Picomolar inhibitors as transition-state probes of 5′-methylthioadenosine nucleosidases

Transition states can be predicted from an enzyme's affinity to related transition-state analogues. 5′-Methylthioadenosine nucleosidases (MTANs) are involved in bacterial quorum sensing pathways and thus are targets for antibacterial drug design. The transition-state characteristics of six MTANs are compared by analyzing dissociation constants (K_d) with a small array of representative transition-state analogues. These inhibitors mimic early or late dissociative transition states with K_d values in the picomolar range. Our results indicate that the K_d ratio for mimics of early and late transition states are useful in distinguishing between these states. By this criterion, the transition states of Neisseria meningitides and Helicobacter pylori MTANs are early dissociative, whereas Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, and Klebsiella pneumoniae MTANs have late dissociative characters. This conclusion is confirmed independently by the characteristic [1′-³H] and [1′-¹⁴C] kinetic isotope effects (KIEs) of these enzymes. Large [1′-³H] and unity [1′-¹⁴C] KIEs are observed for late dissociative transition states, whereas early dissociative states showed close-to-unity [1′-³H] and significant [1′-¹⁴C] KIEs. K_d values of various MTANs for individual transition-state analogues provide tentative information about transition-state structures due to varying catalytic efficiencies of enzymes. Comparing K_d ratios for mimics of early and late transition states removes limitations inherent to the enzyme and provides a better predictive tool in discriminating between possible transition-state structures.