Structural insights into inhibition of lipid I production in bacterial cell wall synthesis

Abstract

Summary Antibiotic-resistant bacterial infection is a serious threat to public health. Peptidoglycan biosynthesis is a well-established target for antibiotic development. MraY (phospho-MurNAc-pentapeptide translocase) catalyzes the first and an essential membrane step of peptidoglycan biosynthesis. It is considered a very promising target for the development of new antibiotics, as many naturally occuring nucleoside inhibitors with antibacterial activity target this enzyme1-4. However, antibiotics targeting MraY have not been developed for clinical use mainly due to a lack of structural insight into inhibition of this enzyme. Here we present the crystal structure of MraY from Aquifex aeolicus (MraYAA) in complex with its naturally occurring inhibitor, muraymycin D2 (MD2). Upon binding MD2, MraYAA undergoes remarkably large conformational rearrangements near the active site, which lead to the formation of a nucleoside-binding pocket and a peptide-binding site. MD2 binds the nucleoside-binding pocket like a two-pronged plug inserting into a socket. Additional interactions it makes in the adjacent peptide-binding site anchor MD2 to and enhance its affinity for MraYAA. Surprisingly, MD2 does not interact with three acidic residues or the Mg2+ cofactor required for catalysis, suggesting that MD2 binds to MraYAA in a manner that overlaps with, but is distinct from its natural substrate, UDP-MurNAc-pentapeptide. We have deciphered the chemical logic of MD2 binding to MraYAA, including how it avoids the need for pyrophosphate and sugar moieties, which are essential features for substrate binding. The conformational plasticity of MraY could be the reason that it is the target of many structurally distinct inhibitors. These findings can inform the design of new inhibitors targeting MraY as well as its paralogs, WecA and TarO.

Fluorescence-based assay for polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA) and identification of novel antimycobacterial WecA inhibitors

“…Function of MurX/MraY in peptidoglycan biosynthesis has been studied extensively and MurX is considered a promising drug target for developing new TB drugs (11,54,61). Some MurX inhibitors are known to kill Mtb much faster than the FDA-approved TB drugs; capuramycin analogues kill 99% of Mtb in 2–7 days, suggesting that targeting MurX will help ease the burden caused by tuberculosis (11,52).…”

Structural basis for catalysis at the membrane-water interface

“…A recent MraY structure in complex with a natural soluble inhibitor, muramycin D2 (MD2), was solved to 2.95 Å resolution [47]. This structure revealed that MD2 binding creates a large conformational change in the MraY and, though elements of MD2 mimic the natural soluble substrate, UDP-MurNAc-pentapeptide, it does not interact directly with any of the key acidic residues previously identified.…”

Synthesis and Medicinal Chemistry of Muraymycins, Nucleoside Antibiotics

“…The X-ray crystal structure of MraY, which is a target enzyme of MRYs, has long been difficult to solve because it is an integral membrane protein. Recently we present the crystal structure of MraY from Aquifex aeolicus (MraY AA ) in complex with MRY D2 64) (Fig. 6).…”