An Optimized Workflow for the Discovery of New Antimicrobial Compounds Targeting Bacterial RNA Polymerase Complex Formation
Abstract
:1. Introduction
2. Results and Discussion
2.1. Drug-Discovery Workflow
- (i)
- (ii)
- The ICBMS-Lyon 1 University in-house library, containing 3120 original synthetic and natural compounds, selected for their scaffold diversity and physicochemical properties.
- (iii)
- The PKRC library, containing 1200 synthetic and natural compounds, focused on protein kinase inhibitors [29].
2.1.1. yBRET Screening
2.1.2. In Vitro Competitive ELISA Assay
2.1.3. Bacterial Growth Inhibition Assay
2.2. Hit Characterization
2.2.1. Antimicrobial Activity
2.2.2. RNA Polymerase Inhibitory Activity
2.2.3. β’ CH Region–σ70 PPI Inhibition Characterization
2.3. Similarity with Indolyl-Urea Inhibitors and Pharmacophore Model Matching
3. Conclusions
4. Materials and Methods
4.1. Chemicals
4.2. yBRET Assay
4.3. Competitive ELISA Assay
4.4. Antibacterial Activity Assays
4.5. In Vitro Transcription Assay
4.6. Alignment of New Compounds on Indolyl-Urea 4
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References and Notes
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Library | Compound | Growth Inhibition at 100 μM (8 h) | MIC (μM) | Binding Inhibition | |||
---|---|---|---|---|---|---|---|
B. subtilis | E. colib | S. cerevisiae | B. subtilis | E. colib | IC50 μM ± SD | ||
Reference | 4 a | 73% | 91% | 0% | 50 | 25 | 8.09 ± 1.1 c |
ReCC | 5 | 19% | 92% | 1% | >100 | 1.56 | 15.11 ± 1.96 |
7 | 13% | 66% | 7% | >100 | 0.78 | 8.56 ± 1.82 | |
ICBMS | 9 | 24% | 24% | 0% | >100 | >100 | 13.93 ± 1.86 |
13 | 40% | 29% | 0% | 50 | 50 | 16.35 ± 1.8 | |
PKRC | 19 | 37% | 0% | 0% | 100 | >100 | 40 ± 4.2 |
20 | 15% | 30% | 0% | 100 | 12.5 | 80 ± 6.56 |
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Caputo, A.; Sartini, S.; Levati, E.; Minato, I.; Elisi, G.M.; Di Stasi, A.; Guillou, C.; Goekjian, P.G.; Garcia, P.; Gueyrard, D.; et al. An Optimized Workflow for the Discovery of New Antimicrobial Compounds Targeting Bacterial RNA Polymerase Complex Formation. Antibiotics 2022, 11, 1449. https://doi.org/10.3390/antibiotics11101449
Caputo A, Sartini S, Levati E, Minato I, Elisi GM, Di Stasi A, Guillou C, Goekjian PG, Garcia P, Gueyrard D, et al. An Optimized Workflow for the Discovery of New Antimicrobial Compounds Targeting Bacterial RNA Polymerase Complex Formation. Antibiotics. 2022; 11(10):1449. https://doi.org/10.3390/antibiotics11101449
Chicago/Turabian StyleCaputo, Alessia, Sara Sartini, Elisabetta Levati, Ilaria Minato, Gian Marco Elisi, Adriana Di Stasi, Catherine Guillou, Peter G. Goekjian, Pierre Garcia, David Gueyrard, and et al. 2022. "An Optimized Workflow for the Discovery of New Antimicrobial Compounds Targeting Bacterial RNA Polymerase Complex Formation" Antibiotics 11, no. 10: 1449. https://doi.org/10.3390/antibiotics11101449