the linker tethered by each compound. MD simulations confirmed that both compounds bind through one of their edges to the catalytic crevice. Compound 5 was additionally hydrogen bonded through its second CAM moiety to the 2OH- group of C2610, a fact compelling the p-nitrophenyl ring of this edge to bend and insert a hydrophobic crevice, formed by nucleosides A2058 and A2059 at the entrance to the exit tunnel. Noteworthy, nucleoside C2610 has been considered as a part of a signal relay pathway linking the exit tunnel sensors to the PTase active site. In contrast, compound 4 was revealed to bind C2611. Nevertheless, this interaction is not stable enough, nor it orientated the edge of compound 4 towards the A2058-A2059 crevice. Due to technical limitations, certain interactions detected by MD simulations purchase GLYX-13 cannot be revealed by footprinting analysis; C2610 does not react with dimethyl sulfate, while C2611 is based paired with G2057. Binding models for the remaining CAM dimers, as generated by MD simulations, are presented in S3 Fig. To experimentally demonstrate that compounds 4 and 5 are capable of binding nucleosides C2611 and C2610, respectively, a crosslinking approach was applied. Specifically, a mixture of E. coli ribosomes together with either 4 or 5, each added to the incubation mixture at concentration equal to 10Ki, were irradiated for 30 min with 365 nm light. Following purification, the irradiation products were analyzed by primer extension. As shown in Fig 5, footprints of R I complex having bound compound 5 mapped to nucleoside C2610, and less to nucleosides A2058 and A2059. Footprinting analysis of the whole irradiated mixture, before purification, indicated that compound 5 was firmly attached to the catalytic PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19757813 crevice of PTase, but did not form crosslinks with this region. In contrast, compound 4 8 / 22 Development of Chloramphenicol Homodimers Fig 4. Binding positions of compounds 4 and 5 on the E. coli ribosome, as detected PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19754877 by Molecular Dynamics simulations. Compounds 4 and 5 have been docked into the 50S ribosomal subunit, by positioning one of their CAM moieties within the CAM crystallographic pocket. Binding position of compound 5; hydrogen bonding with residues of the catalytic center is shown by black dots. Other residues of 23S rRNA placed adjacently to the binding pocket of 5 are ignored for clarity. Binding position of compound 4. doi:10.1371/journal.pone.0134526.g004 crosslinked to C2611, without raising any modification signal in the A2058-A2059 region. It should be mentioned that the concentrations used for compounds 4 and 5 in this series of experiments were much lower than those of CAM utilized previously by Long & Porse. The most plausible explanation for this enhanced affinity is that binding of a dimer to the primary high-affinity site facilitates targeting of a cryptic, low-affinity site via the second edge of the homodimer. Such a site cannot be easily detected by kinetic analysis of CAM binding to the ribosome, due to its high Ki value , and it is the first time that such a position is revealed by using the drug at micromolar concentrations. Antibacterial activity of the CAM dimers and correlation with inhibitory activity on the puromycin reaction The antimicrobial potency of the synthesized CAM dimers was tested against a panel of Gramnegative and Gram-positive bacteria. Two laboratory strains of E. coli possessing the A2058G or A2503C mutations in 23S rRNA, the RosettapLysS E. coli strain expressing the

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