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Article

In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli

1
Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK 2000 Frederiksberg, Denmark
2
Naicons Srl, 20139 Milan, Italy
*
Authors to whom correspondence should be addressed.
Academic Editor: Dorothea K. Thompson
Received: 29 March 2021 / Revised: 8 May 2021 / Accepted: 21 May 2021 / Published: 25 May 2021
(This article belongs to the Special Issue Bacterial Stress Responses and Antibiotic Resistance Phenotypes)
Novel antimicrobials interfering with pathogen-specific targets can minimize the risk of perturbations of the gut microbiota (dysbiosis) during therapy. We employed an in silico approach to identify essential proteins in Escherichia coli that are either absent or have low sequence identity in seven beneficial taxa of the gut microbiota: Faecalibacterium, Prevotella, RuminococcusBacteroides, Lactobacillus, Lachnospiraceae and Bifidobacterium. We identified 36 essential proteins that are present in hyper-virulent E. coli ST131 and have low similarity (bitscore < 50 or identity < 30% and alignment length < 25%) to proteins in mammalian hosts and beneficial taxa. Of these, 35 are also present in Klebsiella pneumoniae. None of the proteins are targets of clinically used antibiotics, and 3D structure is available for 23 of them. Four proteins (LptD, LptE, LolB and BamD) are easily accessible as drug targets due to their location in the outer membrane, especially LptD, which contains extracellular domains. Our results indicate that it may be possible to selectively interfere with essential biological processes in Enterobacteriaceae that are absent or mediated by unrelated proteins in beneficial taxa residing in the gut. The identified targets can be used to discover antimicrobial drugs effective against these opportunistic pathogens with a decreased risk of causing dysbiosis. View Full-Text
Keywords: antimicrobial targets; Escherichia coli; in silico; microbiota antimicrobial targets; Escherichia coli; in silico; microbiota
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MDPI and ACS Style

Svanberg Frisinger, F.; Jana, B.; Donadio, S.; Guardabassi, L. In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli. Antibiotics 2021, 10, 632. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics10060632

AMA Style

Svanberg Frisinger F, Jana B, Donadio S, Guardabassi L. In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli. Antibiotics. 2021; 10(6):632. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics10060632

Chicago/Turabian Style

Svanberg Frisinger, Frida, Bimal Jana, Stefano Donadio, and Luca Guardabassi. 2021. "In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli" Antibiotics 10, no. 6: 632. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics10060632

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