Lumazine synthase catalyzes the penultimate step in the
biosynthesis
of riboflavin, while riboflavin synthase catalyzes the last step. O-Nucleoside, S-nucleoside, and N-nucleoside analogues of hypothetical lumazine biosynthetic
intermediates have been synthesized in order to obtain structure and
mechanism probes of these two enzymes, as well as inhibitors of potential
value as antibiotics. Methods were devised for the selective cleavage
of benzyl protecting groups in the presence of other easily reduced
functionality by controlled hydrogenolysis over Lindlar catalyst.
The deprotection reaction was performed in the presence of other reactive
functionality including nitro groups, alkenes, and halogens. The target
compounds were tested as inhibitors of lumazine synthase and riboflavin
synthase obtained from a variety of microorganisms. In general, the S-nucleosides and N-nucleosides were more
potent than the corresponding O-nucleosides as lumazine
synthase and riboflavin synthase inhibitors, while the C-nucleosides were the least potent. A series of molecular dynamics
simulations followed by free energy calculations using the Poisson–Boltzmann/surface
area (MM-PBSA) method were carried out in order to rationalize the
results of ligand binding to lumazine synthase, and the results provide
insight into the dynamics of ligand binding as well as the molecular
forces stabilizing the intermediates in the enzyme-catalyzed reaction.