Fig. 1: Development of antibacterial agents based on MraY inhibitory natural products with build-up library synthesis strategy.

a Structures of MraY inhibitory natural products have common uridine moiety binding to uridine pocket (red) and other motif with various binding mode in MraY. HS1–4 represent binding hot spot (see details in reference 13, magenta; uridine pocket, green; HS1, purple; HS2, salmon; HS3, cyan; HS4, light brown; HS5, brown; HS6). b Complex structures of these antibiotics bound to MraY. Each carbon colour represents each antibiotic in panel a (salmon; tunicamycin, green; muraymycin D2, cyan; 3′-hydroxy-mureidomycin A, orange; capuramycin). c Overview of a comprehensive in situ evaluation of the build-up library. (1) Natural products are divided into the core and accessory. (2) Reaction site is introduced into both pairs. The reaction ideally proceeds quantitatively and selectively without toxic reagents and by-products. (3) The core and accessory fragments are ligated on the assay plates. The resulting library is directly evaluated by enzymatic and cell-based assays. (4) A comprehensive SAR is obtained and hit analogues are identified. d Core fragments are the core substructures containing uridine from these antibiotics and formyl group attached to them. Each antibiotic type is represented by three capital letters (tunicamycin; TUN, muraymycin; MRY, 3′-hydroxy-mureidomycin; MRD, capuramycin; CAP) and an additional letter (para or meta substituted formyl group; p-CHO or m-CHO). Aldehydes are ligated with hydrazine (named BZXX, PAXX, ACXX, AAXX, or LAXX; XX is a number). e The name of the obtained hydrazone should be indicated with the aldehyde name in front and the hydrazine name behind (e.g. TUNp-BZXX).