# Patent

## Title
Antimicrobial peptides and methods of use

## Abstract

Disclosed herein are novel antimicrobial peptides with useful, improved, or superior properties such as antimicrobial activity, desirable levels of hemolytic activity, and therapeutic index against a broad range of microorganisms including gram-negative and gram-positive bacteria and other organisms having a cellular or structural component of a lipid bilayer membrane. Also provided are methods of making and using such peptides to control microbial growth and in pharmaceutical compositions for treatment or prevention of infections caused by such microorganisms. Certain peptides are disclosed utilizing a structure-based rational design relating to an antimicrobial peptide, V681, with single D-/L-amino acid substitutions or charged residue substitutions in or near the center of the peptide on the nonpolar or polar face. Also disclosed are peptides with one or more amino acids in the D configuration, including peptides with all amino acids in the D configuration. Modified peptide analogs herein can demonstrate one or more properties such as improved antimicrobial activity, specificity, and resistance to degradation. Compositions disclosed herein have useful clinical potential as antibiotics including broad spectrum antibiotics.

## Background
CROSS-REFERENCES TO RELATED APPLICATIONS
This application is the U.S. National Stage of International Application No. PCT/US2005/045393, filed Dec. 15, 2005, which claims benefit of U.S. Provisional Application No. 60/636,220, filed Dec. 15, 2004, both of which are hereby incorporated by reference to the extent not inconsistent with the disclosure herewith.


STATEMENT ON FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under NIH Grant Numbers RO1GM61855 and RO1A148717 awarded by the National Institutes of Health. The government has certain rights in the invention.


BACKGROUND OF THE INVENTION
The present invention broadly relates to novel antimicrobial peptides and methods of making and using such peptides to inhibit microbial growth and in pharmaceutical compositions for treatment or prevention of infections caused by a broad range of microorganisms including gram-positive and gram-negative bacteria.
The extensive clinical use of classical antibiotics has led to the growing emergence of many medically relevant resistant strains of bacteria (1, 2). Moreover, only three new structural classes of antibiotics (the oxazolidinone, linezolid, the streptogramins and the lipopeptide-daptomycin) have been introduced into medical practice in the past 40 years. Therefore, the development of a new class of antibiotics has great significance. The cationic antimicrobial peptides could represent such a new class of antibiotics (3-5). Although the exact mode of action of the cationic antimicrobial peptides has not been established, all cationic amphipathic peptides interact with membranes and it has been proposed that the cytoplasmic membrane is the main target of some peptides, where peptide accumulation in the membrane may cause increased permeability and loss of barrier function (6, 7). Therefore, the development of resistance to these membrane active peptides is less likely because this would require substantial changes in the lipid composition of cell membranes of microorganisms.
Two major classes of the cationic antimicrobial peptides are the α-helical and the β-sheet peptides (3, 4, 8, 9). The β-sheet class includes cyclic peptides constrained in this conformation either by intramolecular disulfide bonds, e.g., defensins (10) and protegrins (11), or by an N-terminal to C-terminal covalent bond, e.g., gramicidin S (12) and tyrocidines (13). Unlike the β-sheet peptides, α-helical peptides are more linear molecules that mainly exist as disordered structures in aqueous media and become amphipathic helices upon interaction with the hydrophobic membranes, e.g., cecropins (14), magainins (15) and melittins (16). Concerning such peptides, we have explored certain factors that may be important in relation to antimicrobial activity.
The major barrier to the use of antimicrobial peptides as antibiotics is their toxicity or ability to lyse eukaryotic cells. This is perhaps not a surprising result if the target is indeed the cell membrane (3-6). To be useful as a broad-spectrum antibiotic, it is necessary to dissociate anti-eukaryotic activity from antimicrobial activity, i.e., increasing the antimicrobial activity and reducing toxicity to normal cells.
A synthetic peptide approach to examining the effect of changes, including small or incremental changes, in hydrophobicity/hydrophilicity, amphipathicity and helicity of cationic antimicrobial peptides can facilitate rapid progress in rational design of peptide antibiotics. Generally, only L-amino acids are the isomers found throughout natural peptides and proteins; D-amino acids are the isomeric forms rarely seen in natural peptides/proteins except in some bacterial cell walls. In certain circumstances, the helix-destabilizing properties of D-amino acids offer a potential systematic approach to the controlled alteration of the hydrophobicity, amphipathicity, and helicity of amphipathic α-helical model peptides (26).
Herein, we disclose the utilization of the structural framework of an amphipathic α-helical antimicrobial peptide, V681 (28), to systematically change peptide amphipathicity, hydrophobicity and helicity by single D- or L-amino acid substitutions in the center of either the polar or nonpolar faces of the amphipathic helix. Peptide V681 has been shown to have excellent antimicrobial activity and strong hemolytic activity (27, 28) and thus served as a potentially useful candidate for our study. By introducing different D- or L-amino acid substitutions, we report here that hydrophobicity/amphipathicity and helicity have dramatic effects on the biophysical and biological activities and, utilizing this method, a significant improvement in antimicrobial activity and specificity can be achieved. In addition, high peptide hydrophobicity and amphipathicity can also result in greater peptide self-association in solution. Since we have developed a useful method to measure self-association of small amphipathic molecules, namely temperature profiling in reversed-phase chromatography (29, 30), this technique was applied for the first time to investigate the influence of peptide dimerization ability on biological activities of α-helical antimicrobial peptides. The advantage of the invention will become apparent in the following description.
SUMMARY OF THE INVENTION
The present invention provides peptide compounds useful as antimicrobial agents and related methods. In embodiments of the invention, the antimicrobial peptides range in size from about 23 to about 26 amino acids in length joined by peptide bonds and have a core amino acid sequence of about 21 amino acids. The amino acids in the peptide compounds can be all in the L configuration, all in the D configuration or in a combination of D or L configurations. The peptides have potent antimicrobial activities and are useful against bacteria, fungi, viruses, and protozoa. The peptides are generally effective in the context of any organism having a cellular or structural component of a lipid bilayer membrane. These peptides are effective compounds for use in human and/or veterinary medicine, or as agents in agricultural, food science, or industrial applications.
Without wishing to be bound by a particular theory, from numerous structure/activity studies on both natural and synthetic antimicrobial peptides it is believed that a number of factors are important for antimicrobial activity. These are identified as including the presence of both hydrophobic and basic residues, an amphipathic nature that segregates basic and hydrophobic residues, and an inducible or preformed secondary structure (α-helical or β-sheet). Also without wishing to be bound by a particular theory, it is believed that by substituting different D-amino acids into the center of the hydrophobic face of an amphipathic α-helical model peptide, disruption of alpha-helical structure can occur. Different D-amino acids can disrupt α-helical structure to different degrees, whilst the destabilized structure can still be induced to fold into an α-helix in hydrophobic medium. An advantage of this method of single D- or L-amino acid substitutions at a specific site is that it provides an opportunity for greater understanding of the mechanism of action of these peptides.
It is recognized that regardless of the ultimate correctness of any mechanistic explanation or hypothesis, the compositions and methods of the invention can nonetheless be operative and useful.
For certain α-helical and β-sheet peptides, there have been attempts to delineate features responsible for anti-eukaryotic or toxic activities and for antimicrobial activities. High amphipathicity (17-20), high hydrophobicity (17, 20-22), as well as high helicity or β-sheet structure (20, 23, 24) may correlate with increased toxicity as measured by hemolytic activity. In contrast, antimicrobial activity may be less dependent on these factors, compared with hemolytic activity (17-21, 23-25). Here, specificity (or therapeutic index (TI) which is defined as the ratio of hemolytic activity and antimicrobial activity) for bacteria over erythrocytes could be increased in one of three ways: increasing antimicrobial activity, decreasing hemolytic activity while maintaining antimicrobial activity, or a combination of both, increasing antimicrobial activity and decreasing hemolytic activity.
The invention provides a method of treating a patient in need of therapy comprising administering to the patient a peptide compound of the invention. The invention provides a method of treating a microbial infection. In a particular embodiment, the microbial infection involves one or more of a bacterium, a virus, a fungus, or a protozoan. In a particular embodiment, the microbial infection involves one or more of each of those kinds of organisms, e.g. two different kinds of bacteria, and so forth.
In an embodiment, the invention provides a method for increasing antimicrobial activity of a peptide compound. In an embodiment, the invention provides a method for decreasing hemolytic activity of a peptide compound while maintaining antimicrobial activity or minimizing a reduction of antimicrobial activity. In an embodiment, the invention provides a method of increasing antimicrobial activity and decreasing hemolytic activity of a peptide compound while maintaining antimicrobial activity or minimizing a reduction of antimicrobial activity.
The inventors discovered the antimicrobial peptides disclosed herein based on the premise that controlled alteration of the hydrophobicity/hydrophilicity, amphipathicity and helicity of an alpha helical peptide would yield a peptide with useful or improved biological activity and specificity (e.g. improved therapeutic index). Exemplified herein are peptides derived from the 26-residue peptide sequence, Ac-KWKSFLKTFKS-AVKTVLHTALKAISS-amide (V681, SEQ ID NO: 1). The terms “derived from” or “derivative” are meant to indicate that the inventive peptides are the same or shorter than the V681 peptide in size and have one or more amino acid residues substituted, or a combination of both; further variations are also described herein. The peptide compound V681 was used as the framework to study the effects of peptide hydrophobicity/hydrophilicity, amphipathicity and helicity on biological activities, for example antimicrobial and hemolytic activities, by substituting one or more amino acid residues at certain locations. These locations can include points at or near the center of the polar and nonpolar faces of the amphipathic helix in addition to other locations. The peptide V681 is disclosed in Zhang et al., 1999 and Zhang et al., 2001.
In an embodiment, the invention provides compositions and methods relating to a peptide selected from the group consisting of SEQ ID NOS:2, 4-14, and 16-25 and other peptides as disclosed herein, e.g. in the Examples. It is noted that SEQ ID NO:1, peptide V681, is exactly equivalent to SEQ ID NOS:3 and 15. See Table 1 which includes peptides with substitutions on the nonpolar face at position X=13 and on the polar face at position X=11. See also Table 2 which includes other peptide analogs.







TABLE 1







Summary of partial sequence listing information.










Peptide
Amino Acid Position


































SEQ ID NO:
Name
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26




































Enantiomer*
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L


































 1
V681
K
W
K
S
F
L
K
T
F
K
S
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


 2
NLL
K
W
K
S
F
L
K
T
F
K
S
A
LL
K
T
V
L
H
T
A
L
K
A
I
S
S


 3
NVL
K
W
K
S
F
L
K
T
F
K
S
A
VL
K
T
V
L
H
T
A
L
K
A
I
S
S


 4
NAL
K
W
K
S
F
L
K
T
F
K
S
A
AL
K
T
V
L
H
T
A
L
K
A
I
S
S


 5
NSL
K
W
K
S
F
L
K
T
F
K
S
A
SL
K
T
V
L
H
T
A
L
K
A
I
S
S


 6
NKL
K
W
K
S
F
L
K
T
F
K
S
A
KL
K
T
V
L
H
T
A
L
K
A
I
S
S


 7
NLD
K
W
K
S
F
L
K
T
F
K
S
A
LD
K
T
V
L
H
T
A
L
K
A
I
S
S


 8
NVD
K
W
K
S
F
L
K
T
F
K
S
A
VD
K
T
V
L
H
T
A
L
K
A
I
S
S


 9
NAD
K
W
K
S
F
L
K
T
F
K
S
A
AD
K
T
V
L
H
T
A
L
K
A
I
S
S


10
NSD
K
W
K
S
F
L
K
T
F
K
S
A
SD
K
T
V
L
H
T
A
L
K
A
I
S
S


11
NKD
K
W
K
S
F
L
K
T
F
K
S
A
KD
K
T
V
L
H
T
A
L
K
A
I
S
S


12
NG
K
W
K
S
F
L
K
T
F
K
S
A
G
K
T
V
L
H
T
A
L
K
A
I
S
S


13
PLL
K
W
K
S
F
L
K
T
F
K
LL
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


14
PAL
K
W
K
S
F
L
K
T
F
K
AL
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


15
PSL
K
W
K
S
F
L
K
T
F
K
SL
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


16
PVL
K
W
K
S
F
L
K
T
F
K
VL
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


17
PKL
K
W
K
S
F
L
K
T
F
K
KL
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


18
PLD
K
W
K
S
F
L
K
T
F
K
LD
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


19
PAD
K
W
K
S
F
L
K
T
F
K
AD
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


20
PSD
K
W
K
S
F
L
K
T
F
K
SD
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


21
PVD
K
W
K
S
F
L
K
T
F
K
VD
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


22
PKD
K
W
K
S
F
L
K
T
F
K
KD
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


23
PG
K
W
K
S
F
L
K
T
F
K
G
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S

































Enantiomer
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D


































24
D-NKD
K
W
K
S
F
L
K
T
F
K
S
A
K
K
T
V
L
H
T
A
L
K
A
I
S
S


25
D-NAL
K
W
K
S
F
L
K
T
F
K
S
A
AL
K
T
V
L
H
T
A
L
K
A
I
S
S


 1
D-V681
K
W
K
S
F
L
K
T
F
K
S
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S





*L-enantiomer unless otherwise indicated in the Enantiomer column or subscript.













TABLE 2







Summary of partial sequence listing information.









SEQ




ID

Amino Acid Position


































NO:
Peptide Name
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26






































Enantiomer*
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L


1
V681
K
W
K
S
F
L
K
T
F
K
S
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


27
F9 to K9
K
W
K
S
F
L
K
T
K
K
S
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


28
F5 to K5
K
W
K
S
K
L
K
T
F
K
S
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


29
F9 to AD9
K
W
K
S
F
L
K
T
AD
K
S
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


30
F5 to AD5
K
W
K
S
AD
L
K
T
F
K
S
A
V
K
T
V
L
H
T
A
L
K
A
I
S
S


31
V13 to R13
K
W
K
S
F
L
K
T
F
K
S
A
R
K
T
V
L
H
T
A
L
K
A
I
S
S


32
L6-AD6,
K
W
K
S
F
AD
K
T
F
K
S
A
V
K
T
V
L
H
T
A
AD
K
A
I
S
S



L21-AD21




























33
L6-KL6,
K
W
K
S
F
K
K
T
F
K
S
A
V
K
T
V
L
H
T
A
K
K
A
I
S
S



L21-KL21




























34
Remove K1

W
K
S
F
L
K
T
F
K
S
A
K
K
T
V
L
H
T
A
L
K
A
I
S
S


35
Remove K1,


K
S
F
L
K
T
F
K
S
A
K
K
T
V
L
H
T
A
L
K
A
I
S
S



W2




























36
Remove S25,
K
W
K
S
F
L
K
T
F
K
S
A
K
K
T
V
L
H
T
A
L
K
A
I





S26




























37
Remove I24,
K
W
K
S
F
L
K
T
F
K
S
A
K
K
T
V
L
H
T
A
L
K
A






S25, S26




























38
non-polar face
K
I
K
S
AD
L
K
T
L
K
S
F
K
K
T
A
A
H
T
L
F
K
V
W
S
S



shuffle




























39
polar face
S
W
S
K
F
L
K
K
F
T
K
A
K
S
H
V
L
T
T
A
L
S
A
I
K
K



shuffle





*L-enantiomer unless otherwise indicated.






In a preferred embodiment, the molecule (peptide) is helical in a hydrophobic environment. We have used circular dichroism spectroscopy to monitor α-helical structure in 50% trifluoroethanol, a mimic of the hydrophobic environment of the cytoplasmic membrane.
In an embodiment, successful peptides that are helical analogs with the desired biological activities have very little alpha-helical structure in benign medium (a non-denaturing medium like 50 mM PO4 buffer containing 100 mM KCl, pH 7) monitored by circular dichroism spectroscopy. In an embodiment, this structural property can have importance in one or more of several potential mechanisms, for example: a) decreasing dimerization of molecule in benign medium (measured as described herein); b) allowing the peptide to more easily penetrate through the cell wall to reach the membrane of the microbe. Furthermore, disruption of the α-helical structure in benign medium can still allow a positively-charged peptide to be attracted to the negatively-charged cell wall surface of the microbe (e.g. lipopolysaccharide), but the lack of structure can decrease the affinity of peptide for this surface which allows the peptide to more easily pass through the cell wall and enter the interface region of the membrane where the peptide is parallel to the surface of membrane. Here the peptide can be induced by the hydrophobic environment of the membrane into its alpha-helical structure. In this alpha-helical structure, we hypothesize that the non-polar face of the peptide can interact with the hydrophobicity of the membrane, and its polar and positively-charged groups on the polar face can interact with the negatively-charged groups of the phospholipids on the surface of the membrane.
In an embodiment, a peptide is net positively-charged and amphipathic/amphiphilic when in an alpha-helical structure. For example, the alpha-helical peptide has a non-polar face or hydrophobic surface on one side of the molecule and a polar and positively-charged surface on the other side of the molecule; i.e., the molecule is amphipathic. Amphipathicity of the molecule can be calculated as described herein.
Certain peptide analogs were studied by temperature profiling in RP-HPLC from 5° C. to 80° C., to evaluate the self-associating ability of the molecules in solution. The ability to self-associate can be another important parameter in understanding peptide antimicrobial and hemolytic activities. It was generally found that a high ability to self-associate in solution was correlated with weak antimicrobial activity and strong hemolytic activity of the peptides. Biological studies showed that strong hemolytic activity of the peptides generally correlated with high hydrophobicity, high amphipathicity and high helicity. In most cases, the D-amino acid substituted peptides possessed an enhanced average antimicrobial activity compared with L-diastereomers. As illustrated herein, the therapeutic index of V681 was improved 90-fold and 23-fold against gram-negative and gram-positive bacteria, respectively (using geometric mean comparison). By replacing the central hydrophobic or hydrophilic amino acid residue on the nonpolar or the polar face of these amphipathic molecules with a series of selected D- and L-amino acids, we further demonstrate that this method can be used for the rational design of other antimicrobial peptides with enhanced activities.
The antimicrobial peptides exemplified in the present invention contain amino acid substitutions in at least one of the two positions selected from the group represented as a and b in the peptide sequence given as KWKSFLKTFKaAbKTVLHTALKAISS (SEQ ID NO:40) wherein a and b are selected from the group consisting of L-leucine, D-leucine, L-valine, D-valine, L-alanine, D-alanine, glycine, L-serine, D-serine, L-lysine, and D-lysine (L, A, S, V, K in L- and D-enantiomeric form and G). Particularly preferred antimicrobial peptides are referred to herein as NKL, D-NKD, NAD, and D-NAL and contain the following amino acid sequences. A most particularly preferred antimicrobial peptide is referred to herein as D-NKD. In an alternative nomenclature, D-NKD can be referred to as D-V13KD.











Peptide



name
Amino acid sequence (one letter code)







NKL






 


D-NKD






 


NAD






 


D-NAL













Here a subscript D following an amino acid residue denotes that the residue is a D-amino acid residue; similarly a subscript L denotes an L-amino acid residue. In the peptide name, an initial D- (not subscripted) denotes all D-amino acids in the peptide except where specified (e.g. D-NAL denotes all D-amino acids with the exception of a single substitution of L-Ala in the center of the non-polar face specified by N). The boxed residues denote the differences at position 13 in the sequence which is in the center of the non-polar face (see FIG. 1).
In an embodiment, a peptide of the invention is integrated in a larger peptide or protein. In an embodiment, a peptide of the invention is covalently or non-covalently associated with another composition. In a particular embodiment, said another composition is a polymer.
The peptides disclosed have antimicrobial activity against a wide range of microorganisms including gram-positive and gram-negative bacteria. Detailed description of the microorganisms belonging to gram-positive and gram-negative bacteria can be found in Medical Microbiology (1991), 3rd edition, edited by Samuel Baron, Churchill Livingstone, N.Y. Examples of potentially susceptible bacteria include, but are not limited to, Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, Bacillus subtilis, Enterococcus faecalis, Corynebacterium xerosis, and Bacillus anthracis. The antimicrobial activities of the inventive peptides have been demonstrated herein against the fore-mentioned gram-positive and gram-negative bacteria because it is well known in the art that these bacteria are considered as model organisms for either gram-negative or gram-positive bacteria and thus any biological activity demonstrated again these model organisms are accepted as an indication of that demonstrated activity against the entire family of gram-negative or gram-positive bacteria.
The antimicrobial peptides of the invention are useful as bactericides and/or bacteriostats for modification of infectivity, killing microorganisms, or inhibiting microbial growth or function and thus useful for the treatment of an infection or contamination caused by such microorganisms.
Also provided are therapeutic or otherwise active compositions suitable for human, veterinary, agricultural or pharmaceutical use, comprising one or more of the antimicrobial peptides of the invention and a suitable pharmaceutical carrier. Such therapeutic compositions can be formulated and administered as known in the art, e.g., for oral, parenteral or topical application for controlling and/or preventing infection by a wide range of microorganisms including gram-positive and gram-negative bacteria.
In an embodiment of the invention, in vitro antimicrobial activity of these peptides demonstrated herein is an accurate predictor of in vivo antimicrobial activity.
Pharmaceutical compositions contain a therapeutically effective amount of one or more of the antimicrobial peptides and a suitable carrier. A therapeutically effective amount of an antimicrobial peptide can be readily determined according to methods well known in the art. For example, the amount will vary depending on the severity of an infection, subject parameters such as the age and the size/weight of a subject with an actual or potential infection of a given microorganism, and the route of administration and the like.
The present invention relates to compositions comprising one or more antimicrobial peptides of the invention in a microbicidal effective amount and a pharmaceutically acceptable carrier. Such compositions may additionally comprise a detergent. The addition of a detergent to such peptide compositions is useful to enhance antibacterial characteristics of the peptides. Although any suitable detergent may be used, the presently preferred detergent is a nonionic detergent such as Tween 20 or 1% NP40. Such antimicrobial pharmaceutical compositions can be formulated and administered in ways, as understood in the art for use local or systemic injection, for oral or topical application. In an embodiment, the antimicrobial peptides of the present invention can comprise from 0.0001% to 50% by weight of such compositions.
It will be understood that a composition for application, e.g. by systemic injection, will contain an antimicrobial peptide in a therapeutically effective amount or a therapeutically effective amount of an antimicrobial peptide can be conjugated to another molecule with specificity for the target cell type. The other molecule can be an antibody, ligand, receptor, or other recognition molecule. In an embodiment, the choice of the peptide is made with consideration of immunogenicity and toxicity for an actually or potentially infected host, effective dose of the peptide, and the sensitivity of the target microbe to the peptide, as known in the art.
In an embodiment, the method of inhibiting the growth of bacteria using the peptides of the invention may further include the addition of one or more other antimicrobial agents (e.g. a conventional antibiotic) for combination or synergistic therapy. The appropriate amount of the peptide administered will typically depend on the susceptibility of a bacterium such as whether the bacterium is Gram negative or Gram positive, and will be easily discernable by one of ordinary skill in the art.
In an embodiment the invention also provides a composition that comprises the peptide, in an amount effective to kill a microorganism, and a suitable carrier. Such compositions may be used in numerous ways to combat microorganisms, for example in household or laboratory antimicrobial formulations using carriers well known in the art.
In an embodiment, the invention provides a peptide comprising SEQ ID NO:2. In an embodiment, the invention provides a peptide comprising a derivative of SEQ ID NO:1. In an embodiment, the invention provides a peptide selected from the group consisting of SEQ ID NO:2, 4-14, 16-25, and a derivative thereof. In an embodiment, a derivative comprises a substitution of at least one amino acid residue. In an embodiment, a derivative includes a substitution of at least one amino acid residue; excepting SEQ ID NO:1. In an embodiment, a derivative comprises a truncation of at least one residue from an end. In an embodiment, a derivative comprises a truncation of at least two residues from an end. In an embodiment, a substitution replaces a hydrophilic residue for a hydrophobic residue. In an embodiment, a substitution replaces a hydrophobic residue for a hydrophilic residue. In an embodiment, a substitution replaces a hydrophilic residue with a different hydrophilic residue. In an embodiment, a substitution replaces a hydrophilic residue with a different hydrophilic residue. In an embodiment, a substitution replaces a residue with a different residue having a similar property, e.g., a polar side chain, a positively charged side chain, a negatively charged side chain, etc. In an embodiment, a substitution replaces an L-residue with a D-residue. In an embodiment, a substitution replaces a D-residue with an L-residue. In an embodiment, all residues are D-residues.
In an embodiment, the invention provides a peptide comprising a sequence KWKSFLKTFKaAbKTVLHTALKAISS (SEQ ID NO:40) wherein a and b are selected from the group consisting of L-leucine, D-Leucine, L-valine, D-valine, L-alanine, D-alanine, glycine, L-serine, D-serine, L-lysine, and D-lysine. In an embodiment, the peptide excludes SEQ ID NO:1.
In an embodiment, the invention provides peptide compositions as described herein, including fragments thereof; wherein the fragment length comprises a continuous stretch of at least about 14, at least about 17, at least about 20, at least about 23, at least about 24, or at least about 25 amino acids. In an embodiment, the invention provides a peptide composition wherein said composition is at least about 70%, at least about 80%, at least about 90%, or at least about 95% homologous to a sequence of a peptide described herein. In an embodiment, the invention provides a nucleic acid capable of encoding a peptide described herein. In an embodiment, a peptide of the invention is intended to be exclusive of one or more of the following peptides: SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:15, and SEQ ID NO:26. In a particular embodiment, a peptide of the invention is exclusive of SEQ ID NO:1.
Where the peptides are to be used as antimicrobial agents, they can be formulated, for example, in buffered aqueous media containing a variety of salts and buffers. Examples of the salts include, but are not limited to, halides, phosphates and sulfates, e.g., sodium chloride, potassium chloride or sodium sulfate. Various buffers may be used, such as citrate, phosphate, HEPES, Tris or the like to the extent that such buffers are physiologically acceptable to the host that is being treated.
Various excipients or other additives may be used, where the peptides are formulated as lyophilized powders, for subsequent use in solution. The excipients may include various polyols, inert powders or other extenders.
“Therapeutically effective” as used herein, refers to an amount of formulation, composition, or reagent, optionally in a pharmaceutically acceptable carrier, that is of sufficient quantity to ameliorate the state of the patient or animal so treated. “Ameliorate” refers to a lessening of the detrimental effect of the disease state or disorder in the recipient of the therapy. In an embodiment, a peptide of the invention is administered to a subject in need of treatment.
Pharmaceutically acceptable carrier preparations for administration include sterile or aqueous or nonaqueous solutions, suspensions, and emulsions. Examples of nonaqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solutions, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Active therapeutic ingredients are often mixed with excipients that are pharmaceutically acceptable and compatible with the active ingredients. Suitable excipients include water, saline, dextrose, glycerol and ethanol, or combinations thereof. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers, such as those based on Ringer's dextrose, and the like. Preservatives and other additives may also be present such as, for example, antioxidants, chelating agents, and inert gases and the like. The actual dosage of the peptides, formulations or compositions containing such peptides can depend on many factors, including the size/weight, age, and health of an organism, however, one of ordinary skill in the art can use the following teachings and others known in the art describing the methods and techniques for determining clinical dosages (Spiker B., Guide to Clinical Studies and Developing Protocols, Raven Press, Ltd., New York, 1984, pp. 7-13, 54-60; Spiker B., Guide to Clinical Trials, Raven Press, Ltd., New York 1991, pp. 93-101; C. Craig. and R. Stitzel, eds., Modern Pharmacology, 2d ed., Little, Brown and Co., Boston, 1986, pp. 127-133; T. Speight, ed., Avery's Drug Treatment: Principles and Practice of Clinical Pharmacology and Therapeutics, 3d ed., Williams and Wilkins, Baltimore, 1987, pp. 50-56; R. Tallarida, R. Raffa and P. McGonigle, Principles in General Pharmacology, Springer-Verlag, new York, 1988, pp. 18-20) to determine the appropriate dosage to use.
In an embodiment, the following dosages are used: generally in the range of about 0.001 mg/kg to about 100 mg/kg and preferably from about 0.001 mg/kg to about 1 mg/kg final concentration are administered per day to an adult in any pharmaceutically acceptable carrier.
In another embodiment, the present invention may be used as a food preservative or in treating food products to control, reduce, or eliminate potential pathogens or contaminants. A peptide of the invention may be used as a disinfectant, for use in or with any product that must remain microbial free or be within certain tolerances. In an embodiment, treatment with a peptide provides at least partial regulation of infection or contamination.
In an embodiment it is also possible to incorporate or distribute the peptides within materials, on devices, or on objects (e.g. on an accessible surface), where microbial growth or viable presence is undesirable, as a method of microbicidal or microbistatic inhibition of microbial growth by administering to the devices or objects a microbicidal or microbistatic effective amount of peptide. In an embodiment, such devices or objects include, but are not limited to, linens, cloth, plastics, latex fabrics, natural rubbers, implantable devices, surfaces, or storage containers.
In an embodiment, the invention provides a method of disinfecting a surface of an article, said method comprising the step of applying to said surface an effective amount of a composition comprising at least one microbial peptide of the invention. In an embodiment, the invention provides a disinfecting solution comprising at least one microbial peptide of the invention and optionally an acceptable carrier.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 illustrates the “host” peptide V681 (SEQ ID NO:1) as a helical wheel/nets and the sequences of the synthetic peptide analogs used in the present studies. Shown are the polar/hydrophilic face (boxed residues) and non-polar/hydrophobic face (circled residues). The hydrophobic face is indicated as an open arc, whilst the hydrophilic face is shown as a solid arc in the helical wheel. The substitution sites are at position 11 (triangled) on the polar face and position 13 (triangled) on the non-polar face. In the peptide sequences, XL and XD denote the L- or D-substituting amino acids. P denotes the polar face and N denotes the non-polar face. Ac denotes Nα-acetyl and amide denotes Cα-amide. One-letter codes are used for the amino acid residues.
FIG. 2 illustrates graphical results of Circular dichroism (CD) spectra of peptides NLD and NLL (panel A) and peptides NKD and NKL (panel B) at pH 7 and 25° C., in 50 mM aq. PO4 containing 100 mM KCl. In both Panel A and Panel B, solid symbols represent the CD spectra of peptide analogs in benign buffer without TFE, whilst open symbols represent CD spectra obtained in the presence of 50% TFE. The symbols used are: in Panel A, circle for NLD and square for NLL; in Panel B, diamond for NKD and triangle for NKL.
FIG. 3 shows graphical results of Circular dichroism (CD) spectra of peptides V681 and D-V681 (panel A), NKL and D-NKD (panel B) and peptides NAD and D-NAL (panel C) at pH 7.4 and 5° C., in 50 mM aq. potassium phosphate buffer (KP buffer) containing 100 mM KCl. In Panels A, B and C, solid symbols represent the CD spectra of peptide analogs in KP buffer without trifluoroethanol (TFE), whilst open symbols represent CD spectra obtained in the presence of 50% TFE; the symbols used are: circles for L-peptides V681, NKL and NAD and diamonds for D-peptides D-V681, D-NKL and D-NAL.
FIG. 4 illustrates the CD temperature denaturation profiles of peptide V681. Panel A shows the change of V681 helical conformation over the temperature range from 5° C. to 80° C. in the hydrophobic medium. The experiment was carried out in 0.05% aq. TFA (pH 2) in the presence of 50% TFE. CD spectra at different temperatures are shown as different lines in the figure; Panel B: shows the stability plot of peptide V681 during CD temperature denaturation.
FIG. 5 illustrates the RP-HPLC temperature profiles of peptide V681 and its analogs. Conditions: RP-HPLC, narrow-bore SB-C8 column (150×2.1 mm ID; 5 μm particle size, 300 Å pore size), linear A-B gradient (1% acetonitrile/min) at a flow-rate of 0.25 ml/min, where eluent A is 0.05% aqueous TFA and eluent B is 0.05% TFA in acetonitrile. Retention data has been collected in 3° C. increments within the temperature range from 5° C. to 80° C. Open symbols represent the temperature profiles of L-amino acid substituted peptides on either the non-polar or polar face of V681 (panels A and C); whereas solid symbols represent the temperature profiles of D-amino acid substituted peptides on either the non-polar or polar face of V681 (panels B and D). In all panels, the substituting amino acids used in either the non-polar or polar face of V681 are Val (circle), Leu (square), Ala (diamond), Ser (triangle), Lys (inverted triangle) and Gly (X). The temperature profile of the random coil control peptide (C1) is shown in the figure (+).
FIG. 6 illustrates the normalized RP-HPLC temperature profiles of peptide V681 and its analogs. Temperature profiles normalized to retention behavior of random coil peptide C1. Column and conditions: see FIG. 4. The retention behavior of the peptides was normalized to that of the random coil peptide C1 through the expression (tRt−tR5 for peptides) minus (tRt−tR5 for C1), where tRt are the retention times at a specific temperature of an antimicrobial peptide or the random coil peptide, and tR5 are the retention times at 5° C. Open symbols represent the temperature profiling of L-amino acid substituted peptides on either the non-polar or polar face of V681 (panels A and C); whereas solid symbols represent D-amino acid substituted peptides on either the non-polar or polar face of V681 (panels B and D). In all panels, amino acids used for substitution in either the non-polar or polar face of V681 are Val (circle), Leu (square), Ala (diamond), Ser (triangle), Lys (inverted triangle) and Gly (X).
FIG. 7 illustrates further peptide analogs including those generated by variations based on several techniques: the position of substitutions, nature of substitutions, multiple substitutions, truncations, and shuffling. FIG. 7A illustrates specific peptide sequences. FIG. 7B illustrates variants based on shuffling of the non-polar face residues. FIG. 7C illustrates variants based on shuffling of the polar face residues.
FIG. 8 illustrates the peptide retention behavior during RP-HPLC with increasing temperature. Column and conditions: RP-HPLC, SB-C8 column (150×2.1 mm ID; 5 μm particle size, 300 Å pore size), linear A-B gradient (0.5% acetonitrile/min) at a flow-rate of 0.35 ml/min, where eluent A is 0.2% aqueous TFA and eluent B is 0.2% TFA in acetonitrile. The retention times of the peptides during the change of temperature are shown in Panel A. In Panel B, the retention time of peptides are normalized to 5° C. through the expression (tRt−tR5), where tRt is the retention time at a specific temperature of an antimicrobial peptide or the random coil peptide, and tR5 is the retention time at 5° C. In Panel C, the retention behavior of the peptides was normalized to that of the random coil peptide C through the expression (tRt−tR5 for peptides) minus (tRt−tR5 for C). In Panels A, B and C, the symbols used are: circles for V681 and D-V681, diamonds for NAD and D-NAL, squares for NKL, D-NKD and triangles for random coil peptide C.
FIG. 9 shows the results of peptide hemolysis of human red blood cells. Closed symbols were used for L-peptides and open symbols were used for D-peptides. Different symbols were used to represent the different concentrations of peptides in the hemolysis study.
FIG. 10 illustrates the peptide stability to proteolysis by trypsin. Closed symbols were used for L-peptides and open symbols were used for D-peptides. Circles denote V681 and D-V681, squares denote NKL and D-NKD, and diamonds denote NAD and D-NAL.
FIG. 11 is a representation of the parent peptide NKL and analogs (with different leucine substitutions) as helical nets showing the non-polar faces. The hydrophobic amino acid residues on the non-polar faces are boxed. The substituting leucine residues are colored red and the amino acid residues involved in the i→i+3 and i→i+4 hydrophobic interactions are colored yellow. The i→i+3 and i→i+4 hydrophobic interactions are shown as black bars and the numbers of hydrophobic interactions on the non-polar face are indicated. One-letter code is used for the amino acid residues.
FIG. 12 illustrates the relationship of peptide hydrophobicity and antimicrobial activity (MIC) and hemolytic activity (MHC). Closed symbols and dotted line represent the relationship between hydrophobicity and hemolytic activity; open symbols and solid line represent the relationship between hydrophobicity and antimicrobial activity. Hydrophobicity was shown as the retention time of peptides in RP-HPLC at room temperature. The lines were drawn to guide the eye.
FIG. 13 illustrates a space-filling model of peptides V681 and V13KL. Hydrophobic amino acids on the non-polar face of the helix are green; hydrophilic amino acids on the polar face of the helix are grey; peptide backbone is colored white. The Lys substitution at position 13 (V13KL) on the non-polar face of the helix is blue. The models were created by the PyMOL v0.98.



DETAILED DESCRIPTION OF THE INVENTION
In general the terms and phrases used herein have their art-recognized meaning, which can be found by reference to standard texts, journal references and contexts known to those skilled in the art. The following definitions are provided to clarify their specific use in the context of the invention.
When used herein, the term “amino acid” is intended to refer to any natural or unnatural amino acid, whether made naturally or synthetically, including any such in L- or D-configuration. The term can also encompass amino acid analog compounds used in peptidomimetics or in peptoids. The term can include a modified or unusual amino acid or a synthetic derivative of an amino acid, e.g. diamino butyric acid and diamino propionic acid and the like.
The antimicrobial peptides of the invention are composed of amino acids linked together by peptide bonds. The peptides are in general in alpha helical conformation under hydrophobic conditions. Sequences are conventionally given from the amino terminus to the carboxyl terminus. Unless otherwise noted, the amino acids are L-amino acids. When all the amino acids are of L-configuration, the peptide is said to be an L-enantiomer. When all the amino acids are of D-configuration, the peptide is said to be a D-enantiomer.
The term “minimal inhibitory concentration” (MIC) refers to the lowest concentration of an antimicrobial agent (e.g., a peptide) required to prevent growth or otherwise modify a function of a microorganism under certain conditions, for example in liquid broth medium, and can be determined for a number of different microorganisms according to standard techniques well known in the art.
The term “minimal hemolytic concentration” (MHC) refers to the lowest concentration of an agent or peptide required to cause hemolysis of blood cells. MHC can be determined with red blood cells (RBC) from various species including human red blood cells (hRBC).
The term “therapeutic index” (TI) is the ratio of minimal hemolytic concentration (MHC) over minimal inhibitory concentration (MIC) of an antimicrobial agent. Larger values generally indicate greater antimicrobial specificity.
The term “stability” can refer to an ability to resist degradation, to persist in a given environment, and/or to maintain a particular structure. For example, a peptide property of stability can indicate resistance to proteolytic degradation and to maintain an alpha-helical structural conformation.
The following abbreviations are used herein: A, Ala, Alanine; M, Met, Methionine; C, Cys, Cysteine; D, Asp, Aspartic Acid; E, Glu, Glutamic Acid; F, Phe, Phenylalanine; G, Gly, Glycine; H, His, Histidine; I, Ile, Isoleucine; K, Lys, Lysine; L, Leu, Leucine; N, Asn, Asparagine; P, Pro, Proline; Q, Glu, Glutamine; R, Arg, Arginine; S, Ser, Serine; T, Thr, Threonine; V, Val, Valine; W, Trp, Tryptophan; Y, Tyr, Tyrosine; RP-HPLC, reversed-phase high performance liquid chromatography; MIC, minimal inhibitory concentration; MHC, minimal hemolytic concentration; CD, circular dichroism spectroscopy; TFE, trifluoroethanol; TFA, trifluoroacetic acid; RBC, red blood cells; hRBC, human red blood cells.
The term “antimicrobial activity” refers to the ability of a peptide of the present invention to modify a function or metabolic process of a target microorganism, for example so as to at least partially affect replication, vegetative growth, toxin production, survival, viability in a quiescent state, or other attribute. In an embodiment, the term relates to inhibition of growth of a microorganism. In a particular embodiment, antimicrobial activity relates to the ability of an inventive peptide to kill at least one bacterial species. In a particular embodiment, the bacterial species is selected from the group consisting of gram-positive and gram-negative bacteria. In an embodiment, the term can be manifested as microbicidal or microbistatic inhibition of microbial growth.
The phrase “improved biological property” is meant to indicate that a test peptide exhibits less hemolytic activity and/or better antimicrobial activity, or better antimicrobial activity and/or less hemolytic activity, compared to the control peptide (e.g. V681), when tested by the protocols described herein or by any other art-known standard protocols. In general, the improved biological property of the peptide is reflected in the therapeutic index (TI) value which is better that that of the control peptide.
The term “microorganism” herein refers broadly to bacteria, fungi, viruses, and protozoa. In particular, the term is applicable for a microorganism having a cellular or structural component of a lipid bilayer membrane. In specific embodiments, the membrane is a cytoplasmic membrane. Pathogenic bacteria, fungi, viruses, and protozoa as known in the art are generally encompassed. Bacteria can include gram-negative and gram-positive bacteria in addition to organisms classified in orders of the class Mollicutes and the like, such as species of the Mycoplasma and Acholeplasma genera. Specific examples of potentially sensitive gram-negative bacteria include, but are not limited to, Escherichia coli, Pseudomonas aeruginosa, Salmonella, Hemophilus influenza, Neisseria, Vibrio cholerae, Vibrio parahaemolyticus and Helicobacter pylori. Examples of potentially sensitive gram-positive bacteria include, but are not limited to, Staphylococcus aureus, Staphylococcus epidermis, Streptococcus agalactiae, Group A streptococcus, Streptococcus pyogenes, Enterococcus faecalis, Group B gram positive streptococcus, Corynebacterium xerosis, and Listeria monocytogenes. Examples of potentially sensitive fungi include yeasts such as Candida albicans. Examples of potentially sensitive viruses include measles virus, herpes simplex virus (HSV-1 and -2), herpes family members (HIV, hepatitis C, vesicular, stomatitis virus (VSV), visna virus, and cytomegalovirus (CMV). Examples of potentially sensitive protozoa include Giardia. 
“Therapeutically effective” as used herein, refers to an amount of formulation, composition, or reagent in a pharmaceutically acceptable carrier or a physiologically acceptable salt of an active compound, that is of sufficient quantity to ameliorate the undesirable state of the patient, animal, material, or object so treated. “Ameliorate” refers to a lessening of the detrimental effect of the disease state or disorder, or reduction in contamination, in the receiver of the treatment.
The peptides of the invention have antimicrobial activity by themselves or when covalently conjugated or otherwise coupled or associated with another molecule, e.g., polyethylene glycol or a carrier protein such as bovine serum albumin, so long as the peptides are positioned such that they can come into contact with a cell or unit of the target microorganism. These peptides may be modified by methods known in the art provided that the antimicrobial activity is not destroyed or substantially compromised.
The invention may be further understood by the following non-limiting examples.
EXAMPLE 1
Derivatives of Peptide V681 with Modified Activity
In the studies described hereinafter, the 26-residue peptide having the sequence Ac-KWKSFLKTFKS-AVKTVLHTALKAISS-amide (V681, SEQ ID NO:1) was utilized as the framework to study the effects of peptide hydrophobicity/hydrophilicity, amphipathicity and helicity by one or more amino acid substitutions in the center of the polar and nonpolar faces of the amphipathic helix on biological activities. These studies demonstrate i) the importance of the peptide self-association parameter in the de novo design of amphipathic α-helical antimicrobial peptides; ii) that disruption of α-helical structure in benign conditions by D-amino acid substitutions or substitutions of hydrophilic/charged L-amino acids on the non-polar face can dramatically alter specificity; and iii) that these substitutions enhance antimicrobial activity, decrease toxicity and improve antimicrobial specificity while maintaining broad spectrum activity for gram-negative and gram-positive bacteria.
Peptide V681, a 26-residue amphipathic antimicrobial peptide with a polar and non-polar face (28), was selected as the native parent peptide in this study (FIG. 1). Its polar face consists of 14 residues: six lysine residues, one histidine, four serines, and three threonines. In contrast, the non-polar face consists of 12 residues: three alanines, two valines, three leucines, two phenylalanines, one isoleucine and one tryptophan residue. In this study, we chose D-/L-amino acid substitution sites at the center of the hydrophobic face (position 13) and at the center of the hydrophilic face (position 11) of the helix, such that these substitution sites were also located in the center of the overall peptide sequence. This was based on our previous model peptide studies (26, 31, 34) that demonstrated that these central location substitutions had the greatest effect on peptide secondary structure. To study the effects of varying hydrophobicity/hydrophilicity on peptide biological activities, in the design of V681 analogs, five L-amino acids (Leu, Val, Ala, Ser, Lys) and Gly were selected out of the 20 natural amino acids as the substituting residues, representing a wide range of hydrophobicity. The hydrophobicity of these six amino acid residues decreases in the order Leu>Val>Ala>Gly>Ser>Lys (26). Based on the relative hydrophobicity of amino acid side-chains (26), leucine was used to replace the native valine on the non-polar face to increase peptide hydrophobicity and amphipathicity; alanine was selected to reduce peptide hydrophobicity/amphipathicity while maintaining high helicity; a hydrophilic amino acid, serine, was selected to decrease the hydrophobicity/amphipathicity of V681 in the non-polar face; positively-charged lysine was used to decrease further peptide hydrophobicity and amphipathicity. In contrast, the same amino acid substitutions on the polar face would have different effects on the alteration of hydrophobicity/hydrophilicity and amphipathicity, since the native amino acid residue is serine on the polar face of V681. As a result, on the polar face, leucine, valine and alanine were used to increase peptide hydrophobicity as well as decrease the amphipathicity of V681, while lysine was selected to increase peptide hydrophilicity and amphipathicity. Previously, Kondejewski et al. (20, 35) and Lee et al. (25) successfully utilized D-amino acid substitutions to dissociate the antimicrobial activity and hemolytic activity of gramicidin S analogs. In the present study, D-enantiomers of the five L-amino acid residues were also incorporated at the same positions on the non-polar/polar face of V681 to change not only peptide hydrophobicity/hydrophilicity and amphipathicity but, more importantly, disrupt peptide helical structure. Since glycine does not exhibit optical activity and has no side-chain, the Gly-substituted analog was used as a reference for diastereomeric peptide pairs.
Since most peptide analogs were made based on a single amino acid substitution in either the polar or nonpolar faces of V681, peptides were divided into two categories, N-peptides (nonpolar face substitutions) and P-peptides (polar face substitutions). Each peptide was named after the substituting amino acid residue, e.g., the peptide analog with L-leucine substitution on the nonpolar face of V681 is called NLL. It is important to note that since the L-valine of the non-polar face and L-serine of the polar face are the original amino acid residues in the V681 sequence (FIG. 1), peptide analogs NVL and PSL are the same peptide as V681.
A control peptide (peptide C) designed to exhibit negligible secondary structure, i.e., a random coil, was employed as a standard peptide for temperature profiling during RP-HPLC to monitor peptide dimerization. As shown in the previous study (29), this 18-residue peptide, with the sequence of Ac-ELEKGGLEGEKGGKELEK-amide (SEQ ID NO:26) clearly exhibited negligible secondary structure, even in the presence of the strong alpha-helix inducing properties of 50% trifluoroethanol (TFE) and at the low temperature of 5° C. ([θ]222=−3,950).
To determine the secondary structure of peptides in different environments, circular dichroism (CD) spectra of the peptide analogs were measured under physiologically related pH and ionic strength (100 mM KCl, 50 mM aq. PO4, pH 7 referred to as benign conditions) and also in 50% TFE to mimic the hydrophobic environment of the membrane. The native peptide, V681, exhibited low alpha-helical content in benign conditions, i.e., [θ]222 of −12,900 compared to −27,300 in 50% TFE, an increase in α-helical content from 45% to 94%, respectively (Table 3). From Table 3, in benign conditions, D-amino acid substituted peptides generally exhibited considerably less α-helical structure compared to their L-diastereomers. The negligible secondary structure characteristics of the D-peptides underlines the helix-disrupting properties of a single D-amino acid substitution, as demonstrated in our previous model α-helical peptide study (26). On the non-polar face, the native L-Val residue was critical in maintaining α-helical structure. Substitution of L-Val with less hydrophobic amino acids (L-Ala, Gly, L-Ser and L-Lys) dramatically decreased the α-helical structure (NVL, [θ]222 of −12,900 to values ranging from −1,300 to −3,450 for NSL, NKL, NG and NAL) (Table 3). Even the substitution with L-Ala, which is known to have the highest α-helical propensity of all 20 amino acids (34), could not stabilize the α-helical structure. This shows the importance of hydrophobicity on the non-polar face in maintaining the α-helical structure. In contrast, substitution with a more hydrophobic amino acid (L-Leu for L-Val) on the non-polar face significantly increased α-helical structure ([θ]222 for peptide NLL of −20,600 compared to peptide NVL of −12,900). It is noteworthy that, on the non-polar face, the magnitude of the helical content of L-peptides in benign buffer was related to the hydrophobicity of the substituting amino acids, i.e., NLL>NVL>NAL>NSL, NKL, again showing the importance of hydrophobicity on the non-polar face in maintaining the α-helical structure. Due to their helix-disruptive ability, on the non-polar face, the D-amino acid substitutions D-Val and D-Leu dramatically decreased α-helical structure in benign medium compared to their L-counterparts. However, whether L- or D-substitutions were made on the non-polar face, high helical structure could be induced by the hydrophobic environment of 50% TFE, a mimic of the membrane's hydrophobicity and α-helix inducing ability (Table 3). From Table 3, it is clear that, although D-amino acid substituted peptides were strongly induced into helical structure in 50% TFE, they were still generally less helical than the L-diastereomers, indicating that D-substitutions were still destabilizing of α-helical structure compared to their L-diastereomers in a hydrophobic environment.







TABLE 3







Circular dichroism data of V681 peptide analogs.










Benignb
50% TFEd












XLe
XDe
XLe
XDe















Peptidesa
[θ]222
% helixc
[θ]222
% helixc
[θ]222
% helixc
[θ]222
% helixc


















NL
−20,600
71
−7,350
25
−28,250
98
−25,750
89


NVf
−12,900
45
−2,800
10
−27,300
94
−26,000
90


NA
−3,450
12
−2,850
10
−28,950
100
−24,650
85


NS
−1,300
4
−1,700
6
−27,550
95
−22,200
77


NK
−1,450
5
−2,000
7
−26,250
91
−23,600
82


NG
−2,250
8


−24,350
84




PL
−10,850
37
−2,950
10
−28,550
99
−26,100
90


PA
−13,600
47
−3,050
11
−27,600
95
−27,300
94


PSf
−12,900
45
−2,800
10
−27,300
94
−26,000
90


PV
−7,550
26
−2,400
8
−23,050
80
−20,800
72


PK
−5,950
21
−2,500
9
−27,350
94
−27,800
96


PG
−4,550
16


−25,950
90





aPeptides are ordered by relative hydrophobicity to the native analog V681 at 5° C. N denotes non-polar face; P denotes polar face (FIG. 1)


bThe mean residue molar ellipticities, [θ]222, (deg · cm2 · dmol−1) at wavelength 222 nm were measured at 25° C. in benign buffer (100 mM KCl, 50 mM PO4 pH 7.0).


cThe helical content (in percentage) of a peptide relative to the molar ellipticity value of the peptide NAL in 50% trifluoroethanol (TFE).


dThe mean residue molar ellipticities (deg · cm2 · dmol−1) at wavelength 222 nm were measured at 25° C. in the benign buffer diluted 1:1 (v/v) with trifluoroethanol (TFE).


eXL and XD denote the L- and D-substitutions, respectively.


fNVL and PSL are the same peptide, which is the native peptide V681.






In this study, the L-substitutions on the polar face in benign medium had dramatically different effects on α-helical structure than the same substitutions on the non-polar face. For example, NLL ([θ]222 of −20,600) differed from PLL ([θ]222−10,850), indicating that Leu stabilized α-helical structure on the non-polar face and destabilized α-helical structure on the polar face. Similarly, Val destabilized α-helical structure on the polar face; on the other hand, Ala and Ser destabilized helical structure on the non-polar face, whilst, Ala and Ser stabilized α-helical structure when substituted in the polar face, compared to the other amino acid substitutions. Taken together, even though Ala had the highest α-helical propensity of all amino acids (34), its α-helical propensity could not overcome the need for hydrophobicity on the non-polar face ([θ]222 for peptides NAL, −3,450 and NLL, −20,600); whereas, on the polar face, peptide PAL exhibited high helical structure in benign ([θ]222−13,600) in contrast to peptide PLL ([θ]222−10,850) (Table 3). It is noteworthy that Val and Leu substitutions on the polar face decreased the amphipathicity of the helix as well as increased the hydrophobicity; however, the lower helical content compared with the native PSL indicated that there should be a balance of amphipathicity and hydrophobicity to enhance the helical content. Similar to the substitutions on the non-polar face, all D-amino acid substitutions on the polar face were destabilizing to α-helical structure in benign medium; however, highly helical structure could be induced by adding 50% TFE. As shown in Table 3, non-polar face substitutions exhibited a greater range of molar ellipticity values in benign conditions than polar face analogs, demonstrating that the amino acid residues on the non-polar face of the helix played a more important role in peptide secondary structure than those on the polar face. As expected, Gly was destabilizing to α-helical structure whether on the non-polar or polar face due to its low α-helical propensity (34).
FIG. 2 shows the CD spectra of the most and the least hydrophobic substitutions on the non-polar face. In benign conditions, peptide NLD showed much less helical structure than NLL due to the helix-destabilizing ability of the D-amino acid; whilst, in 50% TFE, both peptides could be induced to a fully helical structure (FIG. 2, Panel A). In contrast, in benign condition, peptides NKL and NKD were random coils, due to the combined effects of decreasing hydrophobicity and amphipathicity by replacing the native L-Val to D-/L-Lys on the non-polar face; again, in 50% TFE, both of them were induced into highly helical structures, albeit that peptide NKL demonstrated slightly more helical content than peptide NKD.
Next, we prepared the enantiomeric peptides of V681 and analogs NKL and NAD. Peptides V681 and NKL contain all L-amino acids and D-V681 and D-NKD contain all D-amino acids. In the case of NAD and D-NAL, position 13 is D-alanine and L-alanine, respectively (Table 1). Thus, D-V681, D-NKD and D-NAL are opposite in stereochemistry to the corresponding L-peptides, V681, NKL and NAD, respectively. A control peptide C designed to exhibit negligible secondary structure, i.e., a random coil, was employed as a standard peptide for temperature profiling during RP-HPLC to monitor peptide dimerization (53, 19, 29).
To determine the secondary structure of the D-enantiomeric peptides in different environments, CD spectra of the peptide analogs were measured under benign conditions (100 mM KCl, 50 mM KH2PO4/K2HPO4, pH 7.4, referred to as KP buffer) and also in 50% trifluoroethanol (TFE) to mimic the hydrophobic environment of the membrane. As shown in FIG. 3, the parent peptide, V681, was only partially helical in KP buffer; peptides NKL and NAD exhibited negligible secondary structure in KP buffer due to disruption of the non-polar face of the helix by introducing a hydrophilic L-lysine residue into peptide NKL or a helix-disruptive D-alanine residue into peptide NAD. However, in the presence of 50% TFE, all three L-peptides were fully folded α-helical structures with similar ellipticities and helicity (Table 4). As expected, the D-peptides showed spectra that were exact mirror images compared to their L-enantiomers, with ellipticities equivalent but of opposite sign both in benign KP buffer and in 50% TFE (Table 4).







TABLE 4







Biophysical data of peptide analogs.










Hydro-




phobicityb














tR5
tR80
Benign
50% TFE















Peptidea
(min)
(min)
[θ]222c
% helixd
[θ]222c
% helixd
PAe

















V681
96.6
88.8
−13000
46
−27950
99
7.2


D-V681
96.6
88.8
13050
46
28100
100
7.2


NAD
81.2
73.2
−4000
14
−25000
89
4.1


D-NAL
81.2
73.2
4000
14
25050
89
4.1


NKL
74.9
64.7
−1400
5
−27000
96
2.1


D-NKD
74.9
64.7
1500
5
26950
96
2.1





Peptide sequences are shown in Table 1.


Peptides are ordered by decreasing retention time (tR) in RP-HPLC at pH 2 at temperatures of 5° C. and 80° C. which is a measure of overall hydrophobicity.


The mean residue molar ellipticities, [θ]222, (deg · cm2 · dmol−1) at wavelength 222 nm were measured at 5° C. in benign conditions (100 mM KCl, 50 mM PO4 pH 7.4) or in benign buffer containing 50% TFE by circular dichroism spectroscopy. The negative values in molar ellipticity denote the left-handed helices and the positive values denote the right-handed helices.


The helical content (in percentage) of a peptide relative to the molar ellipticity value of the peptide D-V681 in the presence of 50% trifluoroethanol (TFE). PA denotes the dimerization parameter of each peptide during the RP-HPLC temperature profiling, which is the maximal retention time difference of ((tRt − tR5 for peptide analogs) − (tRt − tR5 for control peptide C)) within the temperature range, and (tRt − tR5) is the retention time difference of a peptide at a specific temperature (t) compared with that at 5° C.






We next used temperature profiling during RP-HPLC to determine the self-association ability of the various analogs of V681 which would occur through interaction of the non-polar faces of these amphipathic α-helices. Using model amphipathic α-helical peptides with all 20 amino acid substitutions in the center of the non-polar face, we showed previously that the model amphipathic peptides were maximally induced into an α-helical structure in 40% TFE and that the stability of the α-helix during temperature denaturation was dependent on the substitution (26). In order to investigate the stability of V681 in a hydrophobic environment, we carried out a temperature denaturation study in solution, as monitored by circular dichroism spectroscopy. We used 50% aqueous TFE in 0.05% TFA to mimic the hydrophobic conditions in the reversed-phase column since the hydrophobic environment of a reversed-phase column (hydrophobic stationary phase and the hydrophobic organic solvent in the mobile phase) could induce α-helical structure in a similar manner to TFE. FIG. 4, panel A shows the change of V681 helical conformation over the temperature range from 5° C. to 80° C. in the hydrophobic medium. At 5° C., 50% TFE induced full α-helical structure of V681. During the temperature denaturation, the helical content of V681 decreased with increasing temperature but even at 80° C. V681 remained significantly α-helical. FIG. 4, panel B shows the stability profile of V681 with a transition temperature Tm of 79.3° C., where Tm is defined as the temperature when 50% of α-helical structure is denatured compared with the fully folded conformation of the peptide in 50% TFE at 5° C. These data support the view, that during temperature profiling in RP-HPLC, the peptides are fully helical at low temperatures such as 5° C. and can remain in the α-helical conformation at 80° C. in solution during partitioning in RP-HPLC. In addition, due to their hydrophobic preferred binding domains, the peptides will remain α-helical when bound to the hydrophobic matrix. Overall, these results indicate that V681 is a very stable α-helical peptide in a hydrophobic environment, whether it is in solution (such as 50% TFE), under the conditions of RP-HPLC or in the hydrophobic environment of the membrane.
It is well documented that the formation of a hydrophobic binding domain due to peptide secondary structure can affect peptide interactions with reversed-phase matrices, this effect having been observed especially for amphipathic α-helical peptides (26, 36-39). Indeed, Zhou et al. (39) clearly demonstrated that, because of this preferred binding domain, amphipathic α-helical peptides are considerably more retentive than non-amphipathic peptides of the same amino acid composition. In addition, the chromatography conditions characteristic of RP-HPLC (hydrophobic stationary phase, nonpolar eluting solvent) are able to induce and stabilize helical structure in potentially helical polypeptides (39-41) in a manner similar to that of the helix-inducing solvent TFE. From FIG. 1, it can be seen that the substitution site at position 13, in the center of the nonpolar face of the helix, ensures a maximal effect on the intimate interaction of the substituting side-chain with the reversed-phase stationary phase; thus, any differences in effective hydrophobicity via amino acid substitutions in the preferred binding domain can be readily monitored through consequent differences in RP-HPLC retention time.
The retention time data for the peptides is shown in Table 5 which records retention times at 5° C., the maximal retention times and retention times at 80° C. during the temperature profiling. Temperatures of 5° C. and 80° C. were the lower and upper temperature limits of temperature profiling in RP-HPLC, representing dimerization of the peptides at 5° C. and the monomerization of peptides at 80° C. due to dissociation of the dimers. The maximal retention times represent the threshold points at which peptides transform from dimeric to monomeric form. The retention profiles from 5-80° C. are shown in FIG. 5. Among the non-polar face substituted peptides, peptides with more hydrophobic substitutions (whether L- or D-amino acid substitutions) were more retained during RP-HPLC, i.e., peptides were eluted in the order of Lys, Gly, Ser, Ala, Val and Leu (Table 5). In addition, on the non-polar face, the L-analogs were always more retained than the D-diastereomers (Table 5, FIG. 5). Since the aforementioned preferred binding domain of amphipathic helices is actually the non-polar face of the helix, D-peptides had a smaller preferred binding domain compared with L-diastereomers, due to the helix disruptive ability of D-amino acids, resulting in lower retention times during RP-HPLC. In contrast, on the polar face, the elution order of peptides was not correlated with the order of amino acid side-chain hydrophobicity, e.g., PAL and PSL were more retained than PVL (Table 5); PSD was the most retained peptide among the D-amino acid substituted analogs on the polar face (Table 5). Indeed, on the polar face, peptides PLL and PAL, with the replacement of L-Ser by L-Leu or L-Ala, had increased overall hydrophobicity as revealed by higher retention times compared with V681.
Although amino acid L-Val is much more hydrophobic than L-Ser, the observation that peptide PVL was less retained than the native peptide V681 (with L-Ser at position 11 of the polar face) could be attributed to the helix-disrupting characteristics of the β-branched Val residue (also see Table 3). In contrast, at 80° C., PVL became better retained than PSL. Due to the unfolding of the helical structure at high temperature, the side-chain hydrophobicity of the substituting amino acid in the peptide plays a more important role in the overall hydrophobicity. In a similar manner to the non-polar face substituted peptides, peptides with D-amino acids substituted into the polar face were dramatically less retained than their L-diastereomers. Due to the effect of the preferred binding domain, peptides with substitutions on the non-polar face had a greater retention time range than those with polar face substitutions, e.g., 11.31 min for the L-peptides with non-polar face substitutions versus 2.40 min for the L-peptides with polar face substitutions at 5° C., and 11.05 min versus 3.27 min for the D-peptides with non-polar or polar face substitutions, respectively, at 5° C. (Table 5).
The ability of the D-peptides to self-associate was determined by RP-HPLC temperature profiling. FIG. 8A shows the change in RP-HPLC retention times of the three pairs of enantiomers and the control peptide C over a temperature range of 5° C. to 80° C. As expected, L- and D-peptide enantiomers were totally inseparable over this temperature range, since each pair of peptides is identical in sequence and must adopt identical conformations on interacting with the reversed-phase matrix, whether in an all-L- or all-D-conformation. RP-HPLC retention behavior has been frequently utilized to represent overall peptide hydrophobicity (53, 26). In the present study, the hydrophobicity of the three peptide pairs is in the order V681/D-V681>NAD/D-NAL>NKL/D-NKD (Table 4), which agrees with the change in hydrophobicity of the substitutions at position 13 in order of the most hydrophobic to the least hydrophobic amino acid residue (Val in V681>Ala in NA>Lys in NK) (54). FIG. 8B shows the retention behavior of the peptides after normalization of the retention times to the corresponding retention time at 5° C. in order to highlight differences in the elution behavior of peptides as the temperature is increased from 5° C. to 80° C. For example, the retention times of peptides V681/D-V681 increase with increasing temperature (up to  ̃30° C.) followed by a retention time decrease with a further temperature increase. Such a temperature profile is characteristic of a peptide exhibiting self-association (53, 29, 19). As shown in FIG. 8C, the peptide self-association parameter, PA, represents the maximum change in peptide retention time relative to the random coil peptide C. Since peptide C is a monomeric random coil peptide in both aqueous and hydrophobic media, its retention behavior over the temperature range 5° C. to 80° C. represents only general temperature effects on peptide retention behavior, i.e., a linear decrease in peptide retention time with increasing temperature due to greater solute diffusivity and enhanced mass transfer between the stationary and mobile phases at higher temperatures (55). Thus, after normalization to the retention times of peptide C, the retention behavior of the peptides represents only peptide self-association ability. Note that the higher the PA value, the greater the self-association ability. The order of peptide self-association ability of the three pairs of peptide enantiomers is identical to the order of peptide hydrophobicity, i.e., V681/D-V681 have the highest dimerization ability in solution among the three pairs of peptide enantiomers (PA=7.2, Table 4); in contrast, NAD/D-NAL showed a weaker ability to self-associate when compared to V681/D-V681 (PA=4.1, Table 4); NKL/D-NKD exhibited the lowest dimerization ability (PA=2.1, Table 4). From Table 4, it is also clear that the peptide retention times at 80° C. are dramatically lower than those at 5° C. Apart from the decrease in retention time due to the general temperature effects noted above, unraveling of the α-helix will also occur with increasing temperature, resulting in the loss of the non-polar face of the amphipathic α-helical peptides and, hence, reduced retention times as the peptides become increasingly random coils.







TABLE 5







Relative hydrophobicity and association ability of peptide analogs


during RP-HPLC temperature profiling.










tR (min)b














Peptidesa
5° C.
Max
80° C.
5° C.
80° C.
PA (min)d












Non-polare
ΔtR (X-NVL) (min)c

















NLL
48.16
50.45
47.02
0.06
1.19
4.22


NVLf
48.10
49.99
45.83
0
0
3.63


NAL
43.94
44.88
41.38
−4.16
−4.45
2.59


NSL
40.72
41.08
37.62
−7.38
−8.21
1.82


NKL
36.85
36.91
33.22
−11.25
−12.61
1.10


NG
39.96
40.22
36.74
−8.14
−9.09
1.64


NLD
45.10
46.37
43.03
−3.00
−2.80
3.02


NVD
42.55
43.43
40.15
−5.55
−5.68
2.63


NAD
40.49
41.01
38.00
−7.61
−7.83
2.19


NSD
37.02
37.12
34.08
−11.08
−11.75
1.46


NKD
34.05
34.05
30.96
−14.05
−14.87
1.10












Polare
ΔtR (X-PSL) (min)c

















PLL
48.78
51.23
47.51
0.68
1.68
4.33


PAL
48.25
50.57
46.63
0.15
0.80
4.15


PSLf
48.10
49.99
45.83
0
0
3.63


PVL
47.83
49.93
46.18
−0.27
0.35
3.91


PKL
46.38
47.90
43.89
−1.72
−1.94
3.17


PG
45.86
47.09
43.07
−2.24
−2.76
2.82


PSD
45.47
46.60
42.59
−2.63
−3.24
2.73


PAD
45.19
46.36
42.57
−2.91
−3.26
2.82


PLD
44.73
45.85
42.14
−3.37
−3.69
2.82


PVD
42.96
43.83
40.51
−5.14
−5.32
2.54


PKD
42.20
42.87
39.29
−5.90
−6.54
2.23


Cg
22.74
—
18.64
—
—
—





aPeptides are ordered by relative hydrophobicity to the native L-Val substituted analog on the non-polar face and L-Ser substituted analog on the polar face.


bdenotes the retention times at 5° C., the maximal retention times and the retention times at 80° C. during the temperature profiling.


cdenotes the difference of retention time relative to that of the native peptide V681 (NVL for the non-polar face substitutions and PSL for the polar face substitutions), representing the relative hydrophobicity of the peptide analogs.


dPA denotes the association parameter of each peptide during the RP-HPLC temperature profiling, which is the maximal retention time difference of ((tRt − tR5 for peptide analogs) − (tRt − tR5 for control peptide C)) within the temperature range, and (tRt − tR5) is the retention time difference of a peptide at a specific temperature (t) compared with that at 5° C.


edenotes the amino acid substituted on either the non-polar face (N) or the polar face (P) of the amphipathic native peptide V681 (see FIG. 1).


fNVL and PSL are the same peptide, which is the native peptide V681.


gPeptide C is a random coil control used to calculate PA values, see footnote d.






Elution times during RP-HPLC have frequently been utilized as a measure of relative hydrophobicity of peptide analogs (26, 31). In the current study, peptide analogs differed only by a single amino acid substitution on either the non-polar face or the polar face of V681; thus, the retention time data in Table 5 can be considered to reflect the hydrophobicity difference between peptide analogs. In order to more easily visualize the variation in hydrophobicity of the peptide analogs, the retention time data in Table 5 were normalized relative to that of the native peptide V681 at 5° C. and 80° C., respectively. Hydrophobicity relative to the native peptide V681 indicates an increase or decrease of the apparent peptide hydrophobicity with the different amino acid substitutions on the polar or non-polar face. Again, from Table 5 and FIG. 5, for non-polar face substituted peptides, there was a wide range of peptide hydrophobicity in the order L-Leu>L-Val>L-Ala>L-Ser>Gly>L-Lys at both 5° C. and 80° C. On both the non-polar and polar faces, the relative hydrophobicities of the D-peptides was always less than their L-diastereomers, indicating the helix-disrupting characteristic of D-amino acids also leads to disruption of the preferred binding domain of the helices. On both non-polar and polar faces, peptides exhibited a greater retention time range at 80° C. than at 5° C., also indicating that, due to the unfolding of the helical structures at 80° C., the side-chain hydrophobicity of the substituted amino acids played a more essential role in determining the overall hydrophobicity of the peptide analogs.
The hydrophobicity/hydrophilicity effects of substitutions on the non-polar face relative to the native peptide V681 were large. For example, NVL to NAL, to NSL, and to NKL resulted in decreases in hydrophobicity of −4.45, −8.21 and −12.61 min at 80° C., respectively (Table 5). In fact, the same substitutions, i.e., PVL to PAL, to PSL, and to PKL, resulted in overall hydrophobicity changes of the peptide by +0.45, −0.35 and −2.29 min at 80° C., respectively. This indicates that the polar face substitutions affected overall hydrophobicity of the peptide in a minor way relative to substitutions on the non-polar face. In fact, the effect was of 10 times less for Ala, >20 times less for Ser and >5 times less for Lys.
Since its introduction, the technique of RP-HPLC temperature profiling has been applied on several types of molecules, including cyclic β-sheet peptides (30), monomeric α-helices and α-helices that dimerize (29), as well as α-helices that dimerize to form coiled-coils (42). Although peptides are eluted from a reversed-phase column mainly by an adsorption/desorption mechanism (43), even a peptide strongly bound to a hydrophobic stationary phase will partition between the matrix and the mobile phase when the acetonitrile content becomes high enough during gradient elution. The proposed mechanism of action for temperature profiling of α-helical peptides in RP-HPLC has been explained in detail by Mant, et al. (29). In summary, the mechanism is based on four assumptions: (i) at low temperature, just as an amphipathic α-helical peptide is able to dimerize in aqueous solution (through its hydrophobic, nonpolar face), it will dimerize in solution during partitioning in reversed-phase chromatography; (ii) at higher temperatures, the monomer-dimer equilibrium favors the monomer as the dimer is disrupted; (iii) at sufficiently high temperatures, only monomer is present in solution; and (iv) peptide is always bound in its monomeric helical form to the hydrophobic stationary phase, i.e., the dimer can only be present in solution and disruption of the dimer is required for rebinding to the RP-HPLC matrix.
It is well accepted that the amphipathicity of antimicrobial peptides is necessary for their mechanism of action, since the positively-charged polar face will help the molecules reach the biomembrane through electrostatic interaction with the negatively-charged head groups of phospholipids, and then the nonpolar face of the peptides will allow insertion into the membrane through hydrophobic interactions, causing increased permeability and loss of barrier function of target cells (6, 7). Thus, we believe that peptide self-association (i.e., the ability to dimerize) in aqueous solution is a very important parameter to understand antimicrobial activity. If the self-association ability of a peptide in aqueous media is too strong (forming dimers and burying the non-polar face), it could decrease the ability of the peptide to dissociate and penetrate into the biomembrane and to kill target cells.
FIG. 5 shows the temperature profiling of all L-/D-amino acid substituted peptide analogs during RP-HPLC from 5° C. and 80° C. As mentioned above, the dimerization is temperature-dependent. At low temperatures, peptides exist in a dimer-monomer equilibrium during RP-HPLC partitioning, with the dimeric unbound state favored and dissociation required for rebinding; thus, the retention times are relatively low. With the increase of temperature, equilibrium is shifted toward the monomeric form in solution due to the disruption of the dimer. The higher solution concentration of monomer during partitioning increases the on-rate for the bound state, and the retention time therefore increases. It should be noted that the increased temperature also introduces other general effects on retention time because of lower mobile phase viscosity and a significant increase in mass transfer between the stationary phase and mobile phase. These effects decrease retention time with increasing temperature in a linear fashion, as shown for the random coil control peptide C (FIG. 5). Conversely, for the dimerized peptides, at a given temperature dimers are disrupted and converted to monomers and the retention time reaches the maximal value. Above this critical temperature, one will observe a decrease in retention time with increasing temperature because of the low mobile phase viscosity and increase in mass transfer. In addition, the above described temperature-induced conformational changes, as monitored by CD, may also have an impact by decreasing the retention time with increasing temperature, largely due to the destabilization of peptide α-helical structure and loss of preferred binding domain at high temperatures. To eliminate these general effects during RP-HPLC, the data from FIG. 5 were normalized relative to the temperature profile of the random coil peptide standard C, and normalized to the retention time at 5° C., the latter of which is presented as a dotted line in FIG. 6.
It was observed that the peptide analogs in this study showed dramatic varying dimerization ability in solution (FIG. 6). The maximal values of the change of retention times ((tRt−tR5 for peptide)−(tRt−tR5 for C)) in FIG. 6 were defined as the peptide association parameter (PA) to quantify the association ability of peptide analogs in solution (Table 5). As seen from the data in Table 5, peptides with higher relative hydrophobicity generally showed stronger self-association ability in solution. The PA values of the peptide with non-polar face substitutions were of the same order as their relative hydrophobicity, indicating that the hydrophobicity on the hydrophobic face of the amphipathic helix was essential during dimerization, since the dimers are formed by the binding together of the non-polar faces of two amphipathic molecules. In contrast, the different relationship between PA and the relative hydrophobicity of the peptides with polar face substitutions demonstrated that the hydrophobicity on the polar face of the helices plays a less important role in peptide association. Generally speaking, the PA values of L-peptides were significantly greater than those of their D-diastereomers, indicating the importance of helical structure during dimerization (Table 5). In Table 5, in most cases, the peptides with polar face substitutions had greater PA values than the corresponding peptide analogs with the same amino acid substitutions on the non-polar face. This is exactly what one would expect since polar face substitutions have little effect on the preferred dimerization domain, whereas non-polar face substitutions would dramatically affect the hydrophobicity and dimerization ability of the peptide.
Amphipathicity of the L-amino acid substituted peptides was determined by the calculation of hydrophobic moment (32) using the software package Jemboss version 1.2.1 (33), modified to include the hydrophobicity scale determined in our laboratory (see the Examples section for details) (Table 6). Peptide amphipathicity, for the non-polar face substitutions, was directly correlated with side-chain hydrophobicity of the substituted amino acid residue, i.e., the more hydrophobic the residue the higher the amphipathicity (values of 6.70 and 5.60 for NLL and NKL, respectively); in contrast, on the polar face, peptide amphipathicity was inversely correlated with side-chain hydrophobicity of the substituted amino acid residue, i.e., the more hydrophobic the residue, the lower the amphipathicity (compare PKL and PLL with amphipathicity values of 6.62 and 5.45, respectively, Table 6).
The native sequence, V681 was very amphipathic with a value of 6.35. To place this value in perspective, the sequence of V681 can be shuffled to obtain an amphipathic value of 0.96 (KHAVIKWSIKSSVKFKISTAFKATTI, SEQ ID NO: 41) or a maximum value of 8.10 for the sequence of HWSKLLKSFTKALKKFAKAITSVVST (SEQ ID NO:42). The range of amphipathicity values achieved by single substitutions on the polar and non-polar faces varied from a low of 5.45 for PLL to a high of 6.70 for NLL (Table 6). Even though single substitutions changed the amphipathicity, all the analogs remained very amphipathic, e.g., even with a lysine substitution on the non-polar face, NKL has a value of 5.60.







TABLE 6







Amphipathicity of peptide analogs.












Peptide
Amphipathicitya
Peptide
Amphipathicitya






NLL
6.70
PLL
5.45



NVLb
6.35
PVL
5.82



NAL
5.98
PAL
6.21



NG
5.85
PG
6.35



NSL
5.85
PSLb
6.35



NKL
5.60
PKL
6.62





Amphipathicity was determined by the calculation of hydrophobic moment (31) using hydrophobicity coefficients determined by reversed-phase chromatography (see Materials and Methods for details).


Peptides NVL and PSL are the same peptide as V681.






Concerning the mechanism of action of antimicrobial peptides, many models have been proposed, among which the “barrel-stave” mechanism and the “carpet” model are two (44). In brief, the “barrel-stave” mechanism describes the formation of transmembrane channels/pores by bundles of amphipathic α-helices, as their hydrophobic surfaces interact with the lipid core of the membrane and the hydrophilic surfaces point inward, producing an aqueous pore (45); in contrast, the “carpet” model was proposed for the first time to describe the mechanism of action of dermaseptin S (46), describing the contact of antimicrobial peptides with the phospholipid head group throughout the entire process of membrane permeation which occurs only if there is a high local concentration of membrane-bound peptide. The major difference between the two mechanisms is, in the carpet model, peptides lie at the interface with their hydrophobic surface interacting with the hydrophobic component of the lipids but are not in the hydrophobic core of the membrane, and neither do they assemble the aqueous pore with their hydrophilic faces. A NMR study has shown that the cyclic β-sheet peptide analog of gramicidin S lays in the interface region parallel with the membrane where its hydrophobic surface interacts with the hydrophobic fatty acyl chains and the positively charged residues can still interact with the negatively charged head groups of the phospholipids (47).
Whichever the mechanism, the prerequisite step is the attraction of the peptide molecule to the membrane, followed by insertion into the bilayer. If peptide molecules self-associate in aqueous solution, peptides with lower self-associating ability in an aqueous medium can more easily penetrate into the lipid membrane. From Table 5 and Table 6, peptides with higher relative hydrophobicity on their non-polar face created higher amphipathicity and generally showed stronger self-associating ability in solution; in contrast, for peptides with polar face substitutions, increasing hydrophobicity lowers amphipathicity yet the peptides still strongly self-associate, which indicates that peptide amphipathicity plays a less important role in peptide self-association when changes in amphipathicity are created on the polar face. In addition, self-associating ability is correlated with the secondary structure of peptides, i.e., in this study, disrupting the peptide helical structure by replacing the L-amino acid with its D-amino acid counterpart decreases the PA values (Table 4 and Table 5).
The hemolytic activity of the peptides against human erythrocytes was determined as a major measure of peptide toxicity toward higher eukaryotic cells. As mentioned before, the native peptide V681 (also named as NVL or PSL) had strong hemolytic activity, with a minimal hemolytic concentration (MHC value) of 15.6 μg/ml (Table 7). In this study, due to the alteration of hydrophobicity, amphipathicity and stability, the hemolytic activity of the best variants of peptide V681 was significantly decreased to no detectable activity, a >32 fold decrease for NKL (Table 7).
From Table 7, it is clear that, for the non-polar face substituted peptides, hemolytic activity was correlated with the side-chain hydrophobicity of the substituting amino acid residue, i.e., the more hydrophobic the substituting amino acid, the more hemolytic the peptide, consistent with our previous study on the β-sheet antimicrobial peptide gramicidin S (22). For example, the MHC of peptide NLL was 7.8 μg/ml; in contrast, the MHC was decreased, parallel with the reduction of hydrophobicity, to an undetectable level for peptide NKL. Peptide hydrophobicity and amphipathicity on the non-polar face were also correlated with peptide self-associating ability, thus peptides with less self-association in benign conditions also exhibited less hemolytic activity against eukaryotic cells. In contrast, for polar face substituted peptides, the relationships between self-association, hydrophobicity/amphipathicity and hemolytic activity were less clear. Of course, the hydrophobic non-polar face remained very similar when L-substitutions were made on the polar face; thus, dimerization and hydrophobicity of the non-polar face would be less affected and hemolytic activity would remain relatively strong.
In addition to hydrophobicity/amphipathicity, peptide helicity seemed to have an additional effect on hemolytic activity. In general, on both the non-polar and polar faces, D-amino acid substituted peptides were less hemolytic than their L-diastereomers. For example, NAL had a MHC value of 31.2 μg/ml compared to NAD with a value of 250 μg/ml, an 8-fold decrease in hemolytic activity. Similarly, PVL had a MHC value of 7.8 μg/ml compared to PVD with a value of 125 μg/ml, a 16-fold decrease in hemolytic activity (Table 7). This phenomenon generally correlated with peptide self-associating ability, since D-diastereomeric analogs exhibited weaker self-associating ability than L-analogs. Additionally, D-substitutions disrupt helicity which, in turn, disrupts hydrophobicity of the non-polar face. This result was also consistent with the data of Shai and coworkers (23, 24), who demonstrated that, through multiple D-amino acid substitutions, the helicity of peptides is substantially reduced leading to decreased hemolytic activity. Thus, peptide structure is important in the cytotoxicity towards mammalian cells although these disturbed helices can still maintain antibacterial activity.
As shown in Table 7, peptide analogs with non-polar face substitutions exhibited a greater range of hemolytic activity (7.8 μg/ml to not detectable) than the polar face substitutions (4 to 125 μg/ml), again indicating that the non-polar face of the helix may play a more essential role during the interaction with the biomembrane of normal cells. As expected, the peptides with the polar face substitutions showed stronger hemolytic activity than the peptides with the same amino acid substitutions on the non-polar face, which may be attributed to the different magnitude of the hydrophobicity change by the same amino acid substitutions on different sides of the amphipathic helix. Interestingly, in this study, all polar face substituted peptides except PLD, PVD and PKD showed stronger hemolysis of erythrocytes than V681; in contrast, on the non-polar face, only peptides NLD and NLL were more hemolytic than V681.
The antimicrobial activity of the peptides with either non-polar face or polar face amino acid substitutions against a range of gram-negative microorganisms is shown in Table 7. The geometric mean MIC values from 6 microbial strains in this table were calculated to provide an overall evaluation of antimicrobial activity against gram-negative bacteria. It is apparent that many peptide analogs showed considerable improvement in antimicrobial activity against gram-negative bacteria over the native peptide V681, e.g., peptides NKL and PKD exhibited 2.8-fold and 3.4-fold improvement on the average MIC value compared to V681, respectively (geometric mean comparison; Table 7). Generally, the peptide analogs have high activity against bacterial strains of E. coli (UB 1005 wt and DC2 abs), S. typhimurium C610 abs and P. aeruginosa H187 wt in this study (Table 7).
For gram-negative bacteria, disruption of peptide helicity out weighted other factors in the improvement of antimicrobial activity; i.e., in most cases, the peptides with D-amino acid substitutions showed better antimicrobial activity than L-diastereomers. The exceptions were peptides NSD and NKD. The reason for the low activity of peptides NSD and NKD was possibly the combined effects of the destabilization of the helix, the decrease of hydrophobicity on the non-polar face and the disruption of amphipathicity, highlighting the importance of maintaining a certain magnitude of hydrophobicity and amphipathicity on the non-polar face of the helix for biological activity, i.e., perhaps there is a combined threshold of helicity and hydrophobicity/amphipathicity required for biological activity of α-helical antimicrobial peptides. In this study, peptide self-associating ability (relative hydrophobicity) seemed to have no general relationship to MIC; however, interestingly, for peptides with L-hydrophobic amino acid substitutions (Leu, Val and Ala) in the polar and non-polar faces, the less hydrophobic the substituting amino acid, the more active the peptide against gram-negative bacteria.
Table 8 shows the antimicrobial activity of the peptides against gram-positive microorganisms. By introducing D-/L-amino acid substitutions, we improved the antimicrobial activity of peptide V681 against gram-positive bacteria by as much as 2.7-fold (geometric mean MIC values for V681 were 6.3 μg/ml compared to 2.3 μg/ml for PSD, Table 8). Compared with peptide V681, most of the peptide analogs with increased antimicrobial activity against gram-positive microorganisms were D-amino acid substituted peptides (6 D-peptides versus 1 L-peptide). It was surprising to observe that peptides with polar face substitutions showed an overall greater improvement in MIC than those with non-polar face substitutions. Generally speaking, increasing the hydrophobicity of the native peptide V681 by amino acid substitutions at either the polar or the non-polar face decreased the antimicrobial activity against Gram-positive bacteria, e.g., peptides NLL, PLL, PVL and PAL (Table 8). Amino acid substitutions of D-Ser and D-Lys on the non-polar face significantly weakened the activity, in a similar manner to the anti-Gram-negative activity, indicating again the importance of maintaining a certain magnitude of helicity, hydrophobicity/amphipathicity on the non-polar face of the helix for peptide Gram-positive antimicrobial activity.
Therapeutic index is a widely employed parameter to represent the specificity of antimicrobial reagents. It is calculated by the ratio of MHC (hemolytic activity) and MIC (antimicrobial activity); thus, larger values in therapeutic index indicate greater antimicrobial specificity. As mentioned above, the native peptide V681 is a peptide with good antimicrobial activity coupled with strong hemolytic activity; hence, its therapeutic index is low (1.8 and 2.5 for gram-negative and gram-positive bacteria, respectively) and comparable to general toxins like melittin. In this study, by altering peptide hydrophobicity/hydrophilicity, amphipathicity and helicity, we significantly increased the therapeutic index of peptide V681 against gram-negative bacteria by 90-fold (Table 7) and Gram-positive bacteria by 23-fold (Table 8). As indicated in Tables 7 and 8, there was a greater range of therapeutic indices for peptides with the non-polar face substitutions compared with the polar face substitutions, which was consistent with peptide self-association studies, indicating that the non-polar face of the helix may play a more important role in the mechanism of action.
Table 9 summarizes the data for these peptide analogs with improved therapeutic index values relative to the native peptide V681. From Table 3 and Table 9, it is clear that all peptides with improved therapeutic indices are those showing less stable helical structure in benign medium (either the D-amino acid substituted peptides or the hydrophilic amino acid substituted peptides on the non-polar face). The peptide with the best therapeutic index among all the analogs is NKL with a 90-fold improvement compared with V681 against Gram-negative bacteria; in contrast, peptide NAD is the analog with the broadest specificity against all the tested gram-negative and gram-positive microorganisms, having a 42-fold improvement in therapeutic index against gram-negative bacteria and a 23-fold improvement against gram-positive bacteria. It is noteworthy that the hemolytic activity of these two peptides was extremely weak; in addition, peptides NKL and NAD exhibited improved antimicrobial activity compared to peptide V681 against gram-negative bacteria and identical antimicrobial activity against gram-positive bacteria.
In order to evaluate the biological activities of the D-enantiomeric peptides, namely D-NAL and D-NKD, the hemolytic activity of the peptides against human erythrocytes was determined as the maximal peptide concentration that produces no hemolysis after 18 hours of incubation at 37° C. The parent peptide, V681, exhibited the strongest hemolytic activity with a value of 7.8 μg/ml, compared to peptides NKL and NAD (250.0 μg/ml and 31.3 μg/ml, respectively) (Table 10). The activity of the D-enantiomers was quantitatively equivalent to that of L-enantiomers.
In the studies described above (see Tables 5-7), the hemolytic activities of peptides V681, NAD and NKL were determined as 15.6 μg/ml, 250.0 μg/ml and greater than 250.0 μg/ml, respectively, following incubation for 12 hours at 37° C. instead of the 18 hours incubation used for the D-enantiomers. Hence, a hemolysis time study was carried out to investigate the extent of hemolysis during different periods of incubation and different peptide concentrations in order to explore the relationship between hemolysis and incubation time. As shown in FIG. 9, a hemolysis time study was carried out over 8 hours at peptide concentrations of 8, 16, 32, 64, 125, 250 and 500 μg/ml. The percent hemolysis of cells was determined spectrophotometrically by comparison with the complete hemolysis of cells in water. From FIG. 9, peptides V681, D-V681, NAD and D-NAL exhibited an increase in erythrocyte hemolysis with increasing incubation time at most peptide concentrations. Significantly, peptides NKL and D-NKD showed negligible (less than 10%) or no hemolysis against human red blood cells after 8 hours even at the extremely high peptide concentration of 500 μg/ml. From FIG. 9, it is clear that the enantiomeric peptide pair V681/D-V681 exhibit cell lysis to a significantly greater extent than the NAD/D-NAL peptide pair. Thus, 100% hemolysis was already apparent after just 1 hour incubation for V681 and D-V681 at a peptide concentration of 500 μg/ml, whilst this value was approximately 40% for peptides NAD and D-NAL. In addition, while a small increase in hemolysis was apparent for V681 and D-V681 at a peptide concentration of just 8 μg/ml, negligible hemolysis was seen for NAD and D-NAL at a peptide concentration of 32 μg/ml. It is interesting to note that for our lead compounds, peptides NAD/D-NAL and NKL/D-NKD, D-enantiomers generally exhibited slightly weaker hemolytic activity compared to L-enantiomers at most peptide concentrations, the only exception being NAD and D-NAL at 500 μg/ml, where the activity of the L-peptide is greater at less than 4 hours incubation but weaker from 4 hours onwards.
Pseudomonas aeruginosa strains used in this study are a diverse group of clinical isolates from different places in the world. Antibiotic susceptibility tests show that these Pseudomonas aeruginosa strains share similar susceptibility to most antibiotics except that there is about a 64-fold difference for the range of ciprofloxacin susceptibility (Vasil, M. L. et al unpublished data). Antimicrobial activities of peptide enantiomers against Pseudomonas aeruginosa strains are shown in Table 10. In general, the antimicrobial activity of L- and D-enantiomers against Pseudomonas aeruginosa varied within 4-fold. CP204, a Pseudomonas aeruginosa strain from cystic fibrosis patients, is apparently the most susceptible strain to these peptides with MIC values from 7.8 to 31.3 μg/ml. The geometric mean MIC values from six Pseudomonas aeruginosa strains were calculated to provide an overall evaluation of antimicrobial activity of these peptides against Pseudomonas aeruginosa. Fold improvement was calculated by comparing the geometric mean MIC value of each peptide to that of the parent peptide V681. It is clear that, in most cases, all-D-peptides exhibited slightly better antimicrobial activity than their L-enantiomers.
The therapeutic indices of the peptides against Pseudomonas aeruginosa are shown in Table 10. By replacing L-valine with D-alanine or L-lysine, we significantly increased the therapeutic index against Pseudomonas aeruginosa strains by 4.7 fold (peptide NAD) and 16.7 fold (peptide NKL). In addition, by making enantiomeric D-peptides, we further improved the therapeutic index against Pseudomonas aeruginosa by 7.3 fold (peptide D-NAL) and 26.7 fold (peptide D-NKD) as measured by the standard microtiter dilution method. Peptide D-NKD showed no hemolysis at 500 μg/ml after 8 hours in our time study (FIG. 9) which is a more stringent test of hemolytic activity. The hemolytic activities of V681 were not different when determined by the standard microtiter dilution method at 18 hours or by the time study at 8 hours using a peptide concentration of 500 μg/ml (Table 10 and FIG. 9). Thus, using a peptide concentration of 500 μg/ml, the MHC value of D-NKD increased the fold improvement of the therapeutic index compared to V681 to 53-fold. Our overall conclusion is that the key differences in biological activities lie in the much more dramatic variations in hemolytic activity (MHC values) since the differences in antimicrobial activity between the six peptides are relatively minor (Table 10). Thus, the dramatic increases in therapeutic indices arise from the difference in hemolytic activity.
Table 11 shows peptide antimicrobial activity and therapeutic indices against six different Gram-negative bacterium strains. It is clear to see that, in general, all-L-peptides have equivalent antimicrobial activity against Gram-negative bacteria compared to their D-enantiomers, since MIC values of L- and D-enantiomers are all within a 2-fold difference. In Table 11, geometric mean MIC was calculated to provide an overall view of antimicrobial activity of the peptides against Gram-negative bacteria and was also used to calculate the therapeutic index. Peptides NKL and D-NKD both show a 40-fold improvement in therapeutic index against Gram-negative bacteria compared to peptide V681 as measured by the standard microtiter dilution method. For this improvement in the therapeutic index of peptides against Gram-negative bacteria, peptide hemolytic activity is again the key factor. Using our most stringent test of hemolytic activity, the MHC value of 500 μg/ml for peptide D-NKD showed no hemolysis after 8 hours in our time study (FIG. 9) and the fold improvement of the therapeutic index compared to V681 was 80-fold.
The antimicrobial activity against Gram-positive bacteria and a fungus of L- and D-enantiomeric peptides is compared in Table 12. It is clear that our peptides were effective in killing the Gram-positive bacteria tested. The least sensitive Gram-positive bacterium to the enantiomeric peptides was E. faecalis. The effectiveness of the peptides to lyse cells of the fungus C. albicans was similar to E. faecalis. For Gram-positive bacteria and the fungus, D-peptides again generally showed the same or better antimicrobial activity than L-enantiomers. Although the geometric mean MIC values of peptides NKL/D-NKD were among the two lowest, due to the high MHC values (poor or no hemolytic activity), the therapeutic indices of NKL and D-NKD were the highest against Gram-positive bacteria and the fungus. Similar to that seen against Gram-negative bacteria, the therapeutic index of peptide D-NKD was increased 34.7-fold and 16.7-fold against Gram-positive bacteria and C. albicans, respectively, due to the poor or no hemolytic activity as measured by the standard microtiter dilution method. Using our most stringent test of hemolytic activity, the MHC value of 500 μg/ml for peptide D-NKD showed no hemolysis after 8 hours in our time study (FIG. 9) and the fold improvement of the therapeutic indices compared to V681 were 69- and 33-fold against Gram-negative bacteria and fungus, respectively.
Table 7 to Table 12.







TABLE 7





Antimicrobial (MIC) and hemolytic (MHC) activities of peptide analogs against gram-negative


bacteria and human red blood cells.






























aAntimicrobial activity (minimal inhibitory concentration) is given as the geometric mean of three sets of determinations.


bGM denotes the geometric mean of MIC values from all 6 microbial strains in this table.


cHemolytic activity (minimal hemolytic concentration) was deteremined on human red blood cells (hRBC). When no detectable hemolytic activity was observed at 250.0 μg/ml, a value of 500 μg/ml was used for calculation of the therapeutic index.


dTherapeutic index = MHC (μg/ml)/geometric mean of MIC (μg/ml). Larger values indicate greater antimicrobial specificity.


ewt denotes the wild type strain and abs denotes the antibiotics sensitive strain.


fNVL and PSL are the same peptide, which is the native peptide V681.


gThe boxed results show the two best peptides with broad spectrum activity in terms of the therapeutic index against both Gram-negative and Gram-positive bacteria.













TABLE 8





Antimicrobial (MIC) and hemolytic (MHC) activities of peptide analogs against gram-positive bacteria and


human red blood cells.






























aAntimicrobial activity (minimal inhibitory concentration) is given as the geometric mean of three sets of detereminations.


bGM denotes the genomic mean of MIC values from all 6 microbial strains in this table.


cHemolytic activity (minimal hemolytic concentration) was deteremined on human red blood cells (hRBC). When no detectable hemolytic activity was observed at 250.0 μg/ml, a value of 500 μg/ml was used for calculation of the therapeutic index.


dTherapeutic index = MHC (μg/ml)/geometric mean MIC (μg/ml). Larger values indicate greater antimicrobial specificity.


ewt denotes the wild type strain and methR denotes the methicillin-resistant strain.


fNVL and PSL are the same peptide, which is the native peptide V681.


gThe boxed results show the two best peptides with broad spectrum activity in terms of the therapeutic index against both Gram-negative and Gram-positive bacteria.













TABLE 9







Effect of amino acid substitutions on the biological activity of V681a.











Gram-negative

Gram-positive


















MICb

Thera-

MHCd

MICb

Thera-




(μg/

peutic

(μg/

(μg/

peutic



Peptide
ml)
Folde
indexc
Folde
ml)
Folde
ml)
Folde
indexc
Folde





V681
8.8
1.0
  1.8
 1.0
 15.6
 1.0
 6.3
1.0
 2.5
 1.0


NAL
3.8
2.3
  8.1
 4.5
 31.2
 2.0
 4.5
1.4
 6.9
 2.8


NG
4.1
2.1
 30.2
16.8
 125.0
 8.0
 7.4
0.9
16.8
 6.7


NSL
4.2
2.1
 30.1
16.7
 125.0
 8.0
 7.4
0.9
16.9
 6.8


NKLf










































NVD
3.3
2.7
 19.0
10.6
 62.5
 4.0
 2.8
2.3
22.7
 9.1


NADf








 







 







 

















NSD
6.3
1.4
 79.9
44.4
>250.0
32.1
16.0
0.4
31.3
12.5


NKD
7.7
1.1
 65.0
36.1
>250.0
32.1
18.7
0.3
26.8
10.7


PLD
5.0
1.8
  6.2
 3.4
 31.2
 2.0
 4.7
1.3
 6.7
 2.7


PVD
6.1
1.4
 20.5
11.4
 125.0
 8.0
 6.6
1.0
19.0
 7.6


PAD
4.3
2.0
  3.6
 2.0
 15.6
 1.0
 3.8
1.7
 4.1
 1.6


PSD
2.9
3.0
  5.3
 2.9
 15.6
 1.0
 2.3
2.7
 6.7
 2.7


PKD
2.6
3.4
 11.8
 6.6
 31.2
 2.0
 2.8
2.3
11.0
 4.4





aOnly the peptide analogs with a therapeutic index greater than V681 are included in this table.


bAntimicrobial activity (minimal inhibitory concentration) was given as the geometric mean data of Tables IV & V.


cTherapeutic index = MHC (in μg/ml)/MIC (in μg/ml). Larger values indicate greater antimicrobial specificity.


dHemolytic activity (minimal hemolytic concentration) was deteremined on human red blood cells (hRBC). When no detectable hemolytic activity was observed at 250.0 μg/ml, a value of 500 μg/ml was used for calculation of the therapeutic index and fold increased.


edenotes the fold improvement in activity compared with the corresponding data of the native peptide V681.


fThe boxed results show the two best peptides with broad spectrum activity in terms of the therapeutic index against both Gram-negative and Gram-positive bacteria.













TABLE 10







Hemolytic activities of peptides and MIC against Pseudomonas aeruginosa strains.











Hemolytic
Antimicrobial activity













activity
MIC (μg/ml)c

Therapeutic index



















Peptide
MHC (μg/ml)a
Foldb
PAO 1
WR 5
PAK
PA 14
M 2
CP 204
GMd
Folde
MHC/MICf
Foldg






















V681
7.8
1
15.6
62.5
31.3
62.5
15.6
15.6
27.8
1.0
0.3
1.0


D-V681
7.8
1
15.6
31.3
31.3
15.6
31.3
31.3
24.8
1.1
0.3
1.0


NAD
31.3
4
15.6
62.5
62.5
31.3
7.8
7.8
22.1
1.3
1.4
4.7


D-NAL
31.3
4
7.8
31.3
31.3
7.8
15.6
7.8
13.9
2.0
2.2
7.3


NKL
250.0
32
31.3
250.0
125.0
62.5
31.3
7.8
49.6
0.6
5.0
16.7 


D-NKD
250.0h
32
15.6
62.5
125.0
15.6
31.3
15.6
31.2
0.9
8.0
26.7 (53.4)h


Ciprofloxacini


4
1
4
8
8
64





aMHC denotes the maximal peptide concentration that produces no hemolysis after 18 hours in the standard microtiter dilution method.


bDenotes the fold decrease in hemolytic activity compared to the parent peptide V681.


cMIC is minimal inhibitory concentration that inhibited growth of six Pseudomonas aeruginosa strains. MIC is given based on three sets or more of determinations.


dDenotes the geometric mean of a diverse group of Pseudomonas aeruginosa clinical isolates.


eDenotes the fold improvement in antimicrobial activity (geometric mean data) compared to the parent peptide V681.


fTherapeutic index is the ratio of the MHC value (μg/ml) over the geometric mean MIC value (μg/ml). Large values indicate greater antimicrobial specificity.


gDenotes the fold improvement in therapeutic index compared to the parent peptide V681.


hIn the hemolysis time study, D-V13KD showed no hemolysis at 500 μg/ml at 8 hours, which would increase the fold improvement to 53.4 fold in the therapeutic index.


iRelative susceptibility of these Pseudomonas strains to ciprofloxacin with the number 1 denoting the most susceptible strain.













TABLE 11







Antimicrobial (MIC) and hemolytic (MHC) activities of peptide analogs against Gram-negative


bacteria and human red blood cells.










MICb (μg/ml)



















MHCa
E. coli
E. coli
St
St
Pa
Pa






(μg/ml)
C498
C500
C587
C610
H187
H188


Therapeutic indexf


















Peptides
hRBC
wtc
absc
wtc
absc
wtc
absc
GMd
Folde
MHC/MIC
Foldg





















V681
7.8
6.3
3.1
12.5
3.1
6.3
3.1
5.0
1.0
1.6
1.0


D-V681
7.8
6.3
3.1
12.5
6.3
6.3
6.3
6.3
0.8
1.2
0.8


NAD
31.3
3.1
1.6
12.5
3.1
3.1
1.6
3.1
1.6
10.1
6.3


D-NAL
31.3
3.1
3.1
12.5
3.1
3.1
3.1
3.9
1.3
8.0
5.0


NKL
250.0
3.1
3.1
6.3
3.1
6.3
3.1
3.9
1.3
64.1
40.1 


D-NKD
250.0h
3.1
3.1
6.3
3.1
6.3
3.1
3.9
1.3
64.1
40.1 (80.2)h





aHemolytic activity (maximal peptide concentration with no hemolysis after 18 hours) was determined on human red blood cells (hRBC).


bAntimicrobial activity (minimal inhibitory concentration) is from three sets of determinations.


cE. coli denotes Escherichia coli, St denotes Salmonella typhimurium, Pa denotes Pseudomonas aeruginosa, wt denotes the wild-type lab strain and abs denotes an antibiotic sensitive strain.


dGM denotes the geometric mean of MIC values from all 6 microbial strains in this table.


eDenotes fold improvement in the geometric mean of MIC compared to parent peptide V681.


fTherapeutic index = MHC (μg/ml)/geometric mean of MIC (μg/ml). Larger values indicate greater antimicrobial specificity.


gDenotes fold improvement in the therapeutic index compared to parent peptide V681.


hIn the hemolysis time study, D-V13KD showed no hemolysis at 500 μg/ml at 8 hours which would increase the fold improvement in the therapeutic index to 80.2 fold.













TABLE 12







Antimicrobial (MIC) and hemolytic (MHC) activities of peptide analogs against


Gram-positive bacteria, fungus and human red blood cells.










MICb (μg/ml)





















S.
S.
S.
B.
E.


Therapeutic

Therapeutic



MHCa
aureus
aureus
epidermidis
subtilis
faecalis
C. xerosis

indexe
MICb
indexf






















(μg/ml)
622
623
C621
C971
C625
C875


MHC/

(μg/ml)
MHC/



Peptides
hRBC
wtc
methRc
wtc
wtc
wtc
wtc
GMd
Foldd
MIC
Foldg
C. albicans
MIC
Foldg
























V681
7.8
3.1
6.3
6.3
3.1
6.3
3.1
4.4
1.0
1.8
1.0
12.5
0.6
1.0


D-V681
7.8
6.3
6.3
1.6
1.6
6.3
3.1
3.5
1.3
2.2
1.2
6.3
1.2
2.0


NAD
31.3
1.6
3.1
1.6
3.1
12.5
1.6
2.8
1.6
11.2
6.2
12.5
2.5
4.2


D-NAL
31.3
3.1
3.1
1.6
1.6
12.5
1.6
2.8
1.6
11.2
6.2
12.5
2.5
4.2


NKL
250.0
12.5
12.5
6.3
3.1
50.0
1.6
7.9
0.6
31.6
17.6
50.0
5.0
8.3


D-NKD
250.0h
6.3
6.3
3.1
1.6
12.5
1.6
4.0
1.1
62.5
34.7
25.0
10.0
16.7













(69.4)h


(33.4)h





aHemolytic activity (maximal peptide concentration with no hemolysis after 18 hours) was determined on human red blood cells (hRBC).


bAntimicrobial and antifungal activities (minimal inhibitory concentration) are from three sets of determinations.


cS. aureus denotes Staphylococcus aureus, S. epidermidis denotes Staphylococcus epidermidis, B. subtilis denotes Bacillus subtilis, E. faecalis denotes Enterococcus faecalis, C. xerosis denotes Corynebacterium xerosis, C. albicans denotes Candida albicans, wt denotes the wild type strain and methR denotes the methicillin-resistant clinical strain.


dGM denotes the geometric mean of MIC values from all 6 gram-positive microbial strains in this table. Fold denotes fold improvement in the geometric mean MIC compared to parent peptide V681.


eTherapeutic index = MHC (μg/ml)/geometric mean MIC (μg/ml). Larger values indicate greater antimicrobial specificity.


fDenotes the therapeutic index of the peptides against a fungus C. albicans.


gDenotes fold improvement in the therapeutic index compared to parent peptide V681.


hIn the hemolysis time study, D-V13KD showed no hemolysis at 500 μg/ml at 8 hours which would increase the fold improvement in the therapeutic index to 69.4 fold and 33.4 fold for Gram-positive bacteria and C. albicans, respectively.






FIG. 10 illustrates the stability of L- and D-enantiomeric peptides in the presence of trypsin at a molar ratio of 20,000:1 or 20 mM:1 μM (peptide:trypsin) at 37° C. The assay was carried out for 8 hours; however, only the stability of the peptides in the first 60 minutes is shown in FIG. 10, due to the reason that all three L-peptides were 100% digested by trypsin after 1 hour of incubation at 37° C. It is interesting to see that peptide V681 showed a slightly more resistance against trypsin than NKL and NAD; in contrast, NKL and NAD generally showed a similar trend of degradation in the presence of trypsin. All three peptides were 86-97% digested after 30 minutes. In sharp contrast, D-peptides were completely stable (no degradation) to trypsin even at a 10-fold higher molar concentration ratio of trypsin versus peptide (2 mM peptide:1 μM trypsin) for 8 hours.
As mentioned previously, the “barrel-stave” and the “carpet” mechanisms are the two main theories used to explain the mechanism of action of antimicrobial peptides. However, neither mechanism alone can fully explain the data in this study. For example, the hemolytic activity is correlated to the peptide hydrophobicity and amphipathicity on the non-polar face, which may be consistent with the “barrel-stave” mechanism, i.e., peptides interact with the hydrophobic core of the membrane by their non-polar face to form pores/channels. In contrast, the antimicrobial activity is not correlated with peptide hydrophobicity/amphipathicity, showing that the “barrel-stave” mechanism may not be suitable to explain the mechanism of antimicrobial action. Indeed, the “carpet” mechanism may best explain the interaction between the peptides and the bacterial membrane. Based on the above observations, we propose that both mechanisms are in operation for the peptides used in this study, i.e., the mechanism depends upon the difference in membrane composition between prokaryotic and eukaryotic cells. If the peptides form pores/channels in the hydrophobic core of the eukaryotic bilayer, they would cause the hemolysis of human red blood cells; in contrast, for prokaryotic cells, the peptides lyse cells in a detergent-like mechanism as described in the “carpet” mechanism.
Indeed, it is believed that the extent of interaction between peptide and biomembrane is dependent on the composition of lipid bilayer. For example, Liu, et al. (48-50) utilized a polyleucine-based α-helical transmembrane peptide to demonstrate that the peptide reduced the phase transition temperature to a greater extent in phosphatidylethanolamine (PE) bilayers than in phosphatidylcholine (PC) or phosphatidylglycerol (PG) bilayers, indicating a greater disruption of PE organization. The zwitterionic PE is the major lipid component in prokaryotic cell membranes and PC is the major lipid component in eukaryotic cell membranes (51, 52). In addition, although PE also exists in eukaryotic membranes, due to the asymmetry in lipid distribution, PE is mainly found in the inner leaflet of the bilayer while PC is mainly found in the outer leaflet of the eukaryotic bilayer. We draw the conclusion that the antimicrobial specificity of the antimicrobial α-helical peptides is a result of the composition differences of the lipid bilayer between eukaryotic and bacterial cells.
In support of this proposal, we have selected two examples from our study. The results for peptide NKL, the peptide with the highest therapeutic index against Gram-negative bacteria, can be explained using our combined model. For example, if hemolysis of eukaryotic cells requires insertion of the peptide into the hydrophobic core of the membrane, which depends on the composition of the bilayer, and interaction of the non-polar face of the amphipathic α-helix with the hydrophobic lipid environment, it seems reasonable to assume that disruption of the hydrophobic surface with the Lys substitution (NKL) would both disrupt dimerization of the peptide and its interaction with the hydrophobic lipid. Thus, the peptide is unable to penetrate the hydrophobic core of the membrane and unable to cause hemolysis. On the other hand, if the mechanism for prokaryotic cells allows the interaction of monomeric peptides with the phospholipid headgroups in the interface region, then no insertion into the hydrophobic core of the membrane is required for antimicrobial activity.
The biological activities of the D-enantiomeric peptides illustrated herein are consistent with the proposed model; each enantiomeric peptide pair has the same activities against prokaryotic and eukaryotic cell membranes supporting the prediction that the sole target for these antimicrobial peptides is the cell membrane. This model predicts that hemolysis of eukaryotic cells requires the peptides to be inserted into the hydrophobic core of the membrane, perpendicular to the membrane surface, and interaction of the non-polar face of the amphipathic α-helix with the hydrophobic lipid core of the bilayer. The peptide may thus form transmembrane channels/pores and the hydrophilic surfaces point inward, producing an aqueous pore (“barrel-stave” mechanism). In contrast, antimicrobial activity in prokaryotic cells, while maintaining specificity, requires the peptide to lie at the membrane interface parallel with the membrane surface and interaction of the non-polar face of the amphipathic α-helix with the hydrophobic component of the lipid and interaction of the positively charged residues with the negatively charged head groups of the phospholipid (“carpet” mechanism). What dictates the two different modes of interaction is the difference in lipid composition of prokaryotic and eukaryotic membranes. We refer to this mode of interaction of antimicrobial peptides which combines the above two mechanisms as a “membrane discrimination mechanism”.
Using this model, it is easy to understand why peptide NKL and D-NKD of the present study are non-hemolytic but at the same time possess excellent antimicrobial activity compared to the native sequence V681 or D-V681. Thus, the single substitution of Lys for Val at position 13 (NKL and D-NKD) in the center of the non-polar face disrupts the hydrophobic surface due to the presence of the positive charge, preventing the peptide from penetrating the bilayer as a transmembrane helix in eukaryotic cells. The peptide is then excluded from the bilayer and, hence, is non-hemolytic. In prokaryotic cells, the peptide is also excluded from penetrating the bilayer as a transmembrane helix but this is not required for excellent antimicrobial activity. Instead, the peptide can enter the interface region of the bilayer where disruption of the peptide hydrophobic surface by Lys can be tolerated and antimicrobial activity maintained.
In contrast, the observation that the antimicrobial activity of peptide NLL (with Leu at the substitution site) was worse than that of NKL, while its hemolytic activity was stronger (MIC values of 12.7 μg/ml for NLL versus 3.1 μg/ml for NKL against Gram-negative bacteria; hemolytic activity of 7.8 μg/ml for NLL versus no detectable hemolytic activity for NKL) can also be explained by our combined model. Thus, peptide NLL has a fully accessible non-polar face required for insertion into the bilayer and for interaction with the hydrophobic core of the membrane to form pores/channels (“barrel-stave” mechanism), while the hemolytic activity of peptide NLL is dramatically stronger than peptide NKL. On the other hand, due to the stronger tendency of peptide NLL to be inserted into the hydrophobic core of the membrane than peptide NKL, peptide NLL actually interacts less with the water/lipid interface of the bacterial membrane; hence, the antimicrobial activity is 4-fold weaker than the peptide NKL against Gram-negative bacteria. This supports the view that the “carpet” mechanism is essential for strong antimicrobial activity and if there is a preference by the peptide for penetration into the hydrophobic core of the bilayer, the antimicrobial activity will actually decrease.
The studies disclosed herein demonstrate that a high ability of a peptide to self-associate in solution correlates with weak antimicrobial activity and strong hemolytic activity of the peptides. Biological studies further show that strong hemolytic activity of the peptides generally correlates with high hydrophobicity, high amphipathicity and high helicity. In most cases, the D-amino acid substituted peptides possessed an enhanced average antimicrobial activity compared with L-diastereomers. The therapeutic index of V681 was improved 90-fold and 23-fold against gram-negative and gram-positive bacteria, respectively. Although the antimicrobial peptides exemplified are the analogs having five amino acid (L, V, A, S, K) substitutions at position 11 or 13 in the 26-residue peptide, V681, it is predicted that other substitutions such as ornithine, arginine, histidine or other positively charged residues at these sites would also improve antimicrobial activity of the peptides. It is further predicted that similar substitutions at position 16 or 17 of V681 would yield peptides with enhanced biological activity. Based on the studies disclosed herein, a person of ordinary skill in the art can design antimicrobial peptides with enhanced activities by simply replacing the central hydrophobic or hydrophilic amino acid residue on the nonpolar or the polar face of an amphipathic molecule with a series of selected D-/L-amino acids.
Significant features of two specific antimicrobial peptides generated from this study in structural terms are as follows. In the case of NKL, a positively-charged residue, lysine, is introduced in the center of the hydrophobic face. This substitution disrupts alpha-helical structure in benign medium, decreases dimerization, decreases toxicity to normal cells as measured by hemolytic activity, enhances antimicrobial activity and provides a 90-fold increase in the therapeutic index compared with the starting sequence against Gram-negative bacteria (substitution of starting material having Val 13 with a change to Lys 13). The therapeutic index is the ratio of hemolytic activity/antimicrobial activity. This same peptide has a 17-fold increase in the therapeutic index for Gram-positive bacteria.
In the case of NAD, a D-Ala residue is introduced into the center of the hydrophobic face. This disrupts alpha-helical structure, decreases dimerization, decreases toxicity to normal cells as measured by hemolytic activity, enhances antimicrobial activity and provides a 42-fold increase in the therapeutic index compared to the starting sequence against Gram-negative bacteria (substitution is Val 13 to D-Ala 13). This same peptide has a 23-fold increase in the therapeutic index for Gram-positive bacteria.
Alpha-helical antimicrobial peptides are amphipathic; If the self-association ability of a peptide (forming dimers by interaction of the two non-polar faces of two molecules) is too strong in aqueous media, it could decrease the ability of the peptide monomers to dissociate, pass through the cell wall of microorganisms and penetrate into the biomembranes to kill target cells. It is clearly demonstrated in the studies using the D-enantiomeric peptides that there is a direct correlation of the ability of peptides to dimerize and specificity is generated, that is, disruption of dimerization generates specificity between eukaryotic and prokaryotic cells. From Table 9, the PA values of peptides derived from their temperature profiling data (FIG. 8) reflect the ability of the amphipathic α-helices to associate/dimerize. Clearly, V681 and D-V681, due to their uniform non-polar faces, show the greatest ability to dimerize in aqueous solution and lowest specificity or the strongest ability to lyse human erythrocytes. This is consistent with the view that a peptide with a fully accessible non-polar face tends to form pores/channels in the membranes of eukaryotic cells. In the case of NAD and D-NAL, the introduction of D-Ala and L-Ala into all-L- and all-D-amino acid peptides, respectively, disrupts α-helical structure and, thus, lowers dimerization ability relative to V681 and D-V681 and improves specificity. The introduction of Lys into non-polar position 13 of NKL and D-NKD lowers this dimerization ability even further and improves specificity. Thus, the lack of ability of a peptide to dimerize, as exemplified by its PA value, is an excellent measure of the peptide's ability to be non-hemolytic concomitant with maintenance of sufficient hydrophobicity of the non-polar face to ensure antimicrobial activity. It is important to note that D-enantiomeric peptides exhibited the same self-association ability as their corresponding L-enantiomers; thus, similar biological activities can be expected. This is further supported by the fact that the hemolytic activity and antimicrobial activity of D-peptides against human red blood cells and microbial cells, respectively, were indeed quantitatively equivalent to those of the L-enantiomers. These results further demonstrate that there is no chiral selectivity by the membrane or other stereoselective interactions in the cytoplasm with respect to the hemolytic and antimicrobial activities.
Because of the different results on the hemolytic activity of peptide NAD shown in Tables 7 and 8, and Tables 10 and 11 (250 μg/ml after 12 hours versus 31.3 μg/ml after 18 hours, respectively), albeit using the standard microtiter dilution method (see Methods), it became apparent that an investigation of the relationship between hemolysis and time was required. It is noteworthy that there is no universal protocol of determination of hemolytic activity, which makes it difficult to compare data from different sources. For example, some researchers use 4 hours of incubation and take the minimal concentration of peptide to give 100% hemolysis as peptide hemolytic activity (28, 56); in contrast, some use 12 hours or longer (e.g., 18 hours used herein) of incubation and take the maximal concentration of peptide to give no hemolysis as peptide hemolytic activity (53, 57). Hence, the hemolysis time study is important to understand the process of erythrocyte lysis. It is clear that the degree of cell lysis is correlated with time, which may be the main reason for the different values of hemolytic activity of NAD in the two studies. Regardless, the hemolytic activity of each test peptide can readily be appreciated by a skilled artisan by comparing the value of the test peptide with that of the control peptide (V681) within a given study. Hence, we have established a stringent criterion for toxicity, which is no hemolysis at a peptide concentration of 500 μg/ml after 8 hours. We believe that this time study at this very high peptide concentration gives a much more accurate evaluation of hemolytic activity and this method should be established as the gold standard test.
It is important to note that our lead peptides NAD and NKL are effective against a diverse group of Pseudomonas aeruginosa clinical isolates. Peptide D-NAL exhibited the highest antimicrobial activity against Pseudomonas aeruginosa strains; in contrast, D-NKD has the best overall therapeutic index due to its lack of hemolytic activity. As mentioned before, Pseudomonas aeruginosa is a family of notorious Gram-negative bacterial strains which are resistant to most of current antibiotics, thus, it is one of the most severe threats to human health (58-60). Only a few antibiotics are effective against Pseudomonas, including fluoroquinolones (61), gentamicin (62) and imipenem (63), and even these antibiotics are not effective against all strains. In the studies disclosed herein, MIC values for Pseudomonas aeruginosa and other Gram-negative and Gram-positive bacteria were determined in two different collaborating laboratories; in addition to different media used, the inoculum numbers of cells were also different (see details in the Methods Section), which may explain some variations of MIC values of Pseudomonas aeruginosa strains when comparing the results reported in Table 10 and Table 11.
As shown herein, in general, there is no significant difference in peptide antimicrobial activities against Pseudomonas aeruginosa strains, other Gram-negative and Gram-positive bacteria and a fungus between L- and D-enantiomeric peptides, or among peptides with different amino acid substitutions, i.e., V681, NAD and NKL (Tables 10-12). This observation provides understanding of the mechanism of action of α-helical antimicrobial enantiomeric peptides as follows: there is a dramatic difference in peptide hydrophobicity at position 13 between Val and Lys. The Lys disrupts the continuous non-polar surface due to the positive charge and causes the peptide to locate in the interface region of the microbial membrane. This supports the view that the “carpet” mechanism is essential for strong antimicrobial activity, i.e., for both L- and D-peptide enantiomers, the peptides kill bacteria by a detergent-like mechanism, without penetrating deeply into the hydrophobic core of membrane.
Based on the peptide degradation study, all-D-peptides were totally resistant to enzymatic digestion; hence, this may explain the slightly higher antimicrobial activity of D-peptides than that of their L-enantiomers against Pseudomonas aeruginosa and Gram-positive bacteria. The relatively high susceptibility of L-peptides to trypsin is no doubt due to the presence of multiple lysine residues in sequences, i.e., 6 lysines for V681 and NAD, 7 lysines for NKL, resulting in the fast degradation of the L-peptides in 30 minutes even at a molar ratio of 20,000:1 (peptide:trypsin).
In summary, by comparing the biophysical and biological properties of L- and D-enantiomeric peptides, we showed that L- and D-enantiomeric peptide pairs behave the same in self-association ability in solution, had the same hemolytic activity against human red blood cells, and exhibited similar antimicrobial activity against Pseudomonas aeruginosa strains, and other Gram-negative and Gram-positive bacteria and a fungus. No chiral selectivity was found in the antimicrobial and hemolytic activities of the peptides. Thus, the results disclosed support the “membrane discrimination” model as the mechanism of action for both L- and D-enantiomeric peptides. It is important to note that peptide D-NKD showed dramatic improvements in therapeutic indices compared to the parent peptide V681 i.e., 53-fold against Pseudomonas aeruginosa strains, 80-fold against Gram-negative bacteria, 69-fold against Gram-positive bacteria and 33-fold against C. albicans. The proteolytic stability of D-NKD, its broad spectrum of activity and lack of hemolytic activity demonstrate its clinical potential as a new therapeutic.
Methods for Example 1
Peptide Synthesis and Purification—Syntheses of the peptides Ac-KWKSFLKTFKXD/L-AVKTVLHTALKAISS-amide (SEQ ID NO:43) and Ac-KWKSFLKTFKSAXD/LK-TVLHTALKAISS-amide (SEQ ID NO:44), with substitution sites at positions 11 and 13, respectively were carried out by solid-phase peptide synthesis using t-butyloxycarbonyl chemistry and MBHA (4-methylbenzhydrylamine) resin (0.97 mmol/g), as described previously (26). However, it is understood in the art that there are other suitable peptide synthetic devices or that manual peptide synthesis could be carried out to produce the peptides of the present invention. The crude peptides were purified by preparative reversed-phase chromatography (RP-HPLC) using a Zorbax 300 SB-C8 column (250×9.4 mm I.D.; 6.5 μm particle size, 300 Å pore size; Agilent Technologies) with a linear AB gradient (0.2% acetonitrile/min) at a flow rate of 2 ml/min, where mobile phase A was 0.1% aqueous TFA in water and B was 0.1% TFA in acetonitrile. The purity of peptides was verified by analytical RP-HPLC as described below. The peptides were further characterized by electrospray mass spectrometry and amino acid analysis.
Analytical RP-HPLC of Peptides—Peptides were analyzed on an Agilent 1100 series liquid chromatograph (Little Falls, Del.). Runs were performed on a Zorbax 300 SB-C8 column (150×2.1 mm I.D.; 5 μm particle size, 300 Å pore size) from Agilent Technologies using linear AB gradient (1% acetonitrile/min) and a flow rate of 0.25 ml/min, where solvent A was 0.05% aqueous TFA, pH 2 and solvent B was 0.05% TFA in acetonitrile. Temperature profiling analyses were performed in 3° C. increments, from 5° C. to 80° C.
Characterization of Helical Structure—The mean residue molar ellipticities of peptides were determined by circular dichroism (CD) spectroscopy, using a Jasco J-720 spectropolarimeter (Jasco, Easton, Md.), at 25° C. under benign conditions (50 mM KH2PO4/K2HPO4/100 mM KCl, pH 7), as well as in the presence of an α-helix inducing solvent, 2,2,2-trifluoroethanol (TFE) (50 mM KH2PO4/K2HPO4/100 mM KCl, pH 7 buffer/50% TFE). A 10-fold dilution of a  ̃500 μM stock solution of the peptide analogs was loaded into a 0.02 cm fused silica cell and its ellipticity scanned from 190 to 250 nm. The values of molar ellipticities of the peptide analogs at a wavelength of 222 nm were used to estimate the relative α-helicity of the peptides.
CD Temperature Denaturation Study of Peptide V681—The native peptide V681 was dissolved in 0.05% aqueous TFA containing 50% TFE, pH 2, loaded into a 0.02 cm fused silica cell and peptide ellipticity scanned from 190 to 250 nm at temperatures of 5, 15, 25, 35, 45, 55, 65 and 80° C. The spectra at different temperatures were used to mimic the alteration of peptide conformation during temperature profiling analysis in RP-HPLC. The ratio of the molar ellipticity at a particular temperature (t) relative to that at 5° C. ([θ]t−[θ]u)/([θ]5−[θ]u) was calculated and plotted against temperature in order to obtain the thermal melting profiles, where [θ]5 and [θ]u represent the molar ellipticity values for the fully folded and fully unfolded species, respectively. [θ]u was determined in the presence of 8M urea with a value of 1500 deg cm2 dmol−1 to represent a totally random coil state (31). The melting temperature (Tm) was calculated as the temperature at which the α-helix was 50% denatured (([θ]t−[θ]u)/([θ]5−[θ]u)=0.5) and the values were taken as a measure of α-helix stability.
Determination of Peptide Amphipathicity—Amphipathicity of peptide analogs was determined by the calculation of hydrophobic moment (32) using the software package Jemboss version 1.2.1 (33), modified to include a hydrophobicity scale determined in our laboratory. The hydrophobicity scale used in this study is listed as follows: Trp, 32.31; Phe, 29.11; Leu, 23.42; Ile 21.31; Met, 16.13; Tyr, 15.37; Val, 13.81; Pro, 9.38; Cys, 8.14; Ala, 3.60; Glu, 3.60; Thr, 2.82; Asp, 2.22; Gln, 0.54; Ser, 0.00; Asn, 0.00; Gly, 0.00; Arg, −5.01; His, −7.03; Lys, −7.03 (Hodges, et al. unpublished data). These hydrophobicity coefficients were determined from reversed-phase chromatography at pH 2 of a model random coil peptide with single substitution of all 20 naturally occurring amino acids. In this case, the amphipathicity is valid for neutral and acidic pH since V681 and analogs do not have Asp and Glu residues in their sequences. We propose that this HPLC-derived scale reflects the relative differences in hydrophilicity/hydrophobicity of the 20 amino acid side-chains more accurately than previously determined scales.
Measurement of Antimicrobial Activity—Minimal inhibitory concentrations (MICs) were determined using a standard microtiter dilution method in LB (Luria-Bertani) no-salt medium (10 g of tryptone and 5 g of yeast extract per liter). Briefly, cells were grown overnight at 37° C. in LB and diluted in the same medium. Serial dilutions of the peptides were added to the microtiter plates in a volume of 100 μl followed by 10 μl of bacteria to give a final inoculum of 5×105 colony-forming units/ml. Plates were incubated at 37° C. for 24 hours and MICs determined as the lowest peptide concentration that inhibited growth. Alternatively, minimal inhibitory concentrations were determined using a standard microtiter dilution method in a Mueller-Hinton (MH) medium. Briefly, cells were grown overnight at 37° C. in MH broth and diluted in the same medium. Serial dilutions of the peptides were added to the microtiter plates in a volume of 100 μl followed by 10 μl of bacteria to give a final inoculum of 1×105 colony-forming units/ml. Plates were incubated at 37° C. for 24 hours and MICs determined as the lowest peptide concentration that inhibited growth. However, for MIC determination of Pseudomonas aeruginosa clinical isolates, brain heart infusion (BH1) medium was used instead of MH broth. In addition, the bacteria were diluted to a final inoculum of 1×106 colony-forming units/ml.
Measurement of Hemolytic Activity—Protocol A: Peptide samples were added to 1% human erythrocytes in phosphate buffered saline (0.08M NaCl; 0.043M Na2PO4; 0.011M KH2PO4) and reactions were incubated at 37° C. for 12 hours in microtiter plates. Peptide samples were diluted 2 fold in order to determine the concentration that produced no hemolysis. This determination was made by withdrawing aliquots from the hemolysis assays, removing unlysed erythrocytes by centrifugation (800 g) and determining which concentration of peptide failed to cause the release of hemoglobin. Hemoglobin release was determined spectrophotometrically at 562 nm. The hemolytic titer was the highest 2-fold dilution of the peptide that still caused release of hemoglobin from erythrocytes. The control for no release of hemoglobin was a sample of 1% erythrocytes without any peptide added. The results shown in Tables 5-7 were obtained by using Protocol A. Protocol B: Alternatively, peptide samples were added to 1% human erythrocytes in phosphate buffered saline (100 mM NaCl; 80 mM Na2HPO4; 20 mM NaH2PO4, pH 7.4) and reactions were incubated at 37° C. for 18 hours in microtiter plates. Peptide samples were diluted 2 fold in order to determine the concentration that produced no hemolysis. This determination was made by withdrawing aliquots from the hemolysis assays, removing unlysed erythrocytes by centrifugation (800 g) and determining which concentration of peptide failed to cause the release of hemoglobin. Hemoglobin release was determined spectrophotometrically at 570 nm. The hemolytic titer was the highest 2-fold dilution of the peptide that still caused release of hemoglobin from erythrocytes. The control for no release of hemoglobin was a sample of 1% erythrocytes without any peptide added. Since erythrocytes were in an isotonic medium, no detectable release (<1% of that released upon complete hemolysis) of hemoglobin was observed from this control during the course of the assay. For the hemolysis time study, hemolytic activity of peptides at concentrations of 8, 16, 32, 64, 125, 250 and 500 μg/ml was measured at 0, 1, 2, 4, 8 hours at 37° C. The results shown in Tables 10-12 were obtained by using Protocol B.
Calculation of Therapeutic Index (MHC/MIC Ratio)
it should be noted that both MHC and MIC values were determined by serial 2-fold dilutions. Thus, for individual bacteria and individual peptides the therapeutic index (MHC/MIC, “TI”) could vary by as much as 4 fold if the peptide is very active in both hemolytic and antimicrobial activities; if a peptide has poor or no hemolytic activity, the major variation in the therapeutic index (MHC/MIC) comes from the variation in the MIC value (as much as 2-fold).
Proteolytic Stability Assay
Proteolytic stability of the peptides was carried out with trypsin in a molar ratio of 1:20,000 (trypsin:peptide=0.1 μM:2 mM). The buffer used was 50 mM NH4HCO3 at pH 7.4 for both peptides and enzyme. The mixtures of peptide and trypsin were incubated at 37° C. Samples were collected at time points of 0, 5 min, 10 min, 20 min, 30 min, 1, 2, 4, 8 hours. Equal volumes of 20% aqueous TFA were added to each sample to stop the reaction and peptide degradation was checked by RP-HPLC. Runs were performed on a Zorbax 300 SB-C8 column (150×2.1 mm I.D.; 5 μm particle size, 300 Å pore size) from Agilent Technologies at room temperature using a linear AB gradient (1% acetonitrile/min) and a flow rate of 0.25 ml/min, where eluent A was 0.2% aqueous TFA, pH 2 and eluent B was 0.2% TFA in acetonitrile. The change in integrated peak area of the peptides was used to monitor the degree of proteolysis during the time study.
EXAMPLE 2
Peptide Analogs with Varied Position of Substitution
Further peptides of the invention are generated by varying the position of a substitution. By denoting the center position as “i”, varied positions of substitutions can be generated while retaining a preferred location on the desired face, e.g. the non-polar face. In the relative context of SEQ ID NO:1, for example, the position for substitution is selected from the group consisting of i, i−4, i−8, i+4, and i+8. See FIG. 7A for examples of specific variants achieved by optional positioning of substitutions. Without wishing to be bound by a particular theory, it is hypothesized that a peptide with the substitution at position i of KL (e.g., in SEQ ID NO:6), in the center position of the non-polar face, can have greater biological activity than a peptide with a substitution at a position further away from the center position. According to such theory, the therapeutic index can decrease in the order of KL13>KL9>KL5 (here the numeral indicates the position of the amino acid substitution relative to SEQ ID NO:1). Similarly, the therapeutic index can decrease in the order of AD13>AD9>AD5 (here AD13 corresponds to SEQ ID NO:9). Regardless of such theory, such peptides with varied positions of a substitution can have activity and be useful in compositions and methods of the invention. Successful substitutions at position 13 can also work near the center of the hydrophobic face at position 9, 12, 16 and 17 (see helical net diagram in FIG. 1).
In order to evaluate the biological activities of the peptide analogs with varied position of substitution, we used peptide NKL as a framework to systematically alter the peptide hydrophobicity by replacing alanine residues with hydrophobic leucine residues on the non-polar face of the helix. Peptide sequences are shown in Table 13.







TABLE 13







Sequences of NKL analog peptides.









Num-




ber
Denotation
Peptide sequencesa





1
NKL
Ac-KWKSFLKTFKSAKKTVLHTALKAIS



(SEQ ID NO: 6)
S-amide


 


2
A23L
Ac-KWKSFLKTFKSAKKTVLHTALK IS



(SEQ ID NO: 45)
S-amide


 


3
A12L
Ac-KWKSFLKTFKS KKTVLHTALKAIS



(SEQ ID NO: 46)
S-amide


 


4
A20L
Ac-KWKSFLKTFKSAKKTVLHT LKAIS



(SEQ ID NO: 47)
S-amide


 


5
A12L/A23L
Ac-KWKSFLKTFKS KKTVLHTALK IS



(SEQ ID NO: 48)
S-amide


 


6
A12L/A20L
Ac-KWKSFLKTFKS KKTVLHT LKAIS



(SEQ ID NO: 49)
S-amide


 


7
A12L/A20L/A23L
Ac-KWKSFLKTFKS KKTVLHT LK IS



(SEQ ID NO: 50)
S-amide





aPeptide sequences are shown using the one-letter code for amino acid residues; Ac- denotes Na-acetyl and -amide denotes Ca-amide; in sequences, bold letters denote the substituting amino acids at the non-polar face of NKL (see FIG. 1 for details).






FIG. 12 shows the leucine-substituted peptide analogs represented as helical nets. Since there are three alanine residues on the non-polar face of peptide V13KL, three single Leu-substituted analogs were synthesized with an Ala→Leu substitution at positions 12, 20 and 23; two double Leu-substituted peptides (A12L/A23L and A12L/A20L) and a triple Leu-substituted peptide (A12L/A20L/A23L) were also made to increase hydrophobicity. In FIG. 12, the i→i+3 and i→i+4 hydrophobic interactions are shown as black bars. It is clear that, for single Leu-substituted analogs, the number of hydrophobic interactions created by these substitutions in the three peptides is in the order of A20L>A12L>A23L (9, 8 and 6 hydrophobic interactions, respectively); for peptides with double leucine substitutions, A12L/A20L has more hydrophobic interactions than A12L/A23L (11 versus 8 hydrophobic interactions); peptide A12L/A20L/A23L presented the highest number of i→i+3 and i→i+4 hydrophobic interactions (12 hydrophobic interactions) among all the peptide analogs as expected. In this study, peptides were simply named after the positions of the leucine substitutions.
For the Leu-substituted peptides, the hemolytic activity against human erythrocytes was determined as the maximal peptide concentration that produces no hemolysis after 18 hours of incubation at 37° C. Antimicrobial activity of the peptides was determined on a diverse group of Pseudomonas aeruginosa clinical isolates. Pseudomonas is a family of strains that has become more and more resistant to various traditional antibiotics since 1990s and it is also known to produce proteolytic enzymes which make it even less susceptible to antimicrobial peptides (58-60). Pseudomonas aeruginosa strains used in this study exhibited a wide range of ciprofloxacin susceptibility (a 64-fold difference) (Table 14). The most resistant Pseudomonas aeruginosa strain was CP204, a clinical isolate from cystic fibrosis patients, which was, in contrast, the most susceptible strain to our antimicrobial peptides in this study. This indicates that there is no correlation between antibiotic resistance and the ability of antimicrobial peptides to be effective. The geometric mean MIC values from six Pseudomonas strains in Table 14 were calculated to provide an overall evaluation of antimicrobial activity of the peptides with different hydrophobicities.







TABLE 14







Biological activities of NKL analog peptides.









Antimicrobial activity










Peptide
Hemolytic activity
MIC (μg/ml)b



















Number
Denotation
MHC (μg/ml)
Folda
PAO 1
WR 5
PAK
PA 14
M 2
CP 204
GMc
Foldd





















1
NKL
250.0
1.0
31.3
250.0
125.0
62.5
31.3
7.8
49.6
1.0


2
A23L
62.5
4.0
31.3
62.5
62.5
31.3
31.3
15.6
35.1
1.4


3
A12L
31.3
8.0
15.6
62.5
31.3
31.3
15.6
15.6
24.8
2.0


4
A20L
31.3
8.0
7.8
31.3
31.3
15.6
15.6
7.8
15.6
3.2


5
A12L/A23L
15.6
16.0
15.6
250.0
15.6
62.5
31.3
7.8
31.2
1.6


6
A12L/A20L
8.0
32.0
62.5
125.0
62.5
125.0
62.5
62.5
78.7
0.6


7
A12L/A20L/A23L
4.0
62.5
500.0
500.0
500.0
500.0
500.0
500.0
500.0
0.1



Ciprofloxacine


4
1
4
8
8
64





adenotes the fold increase in hemolytic activity compared to the parent peptide NKL. Hemolytic activity (MHC, the maximal peptide concentration showing no hemolysis after 18 hours) was determined on human red blood cells (hRBC).


bMIC is minimal inhibitory concentration against 6 Pseudomonas aeruginosa clinical isolates.


cdenotes the geometric mean of the MIC values for the 6 Pseudomonas aeruginosa clinical isolates.


ddenotes the fold improvement in antimicrobial activity (geometric mean data) compared to the parent peptide NKL.


eRelative susceptibility of these Pseudomonas strains to ciprofloxacin with the number 1 denoting the most susceptible strain.






The influence of peptide hydrophobicity on biological activities is shown in FIG. 13. It was generally accepted that increasing the hydrophobicity of the non-polar face of the amphipathic α-helical peptides would increase both hemolytic and antimicrobial activities (5-8). In the present study, it is clear that peptide hydrophobicity correlated with peptide hemolytic activity in that the more hydrophobic the peptide the stronger the hemolytic activity to erythrocytes, which is consistent with previous results (53, 64-66). The striking result from our antibacterial assay was that hydrophobicity has two effects on peptide antimicrobial activity: at a relative low level of hydrophobicity, increasing peptide hydrophobicity caused an improvement in antimicrobial activity until an optimum hydrophobicity was reached; in contrast, peptide antimicrobial activity was weakened dramatically with further increases of hydrophobicity beyond the optimum, even resulting in the loss of antimicrobial activity of peptide A12L/A20L/A23L (peptide 7) in this study (FIG. 12).
The results of these studies are consistent with our proposed model of “membrane discrimination” mechanism of action for antimicrobial peptides whose sole target is the biomembrane. We believe that the mechanism depends upon the compositional difference in the lipids between prokaryotic and eukaryotic membranes. It is well-known that eukaryotic cell membranes are in contrast to prokaryotic membranes generally characterized by zwitterionic phospholipids, a relatively large amount of cholesterol and sphigomyelin, and the absence of a high, inside-negative transmembrane potential presented in prokaryotic membranes (51-52, 66-67). Hence, if the peptides form pores/channels in the hydrophobic core of the eukaryotic bilayer, they would cause the hemolysis of erythrocytes; in contrast, for prokaryotic cells the peptides lyse cells in a detergent-like mechanism as described in the carpet mechanism (46).
The observation that there is a correlation between peptide hydrophobicity and hemolytic activity can be explained by the “membrane discrimination” mechanism. Peptides with higher hydrophobicity will penetrate deeper into the hydrophobic core of red blood cell membrane (67), causing stronger hemolysis by forming pores or channels, i.e., A12L/A23L (peptide 5) and A12L/A20L (peptide 6) exhibited stronger hemolytic activity than single Leu-substituted peptides, and A12L/A20L/A23L (peptide 7) showed the strongest hemolytic activity in this study (Table 14). For peptide antimicrobial activity, since the insertion of the molecules into the hydrophobic core is not necessary to lyse bacterial cells during the antibacterial action, peptides only lie at the interface parallel with the membrane allowing their hydrophobic surface to interact with the hydrophobic component of the lipid, and the positive charge residues to interact with the negatively charged head groups of the phospholipids (46, 47). Thus, it is reasonable to assume that increasing peptide hydrophobicity to a certain extent will help peptide molecules to reach the interface from aqueous environment and improve antimicrobial activity. In this study, the improvement of antimicrobial activity from peptide NKL (peptide 1) to peptide A20L (peptide 4) can represent such an advantage of increasing hydrophobicity. In contrast, further increases in hydrophobicity will cause the stronger peptide dimerization in solution which in turn results in the monomer-dimer equilibrium favoring the dimer conformation. Peptide dimers are in their folded α-helical conformation and would be inhibited from passing through the cell wall to reach the target membranes. Hence the antimicrobial activities of peptides A12L/A23L (peptide 5) and A12L/A20L (peptide 6) become weaker with increasing hydrophobicity compared to the single Leu-substituted analogs. We believe that there is a threshold of hydrophobicity controlling peptide antimicrobial activity, that is, one may adjust peptide hydrophobicity to obtain the optimal antimicrobial activity. For the extreme example of the triple-Leu-substituted analog, A12L/A20L/A23L (peptide 7), the loss of antimicrobial activity may be explained as due to its very strong dimerization ability in aqueous environments. Hence, the peptide exists mainly as a dimer in solution and it would not pass through the bacterial cell wall. In contrast, there is no polysaccharide-based cell wall in eukaryotic cells, thus, A12L/A20L/A23L (peptide 7) caused severe hemolysis against human red blood cells where the hydrophobicity of the bilayer causes rapid dissociation of dimers to monomers and entry into the bilayer to form channels/pores.
EXAMPLE 3
Peptide Analogs with Varied Nature of Charge Substitution
Further peptides of the invention are generated by varying the nature of the charged residue selected for the substitution. In the relative context of SEQ ID NO:1, for example, the position for substitution is established as position 13. The amino acid selected for substitution is preferably a charged amino acid and is in particular an amino acid with a net positive charge. Particular examples of charged residues at position 13 are Lys, Arg, Orn, His, diamino butyric acid and diamino propionic acid. We note that Orn has a delta/δ-amino group instead of an epsilon/ε-amino group in Lys, i.e., the side-chain is shorter by one carbon atom; diaminobutanoic acid is one carbon shorter than Orn; i.e., it has a gamma/γ-amino group; diaminopropionic acid is two carbons shorter than Orn, i.e., it has a beta/1-amino group.
See FIG. 7A for a specific variant peptide achieved by optional selection of charged residues for use in substitutions. A peptide with a charged residue in the center of the non-polar face can be active. Without wishing to be bound by a particular theory, it is hypothesized that the activity of a peptide with such a centrally positioned positively charged residue can be modulated depending on the positively charged residue, although there may be difficulty in predicting the precise effect upon an activity parameter such as the therapeutic index as described herein.
EXAMPLE 4
Peptide Analogs with Multiple Substitutions
Further peptides of the invention are generated by using multiple substitutions relative to a reference sequence such as SEQ ID NO:1. In a preferred embodiment, the multiple substitutions are a double substitution. In the relative context of SEQ ID NO:1, for example, the following peptides are made with double substitutions: a) peptide with substitution combination of L6 to AD6 and L21 to AD21; and b) peptide with substitution combination of L6 to KL6 and L21 to KL21. See FIG. 7A for specific variant peptides achieved by optional multiple substitutions.
Without wishing to be bound by a particular theory, it is hypothesized that the activity of a peptide with multiple substitutions (e.g. two substitutions) not in the center position can still be effective. For a particular peptide generated by multiple substitutions, such multiple substitutions can be at least as effective as a single substitution in the center of the non-polar face. Alternatively, a given multiple substitution such as the specific double substitutions shown may not be as effective as the single substitutions described herein due to the removal of two Leu residues instead of one Val residue. A decrease in hydrophobicity can optionally result in a decrease in the therapeutic index. In addition, the double D-Ala substitutions may be more disruptive of the helical structure; such disruption can also yield a decrease in the therapeutic index. Analogous results can be achieved for the double L-Lys substitutions.
EXAMPLE 5
Truncated Peptide Analogs
Further peptides of the invention are generated by truncation of a reference peptide such as SEQ ID NO:1 or a peptide of the invention such as any of SEQ ID NOS: 2 to 25 (except for those peptides that are exactly equivalent to SEQ ID NO:1 such as SEQ ID NO: 3 and 15), or other peptide of the invention as described herein. In a truncated peptide analog, for example, truncation of the N-terminal residue Lys1 or C-terminal residues Ser25 and Ser26 do not substantially affect the biological properties such as activity of the truncated peptide. See FIG. 7A for specific variant peptides achieved by optional truncations in the relative context of peptide NKL (SEQ ID NO:6). Without wishing to be bound by a particular theory, it is hypothesized that truncating the N-terminal residue Lys1 or C-terminal residues Ser25 and Ser26 does not substantially affect the biological properties. It is believed, however, that truncation of Lys1 and Trp2 can substantially decrease the therapeutic index due to removal of the large hydrophobe, Trp. Similarly, truncation of Ser26, Ser25 and Ile24 can substantially decrease the therapeutic index due to removal of the large hydrophobe, Ile.
As further alternatives to truncated analog peptides corresponding to SEQ ID 34, 35, 36, and 37, there is a substitution of K13V (the K at position 13 is replaced by V) for each of those respective peptides.
EXAMPLE 6
Shuffled Peptide Analogs
Further peptides of the invention are generated by shuffling various residues. For residues on the non-polar face, shuffling is performed to generate various non-polar face analogs. It is believed that the overall hydrophobicity of the non-polar face is an important factor in biological activity. The hydrophobic residues on the non-polar face are shuffled wherein a resulting peptide is biologically active. As shown in FIG. 7A and FIG. 7B, the circled residues in the sequence are the shuffled residues on the non-polar face.
For residues on the polar face, shuffling is performed to generate various polar face analogs. It is believed that the polar face is an important factor in maintaining the amphipathicity of the molecule and significant properties such as biological activity. The polar residues on the polar face are shuffled wherein a resulting peptide is biologically active. As shown in FIG. 7A and FIG. 7C, the circled residues in the sequence are the shuffled residues on the polar face.
Shuffling of the non-polar face residues or polar face residues does not substantially change the amphipathicity of the molecule, or the overall hydrophobicity of the non-polar face or the overall hydrophilicity of the polar face. Though a particular sequence may be a preferred or the best analog, other analogs can nonetheless have useful biological properties.
In particular peptides, shuffling the 11 residues on the non-polar face is performed, excluding the substitution site (for example so as to preserve 13-Lys as in NKL), to any combination of sequences that contain 1 W (one tryptophan residue), 2 F, 3 L, 3 A, 1 V and 1 I residue. Similarly, shuffling the 14 residues on the polar face to any combination of sequences that contains 6 K, 4 S, 3 T, and 1H residue is performed.
Peptides are generated having a range of overall hydrophobicity of the non-polar face. The hydrophobicity of the non-polar face can be calculated using a sum of the hydrophobicity coefficients listed in the manuscript. For example, a particular hydrophobicity range is of NKL or NAD the value of a Leu side-chain. Using our scale, the hydrophobicity of the non-polar face of NKL sums up the values for W2, F5, L6, F9, A12, K13, V16, L17, A20, L21, A23, I24 getting a value of 199.7. See Table 15.







TABLE 15







Hydrophobicity coefficients.










Item
Coefficient













Trp 2
32.31



Phe 5
29.11



Leu 6
23.42



Phe 9
29.11



Ala 12
3.60



Lys 13
−7.03



Val 16
13.81



Leu 17
23.42



Ala 20
3.60



Leu 21
23.42



Ala 23
3.60



Ile 24
21.31



SUM
199.7 ± 23.42









Different scales can give different values. For peptides herein, there is significance in the sum of the residues in the hydrophobic surface, using our scale, where the surface hydrophobicity range that generates the desired biological activity is from about 176 to about 224.
The sum of the hydrophobicity coefficients for the polar face should be the value for NKL peptide±the value of a Lys residue.







TABLE 16







Coefficient values.










Item
Coefficient













K1
−7.03



K3
−7.03



S4
0.00



K7
−7.03



T6
+2.82



K10
−7.03



S11
0.00



K14
−7.03



T15
+2.82



H18
−7.03



T19
+2.82



K22
−7.03



S25
0.00



S26
0.00



SUM
−40.75 ± 7.03









Using our scale, the hydrophobicity of the polar face of NKL sums up the values K1, K3, S4, K7, T6, K10, S11, K14, T15, H18, T19, K22, S25 and S26. The range of surface hydrophilicity that generates the desired biological activity is from about −33 to about −48.
EXAMPLE 7
Peptide Analogs with Similar Single Hydrophobicity Substitutions
Further peptides of the invention are generated by making single substitutions of amino acid residues with relatively similar hydrophobicity. Single hydrophobicity substitutions with side-chains of similar hydrophobicity are generated and have biological activity. For example, possible substitutions for each residue in the non-polar face are listed below in Table 17 in the context of peptides NKL and NAD (SEQ ID NOS:6 and 9, respectively).







TABLE 17







Residues for single substitutions.










Residue in NKL or NAD
Substituting residues






Leu
Ile, Val, norleucine, norvaline



Ile
Leu, Val, norleucine, norvaline



Val
Leu, Ile, norleucine, norvaline



Phe
Leu, Ile, Val, norleucine, norvaline



Trp
Phe, Leu, Ile, Val, norleucine, norvaline









EXAMPLE 8
Peptide Analogs of NAD and D-NAL 
Further compositions and methods are provided where the hemolytic activity of NAD or D-NAL is further decreased by decreasing the overall hydrophobicity of the non-polar face. See Kondejewski, L. H., et al. 2002, J. Biol. Chem. 277:67-74. For example, V16 is substituted to A16; or L17 to A17; or both V16, L17 to A16, A17. A decreased hydrophobicity can decrease hemolytic activity as shown for substitutions herein at position 13. The hydrophobicity can decrease approximately in the order NLL>NVL>NAL>NG>NSL>NKL which correlates with the weakening of hemolytic activity (μg/ml) where NLL (7.8), NVL (15.6), NAL (31.2), NG (125), NSL (125) and NKL (no measurable activity). It is recognized that there can be a threshold of hydrophobicity which when excessively decreased can result in peptides where the biological property of antimicrobial activity is substantially reduced.
STATEMENTS REGARDING INCORPORATION BY REFERENCE AND VARIATIONS
All references throughout this application, for example patent documents including issued or granted patents or equivalents; patent application publications; and non-patent literature documents or other source material; are hereby incorporated by reference herein in their entireties, as though individually incorporated by reference, to the extent each reference is at least partially not inconsistent with the disclosure in this application (for example, a reference that is partially inconsistent is incorporated by reference except for the partially inconsistent portion of the reference).
Any appendix or appendices hereto are incorporated by reference as part of the specification and/or drawings.
Where the terms “comprise”, “comprises”, “comprised”, or “comprising” are used herein, they are to be interpreted as specifying the presence of the stated features, integers, steps, or components referred to, but not to preclude the presence or addition of one or more other feature, integer, step, component, or group thereof.
The invention has been described with reference to various specific and preferred embodiments and techniques. However, it should be understood that many variations and modifications may be made while remaining within the true spirit and scope of the invention. It will be apparent to one of ordinary skill in the art that compositions, methods, devices, device elements, materials, procedures and techniques other than those specifically described herein can be applied to the practice of the invention as broadly disclosed herein without resort to undue experimentation. All art-known functional equivalents of compositions, methods, devices, device elements, materials, procedures and techniques described herein are intended to be encompassed by this invention. It is not intended, however, for any claim herein to specifically encompass any precise embodiment existing and legally qualifying in the relevant jurisdiction as prior art for novelty; a claim purportedly encompassing such an embodiment is intended to be of scope so as to just exclude any such precise embodiment.
Whenever a range is disclosed, all subranges and individual values are intended to be encompassed. This invention is not to be limited by the embodiments disclosed, including any shown in the drawings or exemplified in the specification, which are given by way of example or illustration and not of limitation.
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## Claims

1. An isolated peptide having antimicrobial activity, said peptide comprising a sequence SEQ ID NO:1 and having one or more improved biological properties relative to SEQ ID NO:1, wherein said one or more properties are selected from the group consisting of antimicrobial activity, hemolytic activity, stability, and therapeutic index for a microorganism, and wherein the peptide does not have the amino acid sequence set forth in SEQ ID NO:1.

2. The peptide of claim 1 wherein the peptide is selected from the group consisting of SEQ ID NOS:2, 4-14, 16-25, 27-39, and wherein said other peptides are exclusive of SEQ ID NO:3, SEQ ID NO:15, and SEQ ID NO:26.

3. The peptide of claim 1 wherein the peptide has an overall surface hydrophobicity in the range of from about 176 to about 224 or the peptide has an overall surface hydrophilicity in the range of from about −33 to about −48.

4. The peptide of claim 1 wherein the peptide is from about 23 to about 26 amino acids in length.

5. The peptide of claim 1 wherein the peptide comprises a core sequence of KSFLKTFKSAKLKTVLHTALKA (SEQ ID NO:51) or KSFLKTFKSAKDKTVLHTALKA (SEQ ID NO:52).

6. The peptide of claim 1 wherein the peptide is in D-configuration.

7. The peptide of claim 1 having antimicrobial activity, said peptide comprising a sequence KWKSFLKTFKaAbKTVLHTALKAISS (SEQ ID NO:40) wherein a and b are selected from the group consisting of L-leucine, D-Leucine, L-valine, D-valine, L-alanine, D-alanine, glycine, L-serine, D-serine, L-lysine, and D-lysine.

8. The peptide of claim 7 wherein b is L-lysine or D-alanine, wherein b is D-lysine and all other amino acids are D-enantiomers, or wherein b is L-alanine and all other amino acids are D-enantiomers.

9. A therapeutic composition for controlling infection by a microorganism, said composition comprising at least one antimicrobial peptide of claim 1 in a therapeutically effective amount and a pharmaceutically acceptable carrier.

10. The composition of claim 9 wherein the microorganism is selected from the group consisting of a bacterium, a fungus, a virus, and a protozoan.

11. The peptide of claim 1, wherein said derivative comprises a substitution of at least one amino acid residue, a truncation of at least one residue from an end, a truncation of at least two residues from an end; or wherein all residues are D-residues.

12. An isolated peptide comprising a sequence KWKSFLKTFKaAbKTVLHTALKAISS (SEQ ID NO:40) wherein a and b are selected from the group consisting of L-leucine, D-Leucine, L-valine, D-valine, L-alanine, D-alanine, glycine, L-serine, D-serine, L-lysine, and D-lysine, and wherein the peptide does not have the amino acid sequence set forth in SEQ ID NO:1.

13. A method of controlling a microorganism, said method comprising the step of administering a therapeutically effective amount of a composition, wherein said composition comprises at least one antimicrobial peptide of claim 1.

14. The method of claim 13 wherein said microorganism is selected from the group consisting of a gram-negative bacterium and a gram-positive bacterium.

15. A method of treating a subject in need or preventing an infection in a subject caused by a microorganism, wherein said method comprises the step of administering a therapeutically effective amount of a composition to a subject with the infection, said composition comprising at least one antimicrobial peptide of claim 1 and a pharmaceutically acceptable carrier.

16. The method of claim 15 wherein the microorganism is selected from the group consisting of gram-positive bacteria and gram-negative bacteria.

17. A method of disinfecting a surface of an article, said method comprising the step of applying to said surface an effective amount of a composition comprising at least one microbial peptide of claim 1.

18. A disinfecting solution comprising at least one microbial peptide of claim 1 and optionally an acceptable carrier.