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Updated: Oct 20, 2025

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

A Platform for Deep Sequence-Activity Mapping and Engineering Antimicrobial Peptides.

Matthew P DeJong¹, Seth C Ritter¹, Katharina A Fransen¹

¹Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, Minnesota 55455, United States.

ACS Synthetic Biology

|September 10, 2021

Summary

This summary is machine-generated.

A new high-throughput platform, sequence-activity mapping of antimicrobial peptides and proteins via depletion (SAMP-Dep), efficiently analyzes antimicrobial peptide mutants. This method accelerates the discovery of potent antimicrobial agents to combat rising antibiotic resistance.

Keywords:

antimicrobial peptide deep mutational scanning oncocin protein engineering ribosome

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Area of Science:

Microbiology
Biochemistry
Drug Discovery

Background:

Antibiotic resistance necessitates the development of novel antimicrobial agents.
Quantifying antimicrobial peptide and protein (AMP) activity is crucial for understanding sequence-activity relationships and engineering potent mutants.
Existing methods for AMP variant analysis are limited in scope and mechanistic detail.

Purpose of the Study:

To develop a high-throughput platform for efficient sequence-activity mapping of AMPs.
To elucidate the sequence-activity landscape of oncocin mutants for intracellular activity against Escherichia coli.
To identify potent AMP mutants and guide future AMP engineering efforts.

Main Methods:

Developed sequence-activity mapping of AMPs via depletion (SAMP-Dep), a platform utilizing bacterial host cultures, induced intracellular AMP expression, selective pressure, and deep sequencing.
Quantified mutant depletion to determine mutant growth rates.
Mapped the sequence-activity landscape of 170,000 oncocin mutants against Escherichia coli.

Main Results:

SAMP-Dep demonstrated sensitivity and accuracy through clonal validation.
The study revealed an extended oncocin pharmacophore, clarified the C-terminus role in internalization, and identified functional epistasis.
Focused synthetic peptide library design yielded a mutant with a 2-fold enhancement in both intracellular and extracellular activity.

Conclusions:

SAMP-Dep is an efficient platform poised to revolutionize AMP engineering, characterization, and discovery.
The platform enables comprehensive analysis of AMP sequence-activity landscapes.
Findings provide insights into AMP mechanisms and guide the design of enhanced antimicrobial agents.