Intramolecular Cooperativity in the Reaction of Diacyl Phosphates with Serine β-Lactamases

Abstract

Asymmetric diaroyl phosphates (ArCOOPO2−OCOAr′, where Ar = Ph, Ar′ = 4-biphenyl, 2-benzothiophenyl and 2-benzofuranyl), have been prepared, evaluated as serine (classes A, C, D) β-lactamase inhibitors, and compared with respect to the latter with their symmetric “parents”, where Ar = Ar′. The asymmetric compounds, in general, were found to react with the β-lactamases in two modes, corresponding to different orientations with respect to the active site, whereby either of the two aroyl groups may acylate the enzyme to form two different inert acyl-enzymes, E-COAr and E-COAr′. In all cases, the asymmetric compounds, in one orientation, react more rapidly with the enzymes tested than one symmetrical “parent” but not both. From comparisons of activation free energy differences, it was found that the changes in free energy on changing from one aryl group to another, in either the acyl group or the leaving group, were not additive, i.e. that the effect of changing one aroyl group to another depended on the leaving group and vice versa. Thus, intramolecular cooperativity between the aroyl groups must exist, arising either from direct interaction between them or from protein-mediated interaction, or from a combination of both. Such cooperativity brings fresh opportunities and challenges to the search for novel ß-lactamase inhibitors.

Linear Free Energy Relationship Analysis of Transition State Mimicry by 3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) Oxime, a DAHP Synthase Inhibitor and Phosphate Mimic

“…The authors argued that because acarbose, a pseudotetrasaccharide, extended into the +1 to +3 subsites, which the substrates did not occupy, binding cooperativity between the extra residues and the inhibitory valienamine residue at the −1 subsite strengthened the latter’s interactions with the enzyme. That is, cooperativity of ligand binding increased the binding strengths of the inhibitory residue’s interactions with the enzyme, as has been observed in other contexts. − …”

Inhibition of dd-Peptidases by a Specific Trifluoroketone: Crystal Structure of a Complex with the Actinomadura R39 dd-Peptidase

“…A combination of the inhibition kinetics and the crystal structure, both discussed above, suggests that the trifluoromethyl moiety alone does not interact specifically and tightly with the dd -peptidase active site but acts only as part of an electrophilic ketone that does react with the active site serine in a cooperative fashion with the specifically binding d -α-aminopimelyl N-terminus. ,,, …”

“…A combination of the inhibition kinetics and the crystal structure, both discussed above, suggests that the trifluoromethyl moiety alone does not interact specifically and tightly with the DD-peptidase active site but acts only as part of an electrophilic ketone that does react with the active site serine in a cooperative fashion with the specifically binding D-α-aminopimelyl N-terminus. 26,27,30,62 ■ CONCLUSIONS Compound 12 represents the first nanomolar trifluoroketone inhibitor of a DD-peptidase. It owes its potency to the trifluoroketone moiety, elevating it over the less electrophilic aldehyde 11 and other tetrahedral species derived from 7−10, which occupy the active site less favorably.…”

Genetic basis of molecular mechanisms in β-lactam resistant gram-negative bacteria

“…revealed the presence of NDM-1 on a transposon between two copies of ISAba125. Most isolates were resistant to meropenem [58]. MDR E. coli contains not only NDM-1 but also other resistance genes, including qnrB, aac(6c)-ib-cr, and blaSHV-11.…”

“…Several β-lactamase inhibitors have been used to minimize the development of β-lactamase inactivation and target the special features and characters of these enzymes. We must use the inhibitors with high affinity for the active site of the β-lactamase target so that the inhibitor can work efficiently; for example, phosphonates and methylidene penems attain an inhibition similar to classes D, C, and A [58,66]. By mimicking the available natural substrates, β-lactamase can therefore be inhibited.…”