Phosphate Recognition in Structural Biology

Abstract

Drug-discovery research in the past decade has seen an increased selection of targets with phosphate recognition sites, such as protein kinases and phosphatases, in the past decade. This review attempts, with the help of database-mining tools, to give an overview of the most important principles in molecular recognition of phosphate groups by enzymes. A total of 3003 X-ray crystal structures from the RCSB Protein Data Bank with bound organophosphates has been analyzed individually, in particular for H-bonding interactions between proteins and ligands. The various known binding motifs for phosphate binding are reviewed, and similarities to phosphate complexation by synthetic receptors are highlighted. An analysis of the propensities of amino acids in various classes of phosphate-binding enzymes showed characteristic distributions of amino acids used for phosphate binding. This review demonstrates that structure-based lead development and optimization should carefully address the phosphate-binding-site environment and also proposes new alternatives for filling such sites.

New insights into dihydrogenphosphate recognition with dirhenium(i) tricarbonyl complexes bridged by a thiourea moiety

“…Surprisingly, fluoride shows no immediate change in the spectrum, but once one equivalent had been added, a small downfield shift is observed before the peaks broaden and become uninterruptable consistent with proton exchange. 44,51,52 With acetate, a similar behaviour is found to that of the free ligand (Figure 4a and S15a), with a binding constant, p 1 = 3.2, assuming a one to one stoichiometry, suggesting that the presence of the two Re(CO) 3 groups has a marginal affect on the affinity for acetate). With the introduction of TBA H 2 PO 4 in a 50% DMSO-D 6 / CD 3 CN mixture, there is a significant down-field shift of the NH proton signal ( Figure S15c), a change in the methylene peak position, with the singlet broadening and eventually becoming a multiplet implying a conformational change and a more rigid arrangement around the flexible methylene groups - i.e.…”

“…49 Ligands L2 and L3 (Scheme 2) were subsequently prepared in the presence of triethylamine in 70 and 86% yield respectively and using a similar procedure as described for L1. These two ligands were also successfully bonded to two Re(CO) 3 Br moieties in DMSO, and characterised by 1 H NMR spectroscopy ( Figure S3 -S6) and Scheme 2: Synthetic pathway to L2 and L3. The rhenium complexes all proved to be bright yellow in colour and the UV / vis.…”

“…The rhenium complexes all proved to be bright yellow in colour and the UV / vis. spectrum of {Re(CO) 3 Br} 2 (-L2) {Re(CO) 3 Br} 2 (-L3) revealed the anticipated ligand centred (LC) * transition at approximately 290 nm (Table 1), a shoulder at 320 nm, and a broad metal-to-ligand-charge-transfer (MLCT) absorption in the range of 370 to 390 nm ( Figure S7). The corresponding emission spectra of all of the complexes show a weak luminescence around 610 nm (excited at 380 nm) and a quantum yield of approximately half that of [Re(CO) 3 (bpy)Br] ( Figure S8).…”

“…This revealed that there is no change in the relative peak position of any of the observed signals, including that of the thiourea NH resonance, with the addition of up to ten equivalents of the tetrabutylammonium (TBA) salts of NO 3 − , Br − and HSO 4 − , while the addition of the corresponding chloride salt leads to a small downfield shift of the thiourea proton signal ( = 0.25 ppm with ten equivalents, Figure 2a and S9). However a sequential titration with fluoride causes the complete loss of the NH signal, consistent with proton exchange, or even full deprotonation ( Figure S9).…”

“…2,3 One successful approach is the use of metal-based receptors, where positive electrostatic interactions can be combined with an acidic proton to encourage hydrogen bonding, 4 and then exploit a change in the redox, photophysical or magnetic properties to create a sensor. [5][6][7] Low charge selective systems able to operate in aqueous media remains a considerable challenge however.…”