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Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria

Nagarajan, Deepesh and Nagarajan, Tushar and Roy, Natasha and Kulkarni, Omkar and Ravichandran, Sathyabaarathi and Mishra, Madhulika and Chakravortty, Madhulika and Chandra, Nagasuma (2018) Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 293 (10). pp. 3492-3509.

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Official URL: http://dx.doi.org/10.1074/jbc.M117.805499


There is a pressing need for new therapeutics to combat multidrug- and carbapenem-resistant bacterial pathogens. This challenge prompted us to use a long short-term memory (LSTM) language model to understand the underlying grammar, i.e. the arrangement and frequencies of amino acid residues, in known antimicrobial peptide sequences. According to the output of our LSTM network, we synthesized 10 peptides and tested them against known bacterial pathogens. All of these peptides displayed broad-spectrum antimicrobial activity, validating our LSTM-based peptide design approach. Our two most effective antimicrobial peptides displayed activity against multidrug- resistant clinical isolates of Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and coagulase-negative staphylococci strains. High activity against extended-spectrum beta-lactamase, methicillin-resistant S. aureus, and carbapenem-resistant strains was also observed. Our peptides selectively interacted with and disrupted bacterial cell membranes and caused secondary gene-regulatory effects. Initial structural characterization revealed that our most effective peptide appeared to be well folded. We conclude that our LSTM-based peptide design approach appears to have correctly deciphered the underlying grammar of antimicrobial peptide sequences, as demonstrated by the experimentally observed efficacy of our designed peptides.

Item Type: Journal Article
Additional Information: Copy right for the article belong to AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA
Department/Centre: Division of Biological Sciences > Biochemistry
Depositing User: Id for Latest eprints
Date Deposited: 02 Apr 2018 19:58
Last Modified: 31 Oct 2018 13:58
URI: http://eprints.iisc.ac.in/id/eprint/59443

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