Blast from the Past: Reassessing Forgotten Translation Inhibitors, Antibiotic Selectivity, and Resistance Mechanisms to Aid Drug Development  Stefan Arenz, Daniel N. Wilson  Molecular Cell  Volume 61, Issue 1, Pages 3-14 (January 2016) DOI: 10.1016/j.molcel.2015.10.019 Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 1 Overview of Antibiotic Binding Sites on the Ribosome (A–C) Binding sites of dityromycin (PDB: 4NVU), paromomycin (PDB: 3UZ3), THB (PDB: 3UXT), viomycin (PDB: 3KNH), neomycin (PDB: 2QAL), NEG (PDB: 4RBH), TET (PDB: 4G5K), tigecycline (PDB: 4G5T), amicoumacin (PDB: 4RB5), EDE (PDB: 1I95), KSG (PDB: 1VS5), pactamycin (PDB: 4RBB), emetine (PDB: 3J7A), Onc112 (PDB: 4ZER), quinupristin (PDB: 4PEB), erythromycin (PDB: 3OFR), tiamulin (PDB: 3G4S), clindamycin (PDB: 3OFZ), linezolid (PDB: 3DLL), A201A (PDB: 4Z3S), hygromycin A (PDB: 4Z3R), blasticidin S (PDB: 4L6J), and bactobolin A (PDB: 4WWE) (A) on the small subunit, (B) on the large subunit, and (C) with respect to positions of mRNA and A-, P-, and E-site tRNAs (PDB: 4RB5). Molecular Cell 2016 61, 3-14DOI: (10.1016/j.molcel.2015.10.019) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 2 Chemical Structures of Selected Antibiotics (A) THB (with tetracyclic and phenyl moieties highlighted), (B) NEG, (C) dityromycin, (D) AMI (with isocoumarin and tail moieties highlighted), (E) hygromycin A (with aminocyclitol and methyl group highlighted), (F) A201A (with methyl group and D-rhamnose moiety highlighted), (G) bactobolin A (with C6-polyketide and chlorinated hydroxyl-valine residue highlighted), and (H) emetine. Molecular Cell 2016 61, 3-14DOI: (10.1016/j.molcel.2015.10.019) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 3 Antibiotics Targeting the Small Ribosomal Subunit (A–H) Overviews ([A], [C], [E], and [G]) with 30S (yellow), 50S (gray), A-tRNA (orange), P-tRNA (green) and E-tRNA (pink) and enlargements ([B], [D], [F], and [H]) of the binding sites of ([A] and [B]) THB (purple) (PDB: 3UXT), ([C] and [D]) NEG (yellow) (PDB: 4RBH), ([E] and [F]) dityromycin ([DIT], pink) (PDB: 4NVU), and ([G] and [H]) AMI (red) (PDB: 4RB5). Molecular Cell 2016 61, 3-14DOI: (10.1016/j.molcel.2015.10.019) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 4 Antibiotics Targeting the Large Ribosomal Subunit (A–H) Overviews ([A], [C], [E], and [G]) with 30S (yellow), 50S (gray), A-tRNA (orange), P-tRNA (green), and E-tRNA (pink) and enlargements ([B], [D], [F], and [H]) of the binding sites of ([A] and [B]) hygromycin A ([HygA], blue) (PDB: 4Z3R), ([C] and [D]) A201A (yellow) (PDB: 4Z3S), and ([G] and [H]) onc112 (red) (PDB: 4ZER). Molecular Cell 2016 61, 3-14DOI: (10.1016/j.molcel.2015.10.019) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 5 Specificity and Toxicity of Antibiotics (A) Relative position of neomycin ([NEO], brown) to the bacterial A1408 (yellow, PDB: 2QAL) and the eukaryotic equivalent G1645 (purple, PDB: 4UG0). (B and C) Relative position of paromomycin ([PAR], green) to bacterial nucleotides C1409 and G1491 (yellow, PDB: 3UZ3) and corresponding nucleotides of the human mitochondrial (blue, PDB: 3J9M), human cytosolic (brown, PDB: 4UG0), and (C) yeast cytosolic (purple, PDB: 4ULE) ribosomes. (D) Geneticin (GEN, pink) bound to h44 of the 18S rRNA in yeast 80S ribosome (PDB: 4UKZ). (E and F) Position of 23S rRNA nucleotide U2504 in archaeal (Gürel et al., 2009) and eukaryotic ribosomes (blue) compared with its position in bacterial ribosomes (gray), with superimposed positions of (E) anisomycin (red, ANI, PDB: 4UK0) and (F) chloramphenicol (CAM, blue, PDB: 3OFC). (G and H) Conformation of the erythromycin binding site in (G) yeast mitochondrial (PDB: 3J6B), (H) bacterial (PDB: 3OFC), human cytosolic (PDB: 4UG0), yeast cytosolic (PDB: 4ULE), and human mitochondrial (PDB: 3J9M) ribosomes, relative to erythromycin ([ERY], blue, PDB: 3OFR), A-tRNA (orange), and P-tRNA (green). Molecular Cell 2016 61, 3-14DOI: (10.1016/j.molcel.2015.10.019) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 6 Ribosome-Targeting Antibiotic Resistance Mechanisms (A) Crystal structure of the aminoglycoside resistance rRNA methyltransferase NpmA (green) with SAM cofactor (orange) bound to h44 (yellow) of the 16S rRNA with flipped-out nucleotide A1408 (PDB: 4OX9). Conformation of base-paired A1408 in h44 is shown in gray for reference (PDB: 1J5E). (B) Superposition of ERY (blue, PDB: 3OFR) with ErmCL-dimethylated (green) A2058. (C) Comparison of the conformations of nascent chain and 23S rRNA nucleotide U2585 in the pre-attack (light gray, PDB: 1VQN) and the ErmCL-stalled (dark gray, PDB: 3J7Z) state of the ribosome, relative to ERY (blue, PDB: 3OFR), A-tRNA (orange), and P-tRNA (green). (D and E) HygA (yellow, PDB: 4Z3R) binding site with modeled (D) Cfr-mediated C8 methylation of 23S rRNA nucleotide A2503 and (E) Hyg21-mediated phosphorylation of HygA. (F) Cryo-EM structure of TetM-bound (green) ribosomes (PDB: 3J9Y) with superimposed position of TET (orange, PDB: 4G5K) stacked upon C1054 in h34 of 16S rRNA (gray). Molecular Cell 2016 61, 3-14DOI: (10.1016/j.molcel.2015.10.019) Copyright © 2016 Elsevier Inc. Terms and Conditions