Sulfonyl fluorides as privileged warheads in chemical biology

Abstract

Sulfonyl fluoride electrophiles have found significant utility as reactive probes in chemical biology and molecular pharmacology. As warheads they possess the right balance of biocompatibility (including aqueous stability) and protein reactivity. Their functionality is privileged in this regard as they are known to modify not only reactive serines (resulting in their common use as protease inhibitors), but also context-specific threonine, lysine, tyrosine, cysteine and histidine residues. This review describes the application of sulfonyl fluoride probes across various areas of research and explores new approaches that could further enhance the chemical biology toolkit. We believe that sulfonyl fluoride probes will find greater utility in areas such as covalent enzyme inhibition, target identification and validation, and the mapping of enzyme binding sites, substrates and protein-protein interactions.

Fig. 1. SF probes that react with serine: (2-aminoethyl)benzenesulfonyl fluoride (AEBSF); phenylmethylsulfonyl fluoride (PMSF); dansyl fluoride; L-28; AM-374 (palmityl sulfonyl fluoride); AM3506; M-352; PW28; enzyme inhibitors 1–5; and cysteine-reactive probe AdaK(Bio)Ahx₃L₃VS.

Fig. 2. (a) X-ray crystal structure of the PPT1 and palmityl sulfonyl fluoride complex (PDB code 1EXW) highlighting the binding surface. (b) Crystal structure showing dimerisation of outer membrane phospholipase A (OMPLA) induced by palmityl sulfonyl fluoride (green, calcium ions blue spheres) (PDB code ; 1QD6).

Fig. 3. SF probes that react with lysine: FSBA; FSBA–biotin; 6, 7, 8, 9, 10; structure of SF-containing oxadiazole 11 (emission and excitation maxima are quoted for the TTR-conjugate) and crystal structure showing adduct formation with TTR (PDB code ; 4FI7).

Fig. 4. Structure of DPIV (grey) with AEBSF (magenta) adduct with Tyr547J (green). Overlaid is a model of DPIV (pink-brown) with a docked meta-analogue of AEBSF (purple) after reaction with Ser630 (cyan). Covalent docking was performed using the Covalent Docking module from the Schrodinger 2014-3 suite (Schrodinger, LLC).

Fig. 5. AEBSF (magenta) adduct of dscPsaA in complex with galactose (cyan) (PDB 4F8O).

Fig. 6. X-ray structure of PMSF (green) that has reacted with Tyr41 (magenta) in Fe-SOD in Sulfolobus solfataricus (PDB ; 1WB8). The proximal His155 (cyan) and Fe^III (brown) are also highlighted.

Fig. 7. (a) SF probes that react with tyrosine: 5′-FSBAzA; DAS1; DS6B; DS6R; G1-H sepharose resin; DTBSF and complex of biopterin (green) in chicken liver DHFR (PDB 1DR1) showing proximity of Tyr31 (cyan) which reacts with DTBSF; SF-p1 and clickable probe SF-p1-yne (and crystal structure of SF-p1 with DcpS, PDB ; 4QDV). (b) Pie chart showing the distribution of amino acid residues proximal to known SF-reactive tyrosines as determined by analyzing crystal structures in the PDB.

Fig. 8. X-ray structure of PMSF (magenta) with macrophage migration inhibitory factor (MIF) illustrating the reaction with the N-terminal proline residue (green). PDB code 3CE4.

Arjun Narayanan

Lyn H. Jones