In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in <i>Escherichia coli</i>

• Main Authors: Frida Svanberg Frisinger (Author), Bimal Jana (Author), Stefano Donadio (Author), Luca Guardabassi (Author)
• Format: Book
• Published: MDPI AG, 2021-05-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.

Summary

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 <i>Escherichia coli</i> that are either absent or have low sequence identity in seven beneficial taxa of the gut microbiota: <i>Faecalibacterium</i>, <i>Prevotella</i>, <i>Ruminococcus</i>, <i>Bacteroides</i>, <i>Lactobacillus</i>, <i>Lachnospiraceae</i> and <i>Bifidobacterium</i>. We identified 36 essential proteins that are present in hyper-virulent <i>E. coli</i> 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 <i>Klebsiella pneumoniae</i>. 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 <i>Enterobacteriaceae</i> 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.

Item Description

10.3390/antibiotics10060632
2079-6382