Antimicrobial peptides with alpha-core helices
AssigneeLundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
InventorsNannette Y. YOUNT, Michael R. YEAMAN
Life of this patent
Estimating the term…
Abstract
Computational systems and methods are described for identifying new α-helical antimicrobial peptides using a systemic consensus formula. Newly identified α-helical antimicrobial peptides are tested experimentally and show potent microbiocidal activities.
Claims14
A method for treating an infection in a patient in need thereof, comprising administering to the patient a peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:
- 1-14 and sequences derived from anyone of SEQ ID NO:
- 1-14 with one amino acid substitution, wherein the peptide is not longer than 60 amino acid residues in length.
A computer-implemented method of identifying a peptide having antimicrobial activity, comprising:
- identifying a consensus formula from aligned amino acid sequences known to have an antimicrobial activity;
- tuning the consensus formula with a test search against a plurality of proteins with known antimicrobial activity;
- and
- searching in a protein database, with one or more processors, for amino acid fragments matching the consensus formula, wherein the search takes as input one or more criteria selected from the group consisting of location of the fragment in a protein, size of the protein, organism of the protein, and signal peptide of the protein.
A computer-implemented method of identifying an α-helical antimicrobial peptide, comprising:
- searching in a protein database, with one or more processors, for amino acid fragments matching a consensus formula:
- X−[VILMCFWYAG]−[KRHEDNQSTAG]−[KRHEDNQSTAG]−[VILMCFWYAG]−[VILMCFWYAG]−[KRHEDNQSTAG]−[KRHEDNQSTAG]−[VILMCFWYAG]−X−[KRHEDNQSTAG]−[VILMCFWYAG], wherein X denotes any amino acid residue;
- filtering the searched fragments based on presence of a signal peptide in the respective protein;
- and
- evaluating the searched fragments for one or more criteria selected from the group consisting of:
- hydrophobic moment;
- mean hydrophobicity;
- net charge;
- frequencies or ratio of K and R;
- and
- isoelectric point.
Dependencies are inferred from the claim text.