Sarecycline inhibits protein translation inCutibacterium acnes70S ribosome using a two-site mechanism

Abstract

Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.

Scientific Rationale and Clinical Basis for Clindamycin Use in the Treatment of Dermatologic Disease

“…For instance, in E. coli , the 70S bacterial ribosome is composed of the 50S large subunit and the 30S small subunit; the aminoacyl-tRNA site (A-site), peptidyl-tRNA site (P-site), and tRNA exit site (E-site) in the 30S subunit allow for mRNA decoding, and in the 50S subunit, they form the peptidyl transferase center (PTC) and the exit tunnel. After peptide bond formation, deacylated tRNA leaves the ribosome through the E-site, while the peptide chain is extended in the nascent peptide exit tunnel (NPET) in the 50S subunit [ 23 , 24 ]. Generally, the PTC and NPET permit the binding of commonly used antibiotics in dermatology to the 50S subunit of bacterial ribosomes; structural discrepancies in these ribosomal sites lead to selective antibiotic binding affinities and differential effectiveness based on the bacterial species and target site(s) of antibiotics within the ribosome [ 3 , 23 , 25 ].…”

“…After peptide bond formation, deacylated tRNA leaves the ribosome through the E-site, while the peptide chain is extended in the nascent peptide exit tunnel (NPET) in the 50S subunit [ 23 , 24 ]. Generally, the PTC and NPET permit the binding of commonly used antibiotics in dermatology to the 50S subunit of bacterial ribosomes; structural discrepancies in these ribosomal sites lead to selective antibiotic binding affinities and differential effectiveness based on the bacterial species and target site(s) of antibiotics within the ribosome [ 3 , 23 , 25 ].…”

“…In the PTC, clindamycin interferes with the proper orientation of the A- and P-site tRNAs, thereby inhibiting peptide bond formation and also sterically blocking progression of the nascent peptide ( Figure 1 ) [ 26 ]. The macrolide class of antibiotics, whose binding site in the ribosome overlaps with that of clindamycin (lincosamide class), as well as for some tetracycline-class compounds ( Figure 1 ), bind in the beginning of the NPET of the 50S ribosomal subunit close to the PTC and share the same mechanism of protein synthesis inhibition, despite structural differences [ 23 , 25 , 27 ].…”

“…Nitrogen atoms are blue, and oxygen atoms are red in CLI and SAR. Superposition of models with Protein Data Bank (PDB) IDs 8CRX, 4V7V, and 7NSO was used to create this figure [ 23 , 25 , 44 ]. All figures in this review were created using PyMOL Version 2.0 [ 45 ].…”

“…All figures in this review were created using PyMOL Version 2.0 [ 45 ]. Abbreviations and labeling methods follow those presented in [ 23 ].…”