Identification of inhibitors of bacterial RNA polymerase

Yang, Xiao; Ma, Cong; Lewis, Peter J.

doi:10.1016/j.ymeth.2015.05.005

Cited by 20 publications

(19 citation statements)

References 26 publications

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“…An enzyme-linked immunosorbent assay-based inhibitory assay was performed to assess the in vitro inhibition of NusB−NusE heterodimer formation by MC4. 24 Purified NusB was used to coat the 96-well plate, and GST-tagged NusE was used as the probe. MC4 showed positive inhibition of the NusB−NusE interaction with an IC 50 of ∼34.7 ± 0.13 μM.…”

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confidence: 99%

First-In-Class Inhibitor of Ribosomal RNA Synthesis with Antimicrobial Activity against Staphylococcus aureus

et al. 2017

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We report the discovery of the first bacterial ribosomal RNA (rRNA) synthesis inhibitor that has specific antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA). A pharmacophore model was constructed on the basis of the protein-protein interaction between essential bacterial rRNA transcription factors NusB and NusE and employed for an in silico screen to identify potential leads. One compound, (E)-2-{[(3-ethynylphenyl)imino]methyl}-4-nitrophenol (MC4), demonstrated antimicrobial activity against a panel of S. aureus strains, including MRSA, without significant toxicity to mammalian cells. MC4 resulted in a decrease in the rRNA level in bacteria, and the target specificity of MC4 was confirmed at the molecular level. Results obtained from this work validated the bacterial rRNA transcription machinery as a novel antimicrobial target. This approach may be extended to other factors in rRNA transcription, and MC4 could be applied as a chemical probe to dissect the relationship among MRSA infection, MRSA growth rate, and rRNA synthesis, in addition to its therapeutic potential.

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confidence: 99%

First-In-Class Inhibitor of Ribosomal RNA Synthesis with Antimicrobial Activity against Staphylococcus aureus

et al. 2017

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“…Previous studies were aimed at identifying novel antibiotics by targeting the transcriptional machinery of bacteria ( 91 , 92 ). This can include targeting riboswitches ( 66 , 82–84 , 93 ), transcription factors ( 94 , 95 ) or the RNA polymerase itself ( 96 , 97 ). Rifampicin inhibits the bacterial RNAP ( 98 ) by blocking elongation ( 99 ) and is the leading drug to treat mycobacterial infections such as tuberculosis ( 100 ).…”

Section: Resultsmentioning

confidence: 99%

SPRINT: a Cas13a-based platform for detection of small molecules

Iwasaki

Batey

2020

Nucleic Acids Research

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Recent efforts in biological engineering have made detection of nucleic acids in samples more rapid, inexpensive and sensitive using CRISPR-based approaches. We expand one of these Cas13a-based methods to detect small molecules in a one-batch assay. Using SHERLOCK-based profiling of in vitrotranscription (SPRINT), in vitro transcribed RNA sequence-specifically triggers the RNase activity of Cas13a. This event activates its non-specific RNase activity, which enables cleavage of an RNA oligonucleotide labeled with a quencher/fluorophore pair and thereby de-quenches the fluorophore. This fluorogenic output can be measured to assess transcriptional output. The use of riboswitches or proteins to regulate transcription via specific effector molecules is leveraged as a coupled assay that transforms effector concentration into fluorescence intensity. In this way, we quantified eight different compounds, including cofactors, nucleotides, metabolites of amino acids, tetracycline and monatomic ions in samples. In this manner, hundreds of reactions can be easily quantified in a few hours. This increased throughput also enables detailed characterization of transcriptional regulators, synthetic compounds that inhibit transcription, or other coupled enzymatic reactions. These SPRINT reactions are easily adaptable to portable formats and could therefore be used for the detection of analytes in the field or at point-of-care situations.

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“…Transcription is synthesis of RNA from its template DNA strand, which is then translated by the ribosome into proteins (mRNA) or complexes with ribosomal proteins to construct the 70S ribosome (rRNA). This process is highly regulated by transcription factors that modulate the synthesis of RNA by controlling initiation of RNA synthesis, pausing RNAP, terminating transcription, reducing pausing of RNAP, rescuing DNA errors, and recruiting DNA repair enzymes …”

Section: Protein‐protein Interactions As Antibacterial Targetsmentioning

confidence: 99%

Protein‐protein interactions as antibiotic targets: A medicinal chemistry perspective

Cossar

Lewis

McCluskey

2018

Medicinal Research Reviews

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There are 27 small molecule protein-protein interaction (PPI) modulators in Phase I, II, and III clinical trials targeting cancer, viruses, autoimmune disorders, and as immune suppression agents. Targeting PPIs as an antibiotic drug discovery strategy remains in relative infancy by comparison. However, a number of molecules are in development which target PPI within the replisome, divisome, transcriptome, and translatome are showing significant promise at the medicinal chemistry stage of drug development. Hence, the success of future PPI agents as antibiotics will build upon the techniques and design strategies of these molecules.

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Identification of inhibitors of bacterial RNA polymerase

Cited by 20 publications

References 26 publications

First-In-Class Inhibitor of Ribosomal RNA Synthesis with Antimicrobial Activity against Staphylococcus aureus

First-In-Class Inhibitor of Ribosomal RNA Synthesis with Antimicrobial Activity against Staphylococcus aureus

SPRINT: a Cas13a-based platform for detection of small molecules

Protein‐protein interactions as antibiotic targets: A medicinal chemistry perspective

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