There is a pressing need for new therapeutics to combat multi-drug 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 multidrugresistant (MDR) clinical isolates of Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and coagulase-negative staphylococci (CoNS) strains. High activity against extended-spectrum beta-lactamase (ESBL), meticillin-resistant S. aureus (MRSA), 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.Antibiotic resistance is an ever-increasing threat which is gradually rendering our current repertoire of antibiotics obsolete. If no new drugs are developed, deaths due to antimicrobial resistance are expected to exceed 10 million annually by 2050 (1). Antimicrobial peptides (AMPs) are one potential solution to this problem. Naturally occurring AMPs continue to remain an important component of the innate immune system despite their ancient evolutionary origin and widespread prevalence across many forms of life (2). Some derivatives of these such as pexiganan (3), omiganan (4), and OP-145 (5) are currently undergoing late-stage clinical trials (for diabetic foot ulcers, rosacea, and ear infections respectively (6)). Other peptides such as Novexatin (7) and Lytixar (8) are currently undergoing early-stage clinical trials (for the treatment of toenail fungal infections and MRSA respectively (6)). Currently, over 2000 natural and designed antimicrobial peptides are curated in various databases (9-11), and have displayed broad-spectrum activity against Gram positive, Gram negative, fungal, mycobacterial, and protozoal pathogens (9). Designed AMPs vs. MDR isolates.positive charge are attracted and incorporated into negatively charged bacterial membranes. Once inside the membrane, they are believed to cause disruption through three possible mechanisms: toroidal pore formation (12), carpet formation (13), and barrel stave formation (14). Although the specifics of each mechanism differ, all propose peptide-induced membrane rupture, allowing cytoplasmic leak...

Drug resistance is a public health concern that threatens to undermine decades of medical progress. ESKAPE pathogens cause most nosocomial infections, and are frequently resistant to carbapenem antibiotics, usually leaving tigecycline and colistin as the last treatment options. However, increasing tigecycline resistance and colistin’s nephrotoxicity severely restrict use of these antibiotics. We have designed antimicrobial peptides using a maximum common subgraph approach. Our best peptide (Ω76) displayed high efficacy against carbapenem and tigecycline-resistant Acinetobacter baumannii in mice. Mice treated with repeated sublethal doses of Ω76 displayed no signs of chronic toxicity. Sublethal Ω76 doses co-administered alongside sublethal colistin doses displayed no additive toxicity. These results indicate that Ω76 can potentially supplement or replace colistin, especially where nephrotoxicity is a concern. To our knowledge, no other existing antibiotics occupy this clinical niche. Mechanistically, Ω76 adopts an α-helical structure in membranes, causing rapid membrane disruption, leakage, and bacterial death.