Engineering antimicrobial peptides

Inventors

Gabant, Philippe

Assignees

SYNGULON SA

Abstract

Embodiments herein relate to methods, systems and kits for engineering antimicrobial peptides such as bacteriocins, for example to have a desired range of activity in a desired range of culture conditions. The antimicrobial peptides may be engineered to have a particular activity for a particular culture, environmental conditions or a range of conditions. Some embodiments include screening an antimicrobial peptides or several candidate antimicrobial peptides for a desired activity. Some embodiments include an iterative process for engineering antimicrobial peptides such as bacteriocins. In some embodiments, the process is performed by automated machine learning.

Core Innovation

The method generates an antimicrobial peptide with a predetermined level of antimicrobial activity by providing a library of candidate nucleic acids encoding a plurality of candidate antimicrobial peptides. The method translates candidate nucleic acids in vitro in a microfluidic device to produce candidate antimicrobial peptides and detects antimicrobial activity, or a lack thereof, against a microbial organism under selected culture conditions, wherein antimicrobial activity comprises inhibition of growth and/or reproduction.

The method obtains the sequence of one or more translated candidate nucleic acids for which antimicrobial activity is detected and indexes the obtained sequences to the detected antimicrobial activity. The method also obtains the sequence of one or more translated candidate nucleic acids for which a lack of antimicrobial activity is detected and indexes the obtained sequences to the lack of antimicrobial activity. One or more mutations or variations are introduced into the candidate nucleic acids for which antimicrobial activity is detected, based on the indexed sequences, to produce a library of variant nucleic acids encoding variant antimicrobial peptides having a different sequence from the candidate antimicrobial peptide.

For variant antimicrobial peptides encoded by the variant nucleic acids, the method translates in vitro in the microfluidic device to produce the variant antimicrobial peptides and detects antimicrobial activity, or a lack thereof, against the microbial organism under selected culture conditions. The method performs one or more iterations of indexing, introducing mutations or variations, translating, and detecting, using variant nucleic acids from an earlier iteration as candidate nucleic acids in each successive iteration.

The iterations generate an antimicrobial peptide with the predetermined level of antimicrobial activity, wherein the predetermined level comprises a level of antimicrobial activity greater than a reference naturally-occurring antimicrobial peptide, a reference engineered antimicrobial peptide, or the antimicrobial activity detected earlier in the method.

Claims Coverage

The independent claim covers a microfluidic, iterative workflow with four inventive features: in vitro translation and detection, sequence indexing, mutation-based variant library generation, and iteration until a predetermined activity level is reached.

Overall claim coverage emphasizes an iterative microfluidic workflow that links in vitro translation and inhibition detection to sequence indexing and mutation-based generation of variant nucleic acids, repeating until an antimicrobial peptide reaches a predetermined activity level relative to references or earlier results.

Stated Advantages

Documented Applications