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Use of Unnatural Amino Acids to Probe Structure–Activity Relationships and Mode-of-Action of Antimicrobial Peptides

  • Alessandro TossiEmail author
  • Marco Scocchi
  • Sotir Zahariev
  • Renato Gennaro
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 794)

Abstract

Endogenous antimicrobial peptides (AMPs) can have multimodal mechanisms of bacterial inactivation, such as membrane lysis, interference with cell wall biosynthesis or membrane-based protein machineries, or translocation through the membrane to intracellular targets. The controlled variation of side-chain characteristics in their amino acid residues can provide much useful information on structure–activity relationships and mode-of-action, and also lead to improved activities. The small size and relatively low complexity of AMPs make them amenable to solid-phase peptide synthesis, facilitating the use of nonproteinogenic amino acids and vastly increasing the accessible molecular diversity of side chains. Here, we describe how such residues can be used to modulate such key parameters as cationicity, hydrophobicity, steric factors conformational stability, and H-bonding.

Key words

Unnatural amino acids Nonproteinogenic amino acids Antimicrobial peptide Host defence peptide SAR studies Solid-phase peptide synthesis 

Abbreviations

AA

Amino acid

DBU

1,8-Diazabicyclo[5.4.0]undec-7-ene

DCM

Dichloromethane

DIPCDI

Diisopropyl carbodiimide

DKP

Diketopiperazine

DMF

N,N-dimethylformamide

DODT

3,6-Dioxa-1,8-octanedithiol

EDT

Ethaneditiol

Fmoc

Fluorenylmethyloxycarbonyl

HFIP

Hexafluoroisopropanol

HOBt

Hydroxybenzotriazole

ivDde

1-(4,4-Dimethyl-2,6-dioxo-cyclohexylidene)-3-methyl-butyl

Mmt

Monomethoxytrityl

NMP

N-methylpyrrolidone

OSu

Succinimidyl carbonate

PEG-PS

Polyethyleneglycol-polystyrene

PG

Side-chain protecting group

PIP

Piperidine

PyBOP

(Benzotriazol-1-yl-oxy)tripyrrolidinophosphonium hexafluoro phosphate

s.r.v.

Swelled resin volume

SPPS

Solid-phase peptide synthesis

TIPS

Triisopropylsilane

Notes

Acknowledgment

This work was supported by the Friuli Venezia Giulia LR 26 regional grant R3A2.

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Alessandro Tossi
    • 1
    Email author
  • Marco Scocchi
    • 1
  • Sotir Zahariev
    • 2
  • Renato Gennaro
    • 1
  1. 1.Department of Life SciencesUniversity of TriesteTriesteItaly
  2. 2.International Centre for Genetic Engineering and BiotechnologyTriesteItaly

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