Insights Into Resistance Against Lincosamide Antibiotics

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Insights into Resistance against Lincosamide Antibiotics

Jesse A. Sundlov1 and Andrew M. Gulick1,* 1Department of Structural Biology, Hauptman-Woodward Medical Research Institute, State University of New York at Buffalo, Buffalo, NY, USA *Correspondence: [email protected] DOI 10.1016/j.str.2009.11.001

Bacteria utilize multiple strategies to circumvent antibiotics, producing broad speciﬁcity exporters or enzymes that catalyze the modiﬁcation of either antibiotics or their targets. A report in this issue of Structure provides the structural and catalytic mechanisms of LinB, an adenylyltransferase of E. faecium that confers resistance to the lincosamide antibiotic clindamycin.

The emergence of pathogenic bacteria maintain necessary interactions for the the exception of different ligands bound that are resistant to many commonly binding of drug to the target, yet prevent in the active site. In one model, using the used antibiotics has led to a renewed interactions with the modifying enzymes. methylene-bridged nonhydrolyzable ATP interest in understanding the biochemical In this issue of Structure, a report by Morar mimic, AMPCPP, two Mg2+ ions, and basis of antibiotic action and resistance. et al. (2009) takes us one step closer in this the cognate antibiotic clindamycin, the Historically, resistant strains have been regard with the lincosamide antibiotic clin- authors were able to trap LinB primed for identified very soon after the introduction damycin (Figure 1). adenylation of the antibiotic. The active of a novel compound into the clinical Clindamycin is a member of the linco- site of the second model includes pyro- setting. Resistance develops primarily samide family of antibiotics. Lincosa- phosphate, which adopts the same orien- from the ability of bacterial export proteins mides are classified with other macrolide tation as the b and g phosphates of ATP. to rid the cell of the antibiotic by modifica- and streptagramin (MLS) antibiotics, The structures show that LinB is tion of the target protein to reduce antibi- which all share a common binding site composed of two domains: an N-terminal otic activity, or by the production of on the 23S rRNA of the 50S subunit of six-strand b sheet surrounded by two specific enzymes that are responsible for the bacterial ribosome (Roberts, 2008). a helices, and a C-terminal a-helical the chemical inactivation of the antibiotic Resistance is often conferred by ribo- bundle. The helical domain of one proto- molecule (Fischbach and Walsh, 2009). somal methylation catalyzed by members mer rests in the groove between the two The facility of transferring resistance of the erythromycin ribosome methylase domains of the partner monomer, forming factors between organisms and species, (erm) enzymes. In modifying the ribosome a swapped dimer. Catalysis of clindamycin and the evolutionary pressure to do so, target, these enzymes confer resistance adenylation occurs in a cleft at the dimer has led to the current state, where multi- to chemically diverse drugs (Leclercq, interface. Clindamycin binds wholly to drug-resistant bacteria are posing serious 2002). Resistance to the lincosamides is one monomer, stacked between the clinical problems (Nordmann et al., 2007). also provided by chemical modification AMPCPP molecule and the N-terminal With a few notable exceptions, the of the drugs with either phosphate or b sheet. Alternatively, residues from both development of new antibiotics over the adenylate groups; resistance provided monomers contribute to AMPCPP binding. last few decades has focused primarily by these antibiotic-modifying enzymes is One Mg2+ ion is coordinated by the three on the chemical modifications of known thus limited to chemically similar com- phosphates of the nucleotide. Interest- antibiotic scaffolds (Fischbach and Walsh, pounds that are recognized by the ingly, a second Mg2+ ion is observed 2009). In this process, new compounds enzyme active site (Leclercq, 2002). bridging the a-phosphate and the nucleo- are identified from chemical libraries that Structures of clindamycin bound to the philic 30-hydroxyl of clindamycin. This are then screened for efficacy. A more ribosome are known (Schlunzen et al., second cation appears to orient the directed approach involves the rational 2001; Tu et al., 2005), providing an under- 30-hydroxyl for attack on the a-phosphate design of new compounds while simulta- standing of the functional groups on the and was not observed in the related struc- neously considering effectiveness and drug that is responsible for target binding ture of kanamycin nucleotidyl transferase resistance. This prospect of true struc- and the inhibition of ribosomal translation. (Pedersen et al., 1995). This homolog ture-guided antibiotic design, however, In this issue of Structure, Morar et al. contains conserved residues at the posi- relies on a clear understanding of struc- (2009) provide the structural and mecha- tions of the three ligands for the second tures of the antibiotic bound to both its nistic insights into the enzymatic modifi- Mg2+, raising the possibility that other target, as well as to the enzyme that cation of clindamycin. The authors pres- members of this family use two ions in the confers resistance by chemical modifica- ent two X-ray structures of LinB, the catalytic mechanism as well. tion or breakdown of the active drug. The lincosamide antibiotic adenylyltransfer- Structural and kinetic analyses point availability of these structures enables ase from Enterococcus faecium. The two to key residues responsible for substrate the design of improved compounds that models are structurally very similar with binding,specificity, and nucleotidyl transfer

Figure 1. Binding of Clindamycin to Its Target and Resistance Element Clindamycin, a lincosamide antibiotic, has now been structurally characterized bound to both the 24S rRNA of the ribosome (left), the therapeutic target, as well as to the LinB (right), the enzyme that catalyzes the inactivation of the antibiotic through an adenylyltransferase reaction. from ATP. Geometry and distance values are known to exist, the relationship maintain therapeutic activity and are less for these residues and the active site suggests that they evolved in response susceptible to enzymatic degradation. ligands, along with product inhibition to the small molecule antibiotics produced Hopefully, this study, and others like it, studies and solvent isotope effects, point by competing bacteria or even as a self- will result in new strategies to overcome to a direct in-line adenylation reaction. defense mechanism within the bacteria antibiotic resistance. These data are also consistent with prior that produce the antibiotics. Resistance enzymatic characterization of diverse in virulent strains results from the transfer REFERENCES members of this family (Gerratana et al., of these genes from environmental 2001; Magnet and Blanchard, 2005). bacteria to their pathogenic counterparts. Fischbach, M.A., and Walsh, C.T. (2009). Science 325, 1089–1093. The kinetic characterization, in addition Finally, the authors propose an inter- to structural comparisons using the esting analogy from the field of cancer Gerratana, B., Frey, P.A., and Cleland, W.W. (2001). Biochemistry 40, 2972–2977. distance alignment matrix method, allowed biology. Oncogenes are mutated or Morar et al. (2009) to classify LinB as a truncated eukaryotic genes, often incor- Leclercq, R. (2002). Clin. Infect. Dis. 34, 482–492. member of the nucleotidyl transferase porated into cancer-causing viruses, that Magnet, S., and Blanchard, J.S. (2005). Chem. superfamily, joining aminoglycoside nucle- have the capability of transforming a Rev. 105, 477–498. otidyl transferases and nucleotide poly- normal cell into a cancerous one. The Morar, M., Bhullar, K., Hughes, D.W., Junop, M., merases. This classification further sup- wild-type genes from which these onco- and Wright, G.D. (2009). Structure 17, this issue, ports the proposed LinB mechanism, as genes evolved are termed proto-onco- 1649–1659. several crystal structures of these related genes. Adopting this nomenclature, Nordmann, P., Naas, T., Fortineau, N., and Poirel, enzymes with characterized mechanisms Morar et al. (2009) term the normal bacte- L. (2007). Curr. Opin. Microbiol. 10, 436–440. have been solved with trapped active site rial precursors of antibiotic resistance Pedersen, L.C., Benning, M.M., and Holden, H.M. intermediates bound to conserved resi- genes as proto-resistance elements. This (1995). Biochemistry 34, 13305–13311. dues (Pedersen et al., 1995). is an intriguing classification that may Roberts, M.C. (2008). FEMS Microbiol. Lett. 282, The structural and mechanistic data lead to new ways of thinking about the 147–159. presented by the authors solidify the enzymatic strategies that confer resis- Schlunzen, F., Zarivach, R., Harms, J., Bashan, A., evolutionary relationship between antibi- tance. A more complete understanding Tocilj, A., Albrecht, R., Yonath, A., and Franceschi, otic nucleotidyl transferases and the of the evolution of enzymes that confer F. (2001). Nature 413, 814–821. nucleotide polymerases found throughout antibiotic resistance may also contribute Tu, D., Blaha, G., Moore, P.B., and Steitz, T.A. all forms of life. As only a few of the former to the design of novel compounds that (2005). Cell 121, 257–270.