Design and synthesis of amphipathic antimicrobial peptides

iAMAP-SCM: A Novel Computational Tool for Large-Scale Identification of Antimalarial Peptides Using Estimated Propensity Scores of Dipeptides

Antimalarial peptides (AMAPs) varying in length, amino acid composition, charge, conformational structure, hydrophobicity, and amphipathicity reflect their diversity in antimalarial mechanisms. Due to the worldwide major health problem concerning antimicrobial resistance, these peptides possess great therapeutic value owing to their low incidences of drug resistance as compared to conventional antibiotics. Although well-known experimental methods are able to precisely determine the antimalarial activity of peptides, these methods are still time-consuming and costly. Thus, machine learning (ML)-based methods that are capable of identifying AMAPs rapidly by using only sequence information would be beneficial for the high-throughput identification of AMAPs. In this study, we propose the first computational model (termed iAMAP-SCM) for the large-scale identification and characterization of peptides with antimalarial activity by using only sequence information. Specifically, we employed an interpretable scoring card method (SCM) to develop iAMAP-SCM and estimate propensities of 20 amino acids and 400 dipeptides to be AMAPs in a supervised manner. Experimental results showed that iAMAP-SCM could achieve a maximum accuracy and Matthew's coefficient correlation of 0.957 and 0.834, respectively, on the independent test dataset. In addition, SCM-derived propensities of 20 amino acids and selected physicochemical properties were used to provide an understanding of the functional mechanisms of AMAPs. Finally, a user-friendly online computational platform of iAMAP-SCM is publicly available at http://pmlabstack.pythonanywhere.com/iAMAP-SCM. The iAMAP-SCM predictor is anticipated to assist experimental scientists in the high-throughput identification of potential AMAP candidates for the treatment of malaria and other clinical applications.

Mechanistic Landscape of Membrane-Permeabilizing Peptides

Membrane permeabilizing peptides (MPPs) are as ubiquitous as the lipid bilayer membranes they act upon. Produced by all forms of life, most membrane permeabilizing peptides are used offensively or defensively against the membranes of other organisms. Just as nature has found many uses for them, translational scientists have worked for decades to design or optimize membrane permeabilizing peptides for applications in the laboratory and in the clinic ranging from antibacterial and antiviral therapy and prophylaxis to anticancer therapeutics and drug delivery. Here, we review the field of membrane permeabilizing peptides. We discuss the diversity of their sources and structures, the systems and methods used to measure their activities, and the behaviors that are observed. We discuss the fact that "mechanism" is not a discrete or a static entity for an MPP but rather the result of a heterogeneous and dynamic ensemble of structural states that vary in response to many different experimental conditions. This has led to an almost complete lack of discrete three-dimensional active structures among the thousands of known MPPs and a lack of useful or predictive sequence-structure-function relationship rules. Ultimately, we discuss how it may be more useful to think of membrane permeabilizing peptides mechanisms as broad regions of a mechanistic landscape rather than discrete molecular processes.

Characterization of the interactions of a polycationic, amphiphilic, terminally branched oligopeptide with lipid A and lipopolysaccharide from the deep rough mutant of Salmonella minnesota

The lipid A and lipopolysaccharide (LPS) binding and neutralizing activities of a synthetic, polycationic, amphiphilic peptide were studied. The branched peptide, designed as a functional analog of polymyxin B, has a six residue hydrophobic sequence, bearing at its N-terminus a penultimate lysine residue whose α- and E-amino groups are coupled to two terminal lysine residues. In fluorescence spectroscopic studies designed to examine relative affinities of binding to the toxin, neutralization of surface charge and fluidization of the acyl domains, the peptide was active, closely resembling the effects of polymyxin B and its nonapeptide derivative; however, the synthetic peptide does not induce phase transitions in LPS aggregates as do polymyxin B and polymyxin B nonapeptide. The peptide was also comparable with polymyxin B in its ability to inhibit LPS-mediated IL-1 and IL-6 release from human peripheral blood mononuclear cells. The synthetic compound is devoid of antibacterial activities and did not induce conductance fluxes in LPS-containing asymmetric planar membranes. These results strengthen the premise that basicity and amphiphilicity are necessary and sufficient physical properties that ascribe endotoxin binding and neutralizing activities, and further suggest that antibacterial/membrane perturbant and LPS neutralizing activities are dissociable, which may be of value in designing LPS-sequestering agents of low toxicity.

Comparison of pathogen-induced expression and efficacy of two amphibian antimicrobial peptides, MsrA2 and temporin A, for engineering wide-spectrum disease resistance in tobacco

The rapid accumulation of defensive transgene products in plants only on pathogen invasion has clear advantages over their constitutive synthesis. In this study, two antimicrobial peptides from the skin secretions of frogs, MsrA2 (N-methionine-dermaseptin B1) and temporin A, were evaluated for engineering pathogen-induced disease resistance in plants. Both peptides inhibited plant-specific pathogens in vitro at micromolar concentrations that were not toxic to plant protoplasts. The plant-optimized nucleotide sequences encoding MsrA2 and temporin A were transcriptionally fused to the inducible win3.12T poplar promoter, which had strong systemic activity in response to fungal infection, and introduced into tobacco (Nicotiana tabacum L. cv. Xanthi). Transgene expression was very low in the leaves of unstressed plants; however, it was strongly increased after pathogen challenge or wounding. The pathogen responsiveness of the win3.12T promoter was found to be universal rather than species specific, with high activity in response to all pathogens tested. On induction, the amount of MsrA2 was up to 6-7 microg per gram of fresh leaf tissue. Most importantly, the induced accumulation of MsrA2 and temporin A in transgenic tobacco was sufficient to confer resistance to a variety of phytopathogenic fungi, such as Fusarium solani, F. oxysporum, Alternaria alternata, Botrytis cinerea, Sclerotinia sclerotiorum, the oomycete Pythium aphanidermatum and the bacterium Pectobacterium carotovorum. The accumulation of these peptides in transgenic plants did not alter the normal phenotype of tobacco. Thus, the expression of MsrA2 and temporin A in a pathogen-inducible manner enables the development of tobacco, and possibly other plant species, with wide-spectrum disease resistance, which can reduce the use of pesticides and the associated environmental risks.

Folding amphipathic helices into membranes: amphiphilicity trumps hydrophobicity

High amphiphilicity is a hallmark of interfacial helices in membrane proteins and membrane-active peptides, such as toxins and antimicrobial peptides. Although there is general agreement that amphiphilicity is important for membrane-interface binding, an unanswered question is its importance relative to simple hydrophobicity-driven partitioning. We have examined this fundamental question using measurements of the interfacial partitioning of a family of 17-residue amidated-acetylated peptides into both neutral and anionic lipid vesicles. Composed only of Ala, Leu, and Gln residues, the amino acid sequences of the peptides were varied to change peptide amphiphilicity without changing total hydrophobicity. We found that peptide helicity in water and interface increased linearly with hydrophobic moment, as did the favorable peptide partitioning free energy. This observation provides simple tools for designing amphipathic helical peptides. Finally, our results show that helical amphiphilicity is far more important for interfacial binding than simple hydrophobicity.

Amphiphilic laminin peptides at air/water interface--effect of single amino acid mutations on surface properties

Amphiphilic derivative of the laminin peptide YIGSR and three other mutated peptides with mutation at Y with V (valine), I (isoleucine), and L (leucine) have been synthesized. The monolayer formation and the stability of these peptide analogues at air/water interface and the interaction with phospholipid monolayers have been studied using surface pressure-molecular area (pi-A) and surface potential-molecular area (DeltaV-A) isotherms. The single amino acid mutation in the native sequence leads to appreciable changes in surface activity, orientation and insertion into lipid monolayers with LIGSR showing most hydrophobic character while YIGSR showed most polar nature. The morphology of spread monolayers in the most close packed state was carried out using Brewster angle microscopy (BAM). LB films of these amphiphilic peptide derivatives transferred to hydrophilic quartz surfaces and hydrophobically modified surfaces showed significant changes in the work of adhesion as well as spreading behavior of water with the L substituted sequence showing maximum work of adhesion and the native sequence YIGSR, the least work of adhesion. From theoretical estimates, the long-range effects of the different amino acid residues in position 1 on the alkyl chains have been studied from charge on the carbon and hydrogen atoms of the alkyl tails. The present study demonstrates that amphiphilic derivatives of the laminin peptide YIGSR show enhanced activity compared to the original sequence. This work shows that the amino acid substituents on the head group clearly influence the distal methylene groups of the tail. Thus, any mutation of even single amino acid in a peptide sequence influences and plays an important role in determining macroscopic properties such as surface energy and adhesion both at air/solution and solid/solution interfaces.

Analyses of dose-response curves to compare the antimicrobial activity of model cationic alpha-helical peptides highlights the necessity for a minimum of two activity parameters

To assess and compare different model Leu-Lys-containing cationic alpha-helical peptides, their antimicrobial activities were tested against Escherichia coli as target organism over a broad peptide concentration range. The natural cationic alpha-helical peptides magainin 2 and PGLa and the cyclic cationic peptide gramicidin S were also tested between comparison. The dose-response curves differed widely for these peptides, making it difficult to rank them into an activity order over the whole concentration range. We therefore compared five different inhibition parameters from dose-response curves: IC(min) (lowest concentration leading to growth inhibition), IC(50) (concentration that gives 50% growth inhibition), IC(max) (related to minimum inhibition concentration and minimum bactericidal concentration), inhibition concentration factor (IC(F); describing the increase in concentration of the peptide between minimum and maximum inhibition), and activity slope (A(S); related to the Hill coefficient). We found that these parameters were covariant: two of them sufficed to characterize the dose dependence and hence the activity of the peptides. This was corroborated by showing that the dose dependences followed the Hill equation, with a small, constant aberration. We propose that the activity of antimicrobial peptides can readily be characterized by both IC(50) and IC(F) (or A(S)) rather than by a single parameter and discuss how this may relate to investigations into their mechanisms of action.

Tuning the biological properties of amphipathic alpha-helical antimicrobial peptides: rational use of minimal amino acid substitutions

In nature, alpha-helical antimicrobial peptides present the small and flexible residue glycine at positions 7 or 14 with a significant frequency. Based on the sequence of the non-proteinogenic alpha-helical model peptide P1(Aib7), with a potent, broad spectrum antimicrobial activity, six peptides were designed by effecting a single amino acid substitution to investigate how tuning the structural characteristics at position 7 could lead to optimization of selectivity without affecting antimicrobial activity against a broad panel of multidrug resistant bacterial and yeast indicator strains. The relationship between structural features (size/hydrophobicity of the side chain as well as conformation and flexibility) and biological activity, in terms of minimum inhibitory concentration, membrane permeabilization kinetics and lysis of red blood cells are discussed. On conversion of the peptide to proteinogenic residues, these principles allowed development of a potent antimicrobial peptide with a reduced cytotoxicity. However, while results suggest that both hydrophobicity of residue 7 and chain flexibility at this position can be modulated to improve selectivity, position 14 is less tolerant of substitutions.

Pathogen-induced expression of a cecropin A-melittin antimicrobial peptide gene confers antifungal resistance in transgenic tobacco

Expression of defensive genes from a promoter that is specifically activated in response to pathogen invasion is highly desirable for engineering disease-resistant plants. A plant transformation vector was constructed with transcriptional fusion between the pathogen-responsive win3.12T promoter from poplar and the gene encoding the novel cecropin A-melittin hybrid peptide (CEMA) with strong antimicrobial activity. This promoter-transgene combination was evaluated in transgenic tobacco (Nicotiana tabacum L. cv. Xanthi) for enhanced plant resistance against a highly virulent pathogenic fungus Fusarium solani. Transgene expression in leaves was strongly increased after fungal infection or mechanical wounding, and the accumulation of CEMA transcripts was found to be systemic and positively correlated with the number of transgene insertions. A simple and efficient in vitro regeneration bioassay for preliminary screening of transgenic lines against pathogenic fungi was developed. CEMA had strong antifungal activity in vitro, inhibiting conidia germination at concentrations that were non-toxic to tobacco protoplasts. Most importantly, the expression level of the CEMA peptide in vivo, regulated by the win3.12T promoter, was sufficient to confer resistance against F. solani in transgenic tobacco. The antifungal resistance of plants with high CEMA expression was strong and reproducible. In addition, leaf tissue extracts from transgenic plants significantly reduced the number of fungal colonies arising from germinated conidia. Accumulation of CEMA peptide in transgenic tobacco had no deleterious effect on plant growth and development. This is the first report showing the application of a heterologous pathogen-inducible promoter to direct the expression of an antimicrobial peptide in plants, and the feasibility of this approach to provide disease resistance in tobacco and, possibly, other crops.

Design and activity of antimicrobial peptides against sporogonic-stage parasites causing murine malarias

Insects produce several types of peptides to combat a broad spectrum of invasive pathogenic microbes, including protozoans. However, despite this defense response, infections are often established. Our aim was to design novel peptides that produce high rates of mortality among protozoa of the genus Plasmodium, the malaria parasites. Using existing antimicrobial peptide sequences as templates, we designed and synthesized three short novel hybrids, designated Vida1 to Vida3. Each has a slightly different predicted secondary structure. The peptides were tested against sporogonic stages of the rodent malaria parasites Plasmodium berghei (in vitro and in vivo) and P. yoelii nigeriensis (in vitro). The level of activity varied for each peptide and according to the parasite stage targeted. Vida3 (which is predicted to have large numbers of beta sheets and coils but no alpha helices) showed the highest level of activity, killing the early sporogonic stages in culture and causing highly significant reductions in the prevalence and intensity of infection of P. berghei after oral administration or injection in Anopheles gambiae mosquitoes. The secondary structures of these peptides may play a crucial role in their ability to interact with and kill sporogonic forms of the malaria parasite.

Identification of novel hexapeptides bioactive against phytopathogenic fungi through screening of a synthetic peptide combinatorial library

The purpose of the present study was to improve the antifungal activity against selected phytopathogenic fungi of the previously identified hexapeptide PAF19. We describe some properties of a set of novel synthetic hexapeptides whose D-amino acid sequences were obtained through screening of a synthetic peptide combinatorial library in a positional scanning format. As a result of the screening, 12 putative bioactive peptides were identified, synthesized, and assayed. The peptides PAF26 (Ac-rkkwfw-NH(2)), PAF32 (Ac-rkwhfw-NH(2)), and PAF34 (Ac-rkwlfw-NH(2)) showed stronger activity than PAF19 against isolates of Penicillium digitatum, Penicillium italicum, and Botrytis cinerea. PAF26 and PAF32, but not PAF34, were also active against Fusarium oxysporum. Penicillium expansum was less susceptible to all four PAF peptides, and only PAF34 showed weak activity against it. Assays were also conducted on nontarget organisms, and PAF26 and PAF32 showed much-reduced toxicity to Escherichia coli and Saccharomyces cerevisiae, demonstrating selectivity towards certain filamentous fungi. Thus, the data showed distinct activity profiles for peptides differentiated by just one or two residue substitutions. Our conclusion from this observation is that a specificity factor is involved in the activity of these short peptides. Furthermore, PAF26 and PAF32 displayed activities against P. digitatum, P. italicum, and B. cinerea similar to that of the hemolytic 26-amino acid melittin, but they did not show the high toxicity of melittin towards bacteria and yeasts. The four peptides acted additively, with no synergistic interactions among them, and PAF26 was shown to have improved activity over PAF19 in in vivo orange fruit decay experiments.

A synthetic peptide of human apoprotein E with antibacterial activity

In recent years, several endogenous mammalian antibacterial peptides have been described. An amphipathic cationicalpha-helix is a common feature in many cases; therefore, other peptides with this characteristic might also possess antibiotic activity. In fact, a 30-mer peptide of apoprotein E 133-162 (LRVRLASHLRKLRKRLLRDADDLQKRLAVY) was found to have antibiotic activity comparable to those of a classic antibiotic (Gentamicin) and a neutrophil-derived antibiotic peptide (CAP18). Calculation of cationicity, hydrophobicity, and hydrophobic moment and the helical wheel diagram of apoprotein E 133-162 revealed close similarities to CAP18.

MiAMP1, a novel protein from Macadamia integrifolia adopts a Greek key beta-barrel fold unique amongst plant antimicrobial proteins

MiAMP1 is a recently discovered 76 amino acid residue, highly basic protein from the nut kernel of Macadamia integrifolia which possesses no sequence homology to any known protein and inhibits the growth of several microbial plant pathogens in vitro while having no effect on mammalian or plant cells. It is considered to be a potentially useful tool for the genetic engineering of disease resistance in transgenic crop plants and for the design of new fungicides. The three-dimensional structure of MiAMP1 was determined through homonuclear and heteronuclear ((15)N) 2D NMR spectroscopy and subsequent simulated annealing calculations with the ultimate aim of understanding the structure-activity relationships of the protein. MiAMP1 is made up of eight beta-strands which are arranged in two Greek key motifs. These Greek key motifs associate to form a Greek key beta-barrel. This structure is unique amongst plant antimicrobial proteins and forms a new class which we term the beta-barrelins. Interestingly, the structure of MiAMP1 bears remarkable similarity to a yeast killer toxin from Williopsis mrakii. This toxin acts by inhibiting beta-glucan synthesis and thereby cell wall construction in sensitive strains of yeast. The structural similarity of MiAMP1 and WmKT, which originate from plant and fungal phyla respectively, may reflect a similar mode of action.

Biological activities of C-terminal 15-residue synthetic fragment of melittin: design of an analog with improved antibacterial activity

Melittin, the 26-residue predominant toxic peptide from bee venom, exhibits potent antibacterial activity in addition to its hemolytic activity. The synthetic peptide of 15 residues corresponding to its C-terminal end (MCF), which encompasses its most amphiphilic segment, is now being shown to possess antibacterial activity about 5-7 times less compared to that of melittin. MCF, however, is 300 times less hemolytic. An analog of MCF, MCFA, in which two cationic residues have been transpositioned to the N-terminal region from the C-terminal region, exhibits antibacterial activity comparable to that of melittin, but is only marginally more hemolytic than MCF. The biophysical properties of the peptides, like folding and aggregation, correlate well with their biological properties.

Conformation and antimicrobial activity of linear derivatives of tachyplesin lacking disulfide bonds

Tachyplesin is a potent antimicrobial peptide isolated from the hemocytes of the horseshoe crab, Tachypleus tridentatus. Previous studies have shown that the 17-residue peptide has an intrinsic amphipathic structure conferred by two antiparallel beta-sheets held rigidly by two disulfide bonds. Taking its short length into account and the potential of such a small polypeptide to take on multiple conformational states, one may assume that the disulfide bonds are relevant determinants of function. However, in order to gain a global perspective on the tolerance of cysteine residues in tachyplesin to amino acid substitutions, a series of linear peptides have been synthesized and their physicochemical properties analyzed. In these linear peptides, the cysteines have been replaced with amino acids possessing different side-chain properties, i.e., aliphatic hydrophobic (Ala, Leu, Ile, Val, and Met), aromatic hydrophobic (Phe and Tyr), and acidic (Asp). Activity assays using natural and synthetic membranes, and conformational measurements, highlight the subtle influence and variability of the amino acid side-chain properties on peptide structure. While an unequivocal interpretation of the results will have to await more refined structural measurements, our results indicate that a rigidly held disulfide-bonded beta-pleated sheet structure may not be absolutely essential for antimicrobial activity. Furthermore, the results challenge the accepted dogma of structure-activity relationships among antimicrobial peptides and suggest that the maintenance of peptide hydrophobic-hydrophilic balance may be a critical parameter, in addition to structure, in the design of peptides with pharmaceutical relevance.

Structure-activity analysis of brevinin 1E amide, an antimicrobial peptide from Rana esculenta

Brevinin 1E, consisting of 24 amino acid residues, from Rana esculenta has potent antimicrobial and hemolytic activity. From a structural point of view, this peptide has a N-terminal hydrophobic region, a proline hinge region in the middle and a C-terminal loop region delineated by an intra-disulfide bridge, which is a common structural feature of antimicrobial peptides from Rana species. To investigate the structural features for antimicrobial and hemolytic activity, truncated and linearized brevinin 1E amides were synthesized and characterized. A deletion of three amino acids from the N-terminal region did not greatly affect antimicrobial activity but dramatically reduced hemolytic activity. The contribution of the intra-disulfide bridge to antimicrobial and hemolytic activity was somewhat different between brevinin 1E amide and truncated fragments. In brevinin 1E amide, the elimination of the intra-disulfide bridge did not greatly affect antimicrobial and hemolytic activity whereas the elimination of the intra-disulfide bridge in the truncated fragments did not decrease antimicrobial activity but did decrease hemolytic activity. Circular dichroism spectra and the retention time on the C18 reverse phase column revealed that the intra-disulfide bridge (i, i+6) formed an amphipathic loop which increased hydrophobicity and helped to induce the alpha-helical structure in the membrane-mimetic environment. Even though the intra-disulfide bridge and the N-terminal region were responsible for the alpha-helical structure and hydrophobicity, these two structural features were not essential for antimicrobial activity. The hemolytic activity of brevinin 1E amide and its analogs also correlated well with the retention time rather than the alpha-helicity.

Identification and characterization of the antimicrobial peptide corresponding to C-terminal beta-sheet domain of tenecin 1, an antibacterial protein of larvae of Tenebrio molitor

An active fragment was identified from tenecin 1, an antibacterial protein belonging to the insect defensin family, by synthesizing the peptides corresponding to the three regions of tenecin 1. Only the fragment corresponding to the C-terminal beta-sheet domain showed activity against fungi as well as Gram-positive and Gram-negative bacteria, whereas tenecin 1, the native protein, showed activity only against Gram-positive bacteria. CD spectra indicated that each fragment in a membrane-mimetic environment might adopt a secondary structure corresponding to its region in the protein. The leakage of dye from liposomes induced by this fragment suggested that this fragment acts on the membrane of pathogens as a primary mode of action. A comparison between the structure and the activity of each fragment indicated that a net positive charge was a prerequisite factor for activity. To the best of our knowledge this is the first report in which the fragment corresponding to the beta-sheet region in antibacterial proteins, which consists of alpha-helical and beta-sheet regions, has been identified as a primary active fragment.

Modification of a synthetic antimicrobial peptide (ESF1) for improved inhibitory activity

Rational modification of an existing cationic alpha-helical antimicrobial peptide (ESF1) for improved activity by increasing amphipathicity was undertaken. ESF1 and two variants (GR7 and SA3) were synthesized and tested for activity range, minimum inhibitory concentration, and hemolytic activity. Biological activity was related to structure as determined by circular dichroism. The substitution of arginine for glycine in position seven was found to increase antimicrobial activity without effecting hemolysis. Increased activity was related to stronger alpha-helix formation in buffer. Increased beta-sheet formation in micellar SDS was observed and speculated to be due to a stronger ability of the variants to form multimolecule complexes, a feature consistent with existing models of cationic peptide activity.

Structural variations in nisin associated with different membrane mimicking and pH environments

Nisin is a membrane active antimicrobial peptide containing unusual dehydrated amino acid residues. The secondary structure of nisin in aqueous solution, membrane mimicking solvents and at various pH values was investigated using circular dichroism. In aqueous solution nisin is largely randomly coiled. In liposomes and at pH 6 and above, however, the presence of a maximum at 195 nm and a minimum at 190 nm was notable and indicative of beta-turn formation in these environments. This change in structure was speculated to result in an increasing unavailability of the site for initial reaction of peptide and membrane at higher pH.

Design of synthetic antimicrobial peptides based on sequence analogy and amphipathicity

Novel alpha-helical antimicrobial peptides have been devised by comparing the N-terminal sequences of many of these peptides from insect, frog and mammalian families, extracting common features, and creating sequence templates with which to design active peptides. Determination of the most frequent amino acids in the first 20 positions for over 80 different natural sequences allowed the design of one peptide, while a further three were based on the comparison of the sequences of alpha-helical antimicrobial peptides derived from the mammalian cathelicidin family of precursors. These peptides were predicted to assume a highly amphipathic alpha-helical conformation, as indicated by high mean hydrophobic moments. In fact, circular dichroism experiments showed clear transitions from random coil in aqueous solution to an alpha-helical conformation on addition of trifluoroethanol. All four peptides displayed a potent antibacterial activity against selected gram-positive and gram-negative bacteria (minimum inhibitory concentrations in the range 1-8 microM), including some antibiotic resistant strains. Permeabilization of both the outer and cytoplasmic membranes of the gram-negative bacterium, Escherichia coli, by selected peptides was quite rapid and a dramatic drop in colony forming units was observed within 5 min in time-killing experiments. Permeabilization of the cytoplasmic membrane of the gram-positive bacterium, Staphylococcus aureus, was instead initially quite slow, gathering speed after 45 min, which corresponds to the time required for significant inactivation in time-killing studies. The cytotoxic activity of the peptides, determined on several normal and transformed cell lines, was generally low at values within the minimum inhibitory concentration range.

Modulation of membrane activity of amphipathic, antibacterial peptides by slight modifications of the hydrophobic moment

Starting from the sequences of magainin 2 analogs, peptides with slightly increased hydrophobic moment (mu) but retained other structural parameters were designed. Circular dichroism investigations revealed that all peptides adopt an alpha-helical conformation when bound to phospholipid vesicles. Analogs with increased mu were considerably more active in permeabilizing vesicles mainly composed of zwitterionic lipid. In addition, the antibacterial and hemolytic activities of these analogs were enhanced. Correlation of permeabilization and binding indicated that the activity increase is predominantly caused by an increased membrane affinity of the peptides due to strengthened hydrophobic interactions.

Surface activity properties of cysteine-substituted C-terminal melittin analogues

In order to extend our knowledge of factors important in the surface activity of melittin, cysteine was substituted for lysine-21 and lysine-21/glutamine-25 in a pair of synthetic peptide analogues. The first of these changes resulted in only modest effects on secondary structure (determined in 50% trifluoroethanol), emulsification and surface tension properties. Introduction of a second cysteine greatly reduced both the rate of surface tension decay and the equilibrium surface tension attained, although secondary structure (determined in 50% trifluoroethanol) was only slightly affected by this modification. This latter peptide completely lacked emulsification and haemolytic properties and was found to oligomerise readily due to the formation of intermolecular, disulphide bridges. These results indicate that oligomerisation abolishes surface activity in melittin.

Effects of the anti-bacterial peptide cecropin B and its analogs, cecropins B-1 and B-2, on liposomes, bacteria, and cancer cells

Custom designed analogs of the natural anti-bacterial peptide cecropin B (CB) have been synthesized; cecropin B-1 (CB-1) was constructed by replacing the C-terminal segment (residues 26 to 35) with the N-terminal sequence of CB (positions 1 to 10 which include five lysine residues). The second analog, CB-2, is identical to CB-1 except for the insertion of a Gly-Pro residue pair between Pro-24 and Ala-25. These peptides were used to investigate their anti-liposome, anti-bacterial and anti-cancer activities. The strength of anti-liposome activity is reduced two- to three-fold when the analogs are used instead of natural CB based on DL50 analysis. Similarly, the potency of these analogs on certain bacteria is about two- to four-fold lower than those of CB based on LC measurements. In contrast, on leukemia cancer cells, the potency of CB-1 and CB-2 is about two- to three-fold greater than that of natural CB based on IC50 measurements. All CB, CB-1 and CB-2 peptides have comparable helix contents according to CD measurements. These results indicate that the designed cationic lytic peptides, having extra cationic residues, are less effective in breaking liposomes and killing bacteria but more effective in lysing cancer cells. The possible interpretations for these observations are discussed.

Purification, characterisation and cDNA cloning of an antimicrobial peptide from Macadamia integrifolia

An antimicrobial peptide with no significant amino acid sequence similarity to previously described peptides has been isolated from the nut kernels of Macadcamia integrifolia. The peptide, termed MiAMP1, is highly basic with an estimated pI of 10.1, a mass of 8.1 kDa and contains 76 amino acids including 6 cysteine residues. A cDNA clone containing the entire coding region corresponding to the peptide was obtained. The deduced amino acid sequence of the cDNA indicated a 26-amino-acid signal peptide at the N-terminus of the preprotein. Purified MiAMP1 inhibited the growth of a variety of fungal, oomycete and gram-positive bacterial phytopathogens in vitro. Some pathogens exhibited close to 100% inhibition in less than 1 microM peptide (5 microg/ml). Antimicrobial activity was diminished against most, but not all, microbes in the presence of calcium and potassium chloride salts (1 mM and 50 mM, respectively). MiAMP1 was active against bakers yeast, was inactive against Escherichia coli and was non-toxic to plant and mammalian cells. Analysis of genomic DNA indicated that MiAMP1 was encoded on a single copy gene containing no introns. The MiAMP1 gene may prove useful in genetic manipulations to increase disease resistance in transgenic plants.

Interaction of alpha s2- and beta-casein signal peptides with DMPC and DMPG liposomes

Interactions of casein signal peptides (CSP) and derivatives were detected with dimyristoylphosphatidyl-glycerol and -choline liposomes. Fluorescence anisotrophy indicated that the peptides interact better with DMPG than DMPC, inserting at a limited depth in the bilayer. Stronger interaction was detected for derivatives of beta-CSP than of alpha s2-CSP. Tryptophan fluorescence (intrinsic, energy transfer, quenching) showed that the central hydrophobic core of CSP was buried in the bilayer whereas both ends remained outside, adopting a hairpin-like conformation. The secondary structure of the CSP was not affected by their interactions with phospholipids. beta-CSP derivatives show both lytic and fusogenic activities.

Design of active analogues of a 15-residue peptide using D-optimal design, QSAR and a combinatorial search algorithm

This report describes the rational design of novel analogues of a 15-residue antibacterial peptide CAMEL0. A constrained D-optimal design was carried out to derive a training set of 60 analogues. Partial least squares (PLS) models describing quantitative structure-activity relationships (QSARs) were initially derived for the peptides using two published and one novel parameter set. The novel "Design parameters' were based on key structural features identified in hypothetical models of the mechanisms by which peptides interact with cell membranes. In an extension of the PLS method, influence statistics were used to decrease the weighting of compounds having a large effect on model predictions. A combinatorial search algorithm was developed which used PLS models as predictors to select a test set of 39 peptides with high predicted potencies. Within this set, the most potent analogue CAMEL135, which contained seven point mutations from CAMEL0, was identified. For a panel of 24 bacteria, the mean MIC value of CAMEL135 was approximately half of that for CAMEL0. For the parameter sets tested, covariance functions derived from Z-scales gave highest Q2-values for the training set, whilst the model using the the 'Design parameters' gave least error when predicting the activity of the test set. The predictive ability of a third published set of peptide parameters was found to compare favourably with that of the parameters used in the design. Analysis of the PLS models indicates that hydrophobicity and amphipathicity are the most important features influencing activity for this class of compound.