Analogues of Muraymycin Nucleoside Antibiotics with Epimeric Uridine-Derived Core Structures

Abstract

Nucleoside analogues have found widespread application as antiviral and antitumor agents, but not yet as antibacterials. Naturally occurring uridine-derived ‘nucleoside antibiotics’ target the bacterial membrane protein MraY, an enzyme involved in peptidoglycan biosynthesis and a promising target for the development of novel antibacterial agents. Muraymycins represent a nucleoside-peptide subgroup of such MraY-inhibiting natural products. As part of detailed structure-activity relationship (SAR) studies on muraymycins and their analogues, we now report novel insights into the effects of stereochemical variations in the nucleoside core structure. Using a simplified version of the muraymycin scaffold, it was shown that some formal inversions of stereochemistry led to about one order of magnitude loss in inhibitory potency towards the target enzyme MraY. In contrast, epimers of the core motif with retained inhibitory activity were also identified. These 5′,6′-anti-configured analogues might serve as novel chemically tractable variations of the muraymycin scaffold for the future development of uridine-derived drug candidates.

Muraymycin Nucleoside Antibiotics: Structure-Activity Relationship for Variations in the Nucleoside Unit

“…However, synthetically obtained 5 -defunctionalized ( 5 -deoxy') muraymycin C4 that was reported by our group [38] was found to still inhibit MraY in the nM range, even though most naturally occurring muramycins are MraY inhibitors with pM activities [39]. The replacement of (3S)-3-hydroxy-L-leucine with L-leucine resulted in a~25-fold loss of activity [41], but that implied that such simplified analogues may still be employed in SAR studies. The exact structure of the amino acid side chains in the urea dipeptide moiety seems to only have limited impact on MraY inhibition [21].…”

“…We had previously described different solution-phase syntheses of muraymycin analogues, either based on a tripartite [38] or a bipartite [41] strategy. However, we have recently reported a novel synthetic approach towards muraymycin analogues, based on solid-phase peptide synthesis (SPPS) to construct a building block for the complete peptide unit [42].…”

“…Introduction of the propyl linker and the leucine moiety was achieved by reductive amination of 42 with aldehyde 43 [24,34], furnishing 44 in 58% yield (Scheme 5). After hydrogenolytic Cbz cleavage (product 45, quantitative yield), urea dipeptide building block 46 [24,41] was employed in a peptide coupling step to construct the full-length muraymycin scaffold. This was followed by global acidic deprotection and HPLC purification to give target compound 16 (as its bis-TFA salt) in 32% yield over two steps from 45 (Scheme 5).…”

“…For these studies, we used an established fluorescence-based assay for MraY activity, which employs a dansylated version of Park's nucleotide 1 and MraY from S. aureus (heterologously overexpressed in E. coli) [18,39,[48][49][50][51][52]. The obtained inhibitory activities (IC 50 values, also see Supplementary Materials Figures S1-S4, for measured data and inhibition curves) are listed in Table 1, including the potency of previously reported reference compound 8 [24,41]. As target structures 13 and 15 turned out to be nearly inactive as MraY inhibitors in the relevant concentration range (≤100 µM), we also tested them at a significantly higher concentration (1 mM, Table 1).…”

“…Regarding the stereochemistry of the nucleoside moiety, the naturally occurring (6 S)-configuration was found to be preferred. If a 5 -hydroxy group was present, at least either C-5 or C-6 needed to have their naturally occurring configuration in order to retain good inhibitory activity towards MraY in vitro [41]. [24] and the previously reported protecting group-containing analogues 11 and 12 (PMB = p-methoxybenzyl, TBDMS = tert-butyldimethylsilyl) [34].…”