Riboswitches as Drug Targets for Antibiotics

Figures

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  Figure 1. Riboswitch-mediated gene regulation. Bacterial riboswitches regulate the expression of immediate downstream genes by modulating their conformation in response to a change in the concentration of their cognate ligands (L). (Strands involved in the formation of anti-antiterminator/anti-antisequester (cyan and magenta) and terminator/sequester (orange and yellow) are color-coded). In most cases, binding of ligand leads to transcriptional and/or translational termination of downstream gene expression (open reading frame (ORF), marked in yellow). These riboswitches are known as “OFF-switches” (a). In other cases, ligand binding leads to their expression of downstream genes and these riboswitches are called “ON-switches” (b). In the case of translation regulation, the RBS (green box) is either sequestered (a) or released (b) upon ligand binding. In the case of transcriptional regulation, the RNA polymerase is either stalled by a terminator (a) or moves past the antiterminator (b) upon ligand binding. RBS: ribosomal binding site.

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  Figure 2. TPP riboswitch ligands. (a) Chemical structures and binding affinities of ligands taken from various studies [32,45,52,53]. (b) The binding pocket of the TPP riboswitch in complex with TPP (Protein Databank (PDB) ID: 2GDI). The aminopyrimidine and pyrophosphate binding pockets are labelled. Water molecules are shown as red spheres, magnesium ions as green spheres, and hydrogen bonds as dotted lines. The negative charge on TPP is compensated by magnesium ions through direct and indirect hydrogen bonds with the surrounding residues. (c) Superposition of TPP riboswitch binding pocket in complex with different fragments (PDB ID: 4NYA (green), 4NYB (cyan), 4NYC (magenta), 4NYD (yellow), 4NYG (pink) and 2GDI (grey)). The conformational flexibility of G72 is visible.

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  Figure 3. FMN riboswitch ligands. (a) Chemical structures of the FMN riboswitch ligands together with KD or IC50 values taken from various studies [34,61,62,63,64]. (b) The binding pocket of the FMN riboswitch in complex with FMN (PDB ID: 3F2Q, left), riboflavin (PDB ID: 3F4G, middle) and roseoflavin (PDB ID: 3F4H, right). The polar contacts are shown as black dotted lines and the magnesium ion as a green sphere. (c) The binding poses of various ligands within the FMN riboswitch binding pocket—BRX1151 (PDB: 6DN1, pink), BRX1354 (PDB: 6DN2, blue), and BRX1555 (PDB: 6DN3, orange).

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  Figure 4. glmS riboswitch ligands. (a) Chemical structures and structure–activity relationships (SAR) of the GlcN6P derivatives. Positions where changes are well tolerated are marked in green, moderately tolerated in yellow and not tolerated in red. (b) Cartoon representation of ligand-dependent glmS ribozyme activity. The RBS is shown as a green bar and the ORF in yellow. Binding of ligand induces glmS riboswitch self-cleavage to produce an upstream fragment with a 2′,3′- cyclic phosphate end (2′,3′-cP) and a downstream fragment with a 5′-OH end, followed by degradation of the latter by a specific RNase. (c) Snapshot of the binding pocket of the glmS riboswitch in the apo form (PDB ID: 2GCS, left), in complex with glucose-6-phosphate (PDB ID: 2Z74, center), and GlcN6P (PDB ID: 2Z75, right). The nucleophile that ends up in the upstream fragment (2′-OH group of A(-1)) is highlighted with a blue circle and the leaving group (5′-phosphate group of G1) with a red circle.

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  Figure 5. Guanine riboswitch ligands. (a) The binding pocket of the guanine riboswitch in complex with guanine (PDB ID: 6UBU). The solvent accessible surface is shown in wheat colour, the ligand with green colour, polar contacts as black dotted lines and water molecules as red spheres. (b) Chemical structure of the guanine riboswitch ligands.