Unrealized targets in the discovery of antibiotics for Gram-negative … – Nature.com

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Butler, M. S. et al. Analysis of the clinical pipeline of treatments for drug-resistant bacterial infections: despite progress, more action is needed. Antimicrob. Agents Chemother. 66, e0199121 (2022).

Article PubMed Google Scholar

Martnez-Garca, L., Gonzlez-Alba, J. M., Baquero, F., Cantn, R. & Galn, J. C. Ceftazidime is the key diversification and selection driver of VIM-type carbapenemases. mBio 9, e02109e02117 (2018).

Article PubMed PubMed Central Google Scholar

Baquero, F. et al. Allogenous selection of mutational collateral resistance: old drugs select for new resistance within antibiotic families. Front. Microbiol. 12, 757833 (2021).

Article PubMed PubMed Central Google Scholar

Rajer, F., Allander, L., Karlsson, P. A. & Sandegren, L. Evolutionary trajectories toward high-level -lactam/-lactamase inhibitor resistance in the presence of multiple -lactamases. Antimicrob. Agents Chemother. 66, e0029022 (2022).

Article PubMed Google Scholar

Poirel, L., Sadek, M., Kusaksizoglu, A. & Nordmann, P. Co-resistance to ceftazidimeavibactam and cefiderocol in clinical isolates producing KPC variants. Eur. J. Clin. Microbiol. Infect. Dis. 41, 677680 (2022).

Article CAS PubMed Google Scholar

Silver, L. L. Challenges of antibacterial discovery. Clin. Microbiol. Rev. 24, 71109 (2011).

Article CAS PubMed PubMed Central Google Scholar

Baker, S. J., Payne, D. J., Rappuoli, R. & De Gregorio, E. Technologies to address antimicrobial resistance. Proc. Natl Acad. Sci. USA 115, 1288712895 (2018).

Article CAS PubMed PubMed Central Google Scholar

Payne, D. J., Gwynn, M. N., Holmes, D. J. & Pompliano, D. L. Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat. Rev. Drug Discov. 6, 2940 (2007).

Article CAS PubMed Google Scholar

Tommasi, R., Brown, D. G., Walkup, G. K., Manchester, J. I. & Miller, A. A. ESKAPEing the labyrinth of antibacterial discovery. Nat. Rev. Drug Discov. 14, 529542 (2015).

Article CAS PubMed Google Scholar

Brotz-Oesterhelt, H. & Sass, P. Postgenomic strategies in antibacterial drug discovery. Future Microbiol. 5, 15531579 (2010).

Article PubMed Google Scholar

Lewis, K. Platforms for antibiotic discovery. Nat. Rev. Drug Discov. 12, 371387 (2013).

Article CAS PubMed Google Scholar

Muoz, K. A. & Hergenrother, P. J. Facilitating compound entry as a means to discover antibiotics for Gram-negative bacteria. Acc. Chem. Res. 54, 13221333 (2021).

Article PubMed PubMed Central Google Scholar

Zhao, S. et al. Defining new chemical space for drug penetration into Gram-negative bacteria. Nat. Chem. Biol. 16, 12931302 (2020).

Article CAS PubMed PubMed Central Google Scholar

Sadybekov, A. V. & Katritch, V. Computational approaches streamlining drug discovery. Nature 616, 673685 (2023).

Article CAS PubMed Google Scholar

Lluka, T. & Stokes, J. M. Antibiotic discovery in the artificial intelligence era. Ann. NY Acad. Sci. 1519, 7493 (2023).

Article CAS PubMed Google Scholar

Lyu, J. et al. Ultra-large library docking for discovering new chemotypes. Nature 566, 224229 (2019).

Article CAS PubMed PubMed Central Google Scholar

Mobegi, F. M. et al. From microbial gene essentiality to novel antimicrobial drug targets. BMC Genomics 15, 958 (2014).

Article PubMed PubMed Central Google Scholar

Agarwal, P. & Searls, D. B. Can literature analysis identify innovation drivers in drug discovery? Nat. Rev. Drug Discov. 8, 865 (2009).

Article CAS PubMed PubMed Central Google Scholar

Lange, R. P., Locher, H. H., Wyss, P. C. & Then, R. L. The targets of currently used antibacterial agents: lessons for drug discovery. Curr. Pharm. Des. 13, 31403154 (2007).

Article CAS PubMed Google Scholar

Theuretzbacher, U. & Piddock, L. J. V. Non-traditional antibacterial therapeutic options and challenges. Cell Host Microbe 26, 6172 (2019).

Article CAS PubMed Google Scholar

Frearson, J. A., Wyatt, P. G., Gilbert, I. H. & Fairlamb, A. H. Target assessment for antiparasitic drug discovery. Trends Parasitol. 23, 589595 (2007).

Article CAS PubMed PubMed Central Google Scholar

Streker, K. et al. In vitro and in vivo validation of ligA and tarI as essential targets in Staphylococcus aureus. Antimicrob. Agents Chemother. 52, 44704474 (2008).

Article CAS PubMed PubMed Central Google Scholar

Rancati, G., Moffat, J., Typas, A. & Pavelka, N. Emerging and evolving concepts in gene essentiality. Nat. Rev. Genet. 19, 3449 (2018).

Article CAS PubMed Google Scholar

Bosch-Guiteras, N. & van Leeuwen, J. Exploring conditional gene essentiality through systems genetics approaches in yeast. Curr. Opin. Genet. Dev. 76, 101963 (2022).

Article CAS PubMed Google Scholar

Zhang, Z. & Ren, Q. Why are essential genes essential? the essentiality of Saccharomyces genes. Microb. Cell 2, 280287 (2015).

Article CAS PubMed PubMed Central Google Scholar

Chessher, A. Evaluating the suitability of essential genes as targets for antibiotic screening assays using proteomics. Protein Cell 3, 57 (2012).

Article PubMed PubMed Central Google Scholar

Editorial. Putting gene essentiality into context. Nat. Rev. Genet. 19, 1 (2017).

Google Scholar

Chaudhary, A. S., Chen, W., Jin, J., Tai, P. C. & Wang, B. SecA: a potential antimicrobial target. Future Med. Chem. 7, 9891007 (2015).

Article CAS PubMed Google Scholar

Emmerich, C. H. et al. Improving target assessment in biomedical research: the GOT-IT recommendations. Nat. Rev. Drug Discov. 20, 6481 (2021).

Article CAS PubMed Google Scholar

Murima, P., McKinney, J. D. & Pethe, K. Targeting bacterial central metabolism for drug development. Chem. Biol. 21, 14231432 (2014).

Article CAS PubMed Google Scholar

Hedstrom, L. The bare essentials of antibiotic target validation. ACS Infect. Dis. 3, 24 (2017).

Article CAS PubMed Google Scholar

Hogan, A. M. & Cardona, S. T. Gradients in gene essentiality reshape antibacterial research. FEMS Microbiol. Rev. 46, fuac005 (2022).

Article PubMed PubMed Central Google Scholar

Bergmiller, T., Ackermann, M. & Silander, O. K. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genet. 8, e1002803 (2012).

Article CAS PubMed PubMed Central Google Scholar

Dunman, P. M. & Tomaras, A. P. Translational deficiencies in antibacterial discovery and new screening paradigms. Curr. Opin. Microbiol. 27, 108113 (2015).

Article CAS PubMed PubMed Central Google Scholar

Rosconi, F. et al. A bacterial pan-genome makes gene essentiality strain-dependent and evolvable. Nat. Microbiol. 7, 15801592 (2022).

Article CAS PubMed PubMed Central Google Scholar

Kaur, H., Kalia, M. & Taneja, N. Identification of novel non-homologous drug targets against Acinetobacter baumannii using subtractive genomics and comparative metabolic pathway analysis. Microb. Pathog. 152, 104608 (2021).

Article CAS PubMed Google Scholar

Uddin, R., Masood, F., Azam, S. S. & Wadood, A. Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis. Microb. Pathog. 128, 2835 (2019).

Article CAS PubMed Google Scholar

Ramos, P. I. P. et al. An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets. Sci. Rep. 8, 10755 (2018).

Article PubMed PubMed Central Google Scholar

Rafiq, H. et al. A computational subtractive genome analysis for the characterization of novel drug targets in Klebsiella pneumoniae strain PittNDM01. Microb. Pathog. 146, 104245 (2020).

Article CAS PubMed Google Scholar

Uddin, R. & Jamil, F. Prioritization of potential drug targets against P. aeruginosa by core proteomic analysis using computational subtractive genomics and proteinprotein interaction network. Comput. Biol. Chem. 74, 115122 (2018).

Article CAS PubMed Google Scholar

Nazarshodeh, E., Marashi, S. A. & Gharaghani, S. Structural systems pharmacology: a framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria. PLoS ONE 16, e0261267 (2021).

Article CAS PubMed PubMed Central Google Scholar

Bakheet, T. M. & Doig, A. J. Properties and identification of antibiotic drug targets. BMC Bioinformatics 11, 195 (2010).

Article PubMed PubMed Central Google Scholar

Bosch, B. et al. Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell 184, 45794592.e24 (2021).

Article CAS PubMed PubMed Central Google Scholar

Hawkins, J. S. et al. Mismatch-CRISPRi reveals the co-varying expressionfitness relationships of essential genes in Escherichia coli and Bacillus subtilis. Cell Syst. 11, 523535.e9 (2020).

Article CAS PubMed PubMed Central Google Scholar

Luo, H., Gao, F. & Lin, Y. Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes. Sci. Rep. 5, 13210 (2015).

Article CAS PubMed PubMed Central Google Scholar

Arun, P. V. P. S. et al. Identification and functional analysis of essential, conserved, housekeeping and duplicated genes. FEBS Lett. 590, 14281437 (2016).

Article CAS PubMed Google Scholar

Du, W. et al. Two active forms of UDP-N-acetylglucosamine enolpyruvyl transferase in Gram-positive bacteria. J. Bacteriol. 182, 41464152 (2000).

Article CAS PubMed PubMed Central Google Scholar

Naz, S., Ngo, T., Farooq, U. & Abagyan, R. Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens. PeerJ 5, e3765e3765 (2017).

Article PubMed PubMed Central Google Scholar

Klahn, P. & Bronstrup, M. New structural templates for clinically validated and novel targets in antimicrobial drug research and development. Curr. Top. Microbiol. Immunol. 398, 365417 (2016).

CAS PubMed Google Scholar

Miranda, R. R., Parthasarathy, A. & Hudson, A. O. Exploration of chemical biology approaches to facilitate the discovery and development of novel antibiotics. Front. Trop. Dis. 3, 845469 (2022).

Article Google Scholar

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