Structures of Kibdelomycin Bound to Staphylococcus aureus GyrB and ParE Showed a Novel U-Shaped Binding Mode

Abstract

Bacterial resistance to antibiotics continues to pose serious challenges as the discovery rate for new antibiotics fades. Kibdelomycin is one of the rare, novel, natural product antibiotics discovered recently that inhibits the bacterial DNA synthesis enzymes gyrase and topoisomerase IV. It is a broad-spectrum, Gram-positive antibiotic without cross-resistance to known gyrase inhibitors, including clinically effective quinolones. To understand its mechanism of action, binding mode, and lack of cross-resistance, we have co-crystallized kibdelomycin and novobiocin with the N-terminal domains of Staphylococcus aureus gyrase B (24 kDa) and topo IV (ParE, 24 and 43 kDa). Kibdelomycin shows a unique "dual-arm", U-shaped binding mode in both crystal structures. The pyrrolamide moiety in the lower part of kibdelomycin penetrates deeply into the ATP-binding site pocket, whereas the isopropyl-tetramic acid and sugar moiety of the upper part thoroughly engage in polar interactions with a surface patch of the protein. The isoproramic acid (1,3-dioxopyrrolidine) and a tetrahydropyran acetate group (Sugar A) make polar contact with a surface area consisting of helix α4 and the flexible loop connecting helices α3 and α4. The two arms are connected together by a rigid decalin linker that makes van del Waals contacts with the protein backbone. This "dual-arm", U-shaped, multicontact binding mode of kibdelomycin is unique and distinctively different from binding modes of other known gyrase inhibitors (e.g., coumarins and quinolones), which explains its lack of cross-resistance and low frequency of resistance. The crystal structures reported in this paper should enable design and discovery of analogues with better properties and antibacterial spectrum.

Kibdelomycin Is a Bactericidal Broad-Spectrum Aerobic Antibacterial Agent

“…There was a moderate (4-fold) shift in its MIC for coumermycin-resistant S. aureus harboring three mutations in GyrB (Q136E, I175T, L455I) (9). These findings were nicely explained by several kibdelomycinbound crystal structures of GyrB and ParE (12). Most importantly, this study, kibdelomycin did not show a shift in its MIC for many well-characterized highly quinolone-resistant S. aureus strains harboring multiple mutations in GrlA and GyrA and S. pneumoniae strains harboring mutations in ParC and GyrA ( Table 2).…”

“…Kibdelomycin selectively inhibits bacterial DNA synthesis by specifically inhibiting the ATPase activity of bacterial gyrase B (GyrB) and topoisomerase IV (ParE). It binds the GyrB and ParE enzymes in a unique U-shaped binding mode with multipoint contacts (12). Kibdelomycin selectively inhibited C. difficile without affecting many other anaerobic gut bacteria, including Bacteroides species (11).…”

“…It showed potent in vivo activity against C. difficile infection without systemic exposure (11). We recently reported an X-ray crystal structure of kibdelomycin bound to S. aureus and E. coli GyrB and ParE (12). The crystal structure showed that kibdelomycin binds uniquely in a U-shaped multicontact binding mode, occupying the ATP binding site with extension to another part of the pocket (12).…”

“…We recently reported an X-ray crystal structure of kibdelomycin bound to S. aureus and E. coli GyrB and ParE (12). The crystal structure showed that kibdelomycin binds uniquely in a U-shaped multicontact binding mode, occupying the ATP binding site with extension to another part of the pocket (12). Kibdelomycin exhibits a low frequency of resistance and shows no cross-resistance in S. aureus strains resistant to other known gyrase inhibitors, such as novobiocin, coumermycin, and quinolones, which is consistent with the novel dual-arm U-shaped binding mode described above.…”

Synthesis, Crystal Studies and Pharmacological Role Prediction of 3-Iodo-2- Methyl-1 Phenyl Sulfonyl-1h Indole

“…Hence, the inhibitors of this enzyme may control the population of this mycobacterium. The crystal structure of Staphylococcus Gyrase in complex with novobiocin (PDB code: 4URO) was used in docking studies to describe the antibacterial role [13]. DNA gyrase of bacteria is an essential topoisomerase that supercoils DNA through a process of strand breakage/resealing and DNA wrapping [14].…”