absolute rate constants were determined for the group which included glycine, alanine, valine, leucine, isoleucine and proline. By comparing reactivities with selected methyl esters, it was found that exchange on the carboxylic acid occurs 3–10 times faster than exchange on the amino group. No simple correlation is observed between the rates of H–D exchange on the acid group and the size of the alkyl group. However, the rates of exchange on the amine decrease with increasing gas-phase basicity. Glycine, the least basic amino acid, exchanges its amine hydrogens the fastest. These results are useful for determining the interaction of methanol with protonated amino acids and can provide insight into the H–D exchange reactions observed with polyprotonated proteins produced by electrospray ionization.     

The use of heated capillary dissociation and collision-induced dissociation to determine the strength of noncovalent bonding interactions in gas-phase peptide-cyclodextrin complexes

Complexes of four peptides and permethylated-β-cyclodextrin are produced in the gas phase by using electrospray ionization. The four peptides—bradykinin (BK), des-Arg-1 bradykinin (dR¹BK), des-Arg-9-bradykinin (dR⁹BK), and Gly-5-Gly-8-bradykinin (G⁵G⁸BK)—were chosen because the relative inclusion and protonation sites varied with each peptide. Collision-induced dissociation (CID) was performed to determine the dissociation threshold of the four complexes. Heated capillary dissociation (HCD) was used to determine the dissociation temperatures of the peptide complexes. CID and HCD indicate the same ordering of stability in the complexation of the peptides to the oligosaccharides. Increasing strength of interaction follows the order dR⁹BK < BK < dR¹BK ≈ G⁵G⁸BK. The absence of Arg-9 destabilizes the complex, whereas the absence of Arg-1 stabilizes it relative to BK. Replacing both Phe residues with Gly similarly strengthens the interaction, suggesting that the Phe destabilizes the complex. CID and HCD are useful methods for obtaining relative strengths of interaction in noncovalent bound complexes.     

“Slow” metastable decomposition of oligosaccharide cations produced in an external source fourier transform mass spectrometer

Unimolecular metastable decomposition of cucyclodextrin cations is observed in a fast-atom bombardment Fourier transform mass spectrometry instrument. Cleavage reactions occur at the glycosidic bonds to produce oligomeric fragment ions. The first-order rate constant for the decay of the protonated parent was measured and found to be (4.2 ± 1.0) × 10²s^?1.     

A novel and rapid encoding method based on mass spectrometry for "one-bead-one-compound" small molecule combinatorial libraries

A novel and efficient encoding method based on mass spectrometry for "one-bead-one-compound" small molecule combinatorial libraries has been developed. The topologically segregated bifunctional resin beads with orthogonal protecting groups in the outer and inner regions are first prepared according to our previously published procedure. Prior to library synthesis, the inner core of each bead is derivatized with 3-4 different coding blocks on a cleavable linker. Each functional group on the scaffold is encoded by an individual coding block containing a functional group with the same chemical reactivity. During the library synthesis, the same chemical reactions take place on the scaffold (outer layer of the bead) and coding blocks (inner core of the bead) concurrently. After screening, the coding tags in the positive beads are released, followed by molecular mass determination using matrix-assisted laser desorption ionization Fourier transform mass spectrometry. The chemical structure of library compounds can be readily identified according to the molecular masses of the coding tags. The feasibility and efficiency of this approach were demonstrated by the synthesis and screening of a model small molecule library containing 84 672 member compounds, with a model receptor, streptavidin. Streptavidin binding ligands with structural similarity (17) were identified. The decoding results were clear and unambiguous.     

Fragmentation behavior of disaccharides during desorption–ionization

The fragmentation behavior of native and singly derivatized protonated disaccharides were examined by fast ion bombardment Fourier transform mass spectrometry to determine the origin of various fragment ions produced during desorption–ionization. The lack of interfering matrix ions in this technique allowed the investigation of model disaccharides. Three major product ions were observed, corresponding in mass to a loss of H₂O, a loss of a monosaccharide unit and a combination of both losses. The oxygen of the lost H₂O molecule originates from an oxygen attached to the anomeric carbon. The other two product ions come from two different monosaccharide units and are due to competing processes. The relative ion intensities of these two fragment ions are governed by the basicities of the fragments. The basicity of the reducing end increases when the hemiacetal is converted into the methyl glycoside. This increase in basicity is due to the increased size of the alkyl group and the ability of the alkyl group to prevent the opening of the reducing glycosidic ring.