Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective

Abstract

The enzyme MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) catalyzes the first cytoplasmatic step in the synthesis of murein precursors. This function is of vital relevance for bacteria, and the enzyme therefore represents an important target protein for the development of novel antibacterial compounds. Several X-ray structures of liganded and un-liganded MurA have been published, which may be used for rational drug design. MurA, however, contains a highly flexible surface loop, which is involved in substrate and inhibitor binding. In the available X-ray structures, the conformation of this surface loop varies, depending on the presence or absence of ligands or substrate and probably also on the crystal packing. The uncertainty of the low-energy, or “resting state” conformation of this surface loop hampers the application of rational drug design to this class of enzymes. We have therefore performed an extensive molecular dynamics study of the enzyme in order to identify one or several low-energy conformers. The results indicate that, at least in some of the X-ray structures, the conformation of the flexible surface loop is influenced by crystallographic contacts. Furthermore, three partially helical foldamers of the surface loop are identified which may resemble the resting states of the enzyme or intermediate states that are “traversed” during the substrate binding process. Another, very important aspect for the development of novel antibacterial compounds is the inter- and intra-species variability of the target structure. We present a comparison of MurA sequences from 163 organisms which were analyzed under the aspects of enzyme mechanism, structure and drug design. The results allow us to identify the most promising binding sites for inhibitor interaction, which are present in MurA enzymes of most species and are expected to be insusceptible to resistance-inducing mutations.