Structural conservation of antibiotic interaction with ribosomes

Abstract

The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic–ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA–ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.

Characterization of Dichloroisoeverninic Acid Biosynthesis and Chemoenzymatic Synthesis of New Orthosomycins

“…Specific details of the orthosomycins’ interactions with the ribosome were fully described in crystallography and cryo-EM imaging. − , A comprehensive view of the orthosomycin binding site on the 50S ribosomal subunit reveal it to be unique from all other ribosomal-targeting natural products . The orthosomycins bind in an extended conformation in the minor grooves of helices 89 and 91 formed by 23S rRNA.…”

“…The A 1 -ring DCIE is conserved among all class I orthosomycins and has been speculated to play a key role in the distinct mechanism of action of everninomicin by forming multiple putative interactions within the pocket formed by ribosomal proteins uL16 and CTC in the 50S subunit . These interactions include potential hydrophobic, ionic, and dipolar interactions, which vary between everninomicin and avilamycin type orthosomycins (Figure C,D). − We seek to revitalize the everninomicins as clinical candidates by interrogating these interactions and developing analogs with improved properties. While a total synthesis of Evn A (Ziracin) has been completed, its application to access analogs is challenging as the synthesis consists of over 130 steps. − It was demonstrated that the formation of suspended aggregates in formulations of Evn A correlated to adverse reactions, and we hypothesize that the amphipathic nature of Evn A, characterized by alternating hydrophobic and hydrophilic functionality, is a driver of aggregation .…”

An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance

“…There are three x-ray crystal structures and one cryo–electron microscopy (cryo-EM) structure of clindamycin bound to ribosomes of the diverse bacterial species Deinococcus radiodurans ( 6 ) and Escherichia coli ( 22 , 23 ), as well as the archaeon Haloarcula marismortui ( 24 ), the latter bearing a G2099A (equivalent to A2058 in E. coli ) mutation that permits lincosamide binding. In addition, there are two x-ray crystal structures of IBX bound to wild-type (WT) and Erm-methylated ribosomes of Thermus thermophilus ( 19 ).…”

Oxydifficidin, a potentNeisseria gonorrhoeaeantibiotic due to DedA assisted uptake and ribosomal protein RplL sensitivity

“…(30,31) Antibiotics that bind away from these two hot spots also showed no cross resistance. (30)(31)(32) The activity of avilamycin, which binds in a unique site in the 50S subunit at the entrance to the A-site tRNA accommodating corridor was also not affected by the L7/L12 R76C mutation. (33) In the case of thiostrepton A (34), which targets the L11 protein GTPaseassociated center and is part of the only class of antibiotics known to bind the ribosome in the vicinity of L10/L7 stalk, we also observed no change in MIC for N. gonorrhoeae with the L7/L12 R76C mutation.…”