Mapping the Suramin-Binding Sites of Human Neutrophil Elastase:  Investigation by Fluorescence Resonance Energy Transfer and Molecular Modeling

Neutrophil elastase (NE), a mediator of inflammation, binds with high affinity numerous anionic molecules including suramin, a polysulfated naphthylurea, which inhibits it with a K i of 0.2 μM and a 4:1 suramin:NE stoichiometry and thus constitutes a potential therapeutic agent. In an attempt to locate the suramin molecules on NE, we investigated the NE−suramin interaction using steady-state and time-resolved fluorescence spectroscopy. The time-resolved intensity decay of NE, a protein with three Trp residues, in positions 27, 141, and 237 (chymotrypsin numbering system) was best described by a three-exponential function with lifetimes ranging from 0.22 to 2.28 ns. Comparison of the accessibility of the three lifetime classes to the fluorescence quenchers acrylamide and iodide with the computed solvent accessibility of the three Trp residues in the crystal structure of NE indicates that the main, if not the sole, contribution to the 2.28 ns lifetime class is brought about by the fully buried Trp 141 residue. The addition of suramin to NE induces a sharp decrease in NE fluorescence and a corresponding increase in suramin fluorescence due to an efficient fluorescence resonance energy transfer (FRET) between the Trp residues of NE, acting as donors, and the naphthalene rings of suramin, behaving as acceptors. From the fate of the longest lifetime class in the presence of variable suramin concentrations, we deduce that two suramins are bound at less than 17 Å from Trp 141, whereas the two others are located at least 29 Å from Trp 141. Moreover, neither the binding of suramin to NE nor the FRET process was modified when NE was complexed with a peptide chloromethylketone inhibitor, suggesting that suramin does not directly interfere with the substrate binding site of NE. These data were used as constraints to model the NE−suramin complex.