Preparation of Fluorinated Linkers:  Use of ¹⁹F NMR Spectroscopy to Establish Conditions for Solid-Phase Synthesis of Pilicide Libraries

Abstract

Three fluorinated linkers which are analogues of linkers commonly used in solid-phase peptide synthesis have been prepared. One of the linkers was used in combination with gel-phase 19F NMR spectroscopy to develop conditions for solid-phase synthesis of two libraries of pilicides, i.e. compounds designed to inhibit assembly of adhesive pili in uropathogenic Escherichia coli. Attachment to and cleavage from the linker could be monitored based on the chemical shift of the fluorine atom of the linker. In addition, use of the linker as internal standard allowed quantification and optimization of reactions occurring further away from the linker when fluorinated building blocks were employed. Importantly, high-quality 19F NMR spectra were obtained for compounds linked to a TentaGel resin in a standard NMR tube using an ordinary NMR instrument.

Chemical Biology Applied to the Study of Bacterial Pathogens

“…In contrast to inhibitors discovered by screening compound libraries, pilicides were developed using a rational design approach (12). Pilus biogenesis requires the chaperone protein to bind its natural ligands (52), so the solved crystal structure of the PapD-PapG complex was used to chemically design molecular mimetics that would bind within the active site of periplasmic chaperones PapD and FimC (12).…”

“…Pilus biogenesis requires the chaperone protein to bind its natural ligands (52), so the solved crystal structure of the PapD-PapG complex was used to chemically design molecular mimetics that would bind within the active site of periplasmic chaperones PapD and FimC (12). A library of pilicides was synthesized and demonstrated to be effective at inhibiting pilus formation (13).…”

Monitoring Reactions on Solid Phases with Raman Spectroscopy

“…The traditionally used procedures for the identification of compounds, such as elemental analysis and cleavage, cause drawbacks in solid‐phase chemistry due to the loss of material and are nowadays replaced or supplemented by new techniques for the on‐bead analysis of reactions. The most important methods, which offer several advantages such as non‐destructive analysis, have been introduced with the development of gel‐phase NMR analysis, the use of the magic‐angle spinning technique and 19 F NMR monitoring of reactions through introduction of fluorine linkers . IR and Raman measurements, both of which offer the advantage of very fast measurements, have also been used for monitoring reactions on polymeric material .…”

“…The most important methods, which offer severala dvantages such as non-destructive analysis, have been introduced with the development of gelphase NMR analysis, [15,16] the use of the magic-angle spinning technique [17,18] and 19 FNMR monitoring of reactions through introduction of fluorine linkers. [19,20] IR and Raman measurements, both of which offer the advantageofvery fast measurements, have also been used for monitoring reactionso np olymeric material. [21][22][23][24] Whereas IR analysish as already found its way into standard proceduresf or monitorings olid-phase reactions [25][26][27] and, in selected examples,t he progress of the reaction, [27][28][29][30][31] Raman and surface-enhanced Raman spectroscopy has been reported only in af ew applicationsf or the identification of smallc ompounds on solid phases,p robablyd ue to the limiteda vailability of Raman instruments.…”

Synthesis and application of N‐[1‐(4‐(4‐fluorophenyl)‐2,6‐dioxocyclohexylidene)ethyl] (Fde)‐protected amino acids for optimization of solid‐phase peptide synthesis using gel‐phase 19F NMR spectroscopy

“…Gel-phase 19 F NMR spectroscopy is a useful and robust method to monitor the progress of reactions on solid support as exemplified in several recent publications [1][2][3][4][5][6][7][8][9]. Fluorinated linkers and building blocks, and fluorinated protective groups allow quantitative and qualitative analysis of the reaction outcome.…”