More than 3000 antimicrobial peptides (AMPs) have been discovered, seven of which have been approved by the U.S. Food and Drug Administration (FDA). Now commercialized, these seven peptides have mostly been utilized for topical medications, though some have been injected into the body to treat severe bacterial infections. To understand the translational potential for AMPs, we analyzed FDA-approved drugs in the FDA drug database. We examined their physicochemical properties, secondary structures, and mechanisms of action, and compared them with the peptides in the AMP database. All FDA-approved AMPs were discovered in Gram-positive soil bacteria, and 98% of known AMPs also come from natural sources (skin secretions of frogs and toxins from different species). However, AMPs can have undesirable properties as drugs, including instability and toxicity. Thus, the design and construction of effective AMPs require an understanding of the mechanisms of known peptides and their effects on the human body. This review provides an overview to guide the development of AMPs that can potentially be used as antimicrobial drugs.

Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures—formed by a single sequence—may be a key feature in preventing bacterial resistance and could explain why sequence–function relationships in AMPs remain elusive.

In the age of failing small-molecule antibiotics, tapping the near-infinite structural and chemical repertoire of antimicrobial peptides (AMPs) offers one of the most promising routes toward developing next-generation antibacterial compounds. One of the key impediments en route is the lack of methodologies for systematic rational design and optimization of new AMPs. Here we present a new simulation-guided rational design approach and apply it to develop a potent new AMP. We show that unbiased atomic detail molecular dynamics (MD) simulations are able to predict structures formed by evolving peptide designs enabling structure-based rational fine-tuning of functional properties. Starting from a 14-residue poly leucine template we demonstrate the design of a minimalistic potent new AMP. Consisting of only four types of amino acids (LDKA), this peptide forms large pores in microbial membranes at very low peptide-to-lipid ratios (1:1000) and exhibits low micromolar activity against common Gram-positive and Gram-negative pathogenic bacteria. Remarkably, the four amino acids were sufficient to encode preferential poration of bacterial membranes with negligible damage to red blood cells at bactericidal concentrations. As the sequence is too short to span cellular membranes, pores are formed by stacking of channels in each bilayer leaflet.

Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.

Copper(II) 2,2'-bipyridine (Cu(II) (bpy))-catalyzed alkaline hydrogen peroxide (AHP) pretreatment was performed on three biomass feedstocks including alkali pre-extracted switchgrass, silver birch, and a hybrid poplar cultivar. This catalytic approach was found to improve the subsequent enzymatic hydrolysis of plant cell wall polysaccharides to monosaccharides for all biomass types at alkaline pH relative to uncatalyzed pretreatment. The hybrid poplar exhibited the most significant improvement in enzymatic hydrolysis with monomeric sugar release and conversions more than doubling from 30% to 61% glucan conversion, while lignin solubilization was increased from 36.6% to 50.2% and hemicellulose solubilization was increased from 14.9% to 32.7%. It was found that Cu(II) (bpy)-catalyzed AHP pretreatment of cellulose resulted in significantly more depolymerization than uncatalyzed AHP pretreatment (78.4% vs. 49.4% decrease in estimated degree of polymerization) and that carboxyl content the cellulose was significantly increased as well (fivefold increase vs. twofold increase). Together, these results indicate that Cu(II) (bpy)-catalyzed AHP pretreatment represents a promising route to biomass deconstruction for bioenergy applications.

BackgroundOne route for producing cellulosic biofuels is by the fermentation of lignocellulose-derived sugars generated from a pretreatment that can be effectively coupled with an enzymatic hydrolysis of the plant cell wall. While woody biomass exhibits a number of positive agronomic and logistical attributes, these feedstocks are significantly more recalcitrant to chemical pretreatments than herbaceous feedstocks, requiring higher chemical and energy inputs to achieve high sugar yields from enzymatic hydrolysis. We previously discovered that alkaline hydrogen peroxide (AHP) pretreatment catalyzed by copper(II) 2,2΄-bipyridine complexes significantly improves subsequent enzymatic glucose and xylose release from hybrid poplar heartwood and sapwood relative to uncatalyzed AHP pretreatment at modest reaction conditions (room temperature and atmospheric pressure). In the present work, the reaction conditions for this catalyzed AHP pretreatment were investigated in more detail with the aim of better characterizing the relationship between pretreatment conditions and subsequent enzymatic sugar release.ResultsWe found that for a wide range of pretreatment conditions, the catalyzed pretreatment resulted in significantly higher glucose and xylose enzymatic hydrolysis yields (as high as 80% for both glucose and xylose) relative to uncatalyzed pretreatment (up to 40% for glucose and 50% for xylose). We identified that the extent of improvement in glucan and xylan yield using this catalyzed pretreatment approach was a function of pretreatment conditions that included H2O2 loading on biomass, catalyst concentration, solids concentration, and pretreatment duration. Based on these results, several important improvements in pretreatment and hydrolysis conditions were identified that may have a positive economic impact for a process employing a catalyzed oxidative pretreatment. These improvements include identifying that: (1) substantially lower H2O2 loadings can be used that may result in up to a 50-65% decrease in H2O2 application (from 100 mg H2O2/g biomass to 35–50 mg/g) with only minor losses in glucose and xylose yield, (2) a 60% decrease in the catalyst concentration from 5.0 mM to 2.0 mM (corresponding to a catalyst loading of 25 μmol/g biomass to 10 μmol/g biomass) can be achieved without a subsequent loss in glucose yield, (3) an order of magnitude improvement in the time required for pretreatment (minutes versus hours or days) can be realized using the catalyzed pretreatment approach, and (4) enzyme dosage can be reduced to less than 30 mg protein/g glucan and potentially further with only minor losses in glucose and xylose yields. In addition, we established that the reaction rate is improved in both catalyzed and uncatalyzed AHP pretreatment by increased solids concentrations.ConclusionsThis work explored the relationship between reaction conditions impacting a catalyzed oxidative pretreatment of woody biomass and identified that significant decreases in the H2O2, catalyst, and enzyme loading on the biomass as well a...

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BackgroundAlkaline hydrogen peroxide pretreatment catalyzed by Cu(II) 2,2′-bipyridine complexes has previously been determined to substantially improve the enzymatic hydrolysis of woody plants including hybrid poplar as a consequence of moderate delignification. In the present work, cell wall morphological and lignin structural changes were characterized for this pretreatment approach to gain insights into pretreatment outcomes and, specifically, to identify the extent and nature of lignin modification.ResultsThrough TEM imaging, this catalytic oxidation process was shown to disrupt cell wall layers in hybrid poplar. Cu-containing nanoparticles, primarily in the Cu(I) oxidation state, co-localized with the disrupted regions, providing indirect evidence of catalytic activity whereby soluble Cu(II) complexes are reduced and precipitated during pretreatment. The concentration of alkali-soluble polymeric and oligomeric lignin was substantially higher for the Cu-catalyzed oxidative pretreatment. This alkali-soluble lignin content increased with time during the catalytic oxidation process, although the molecular weight distributions were unaltered. Yields of aromatic monomers (including phenolic acids and aldehydes) were found to be less than 0.2 % (wt/wt) on lignin. Oxidation of the benzylic alcohol in the lignin side-chain was evident in NMR spectra of the solubilized lignin, whereas minimal changes were observed for the pretreatment-insoluble lignin.ConclusionsThese results provide indirect evidence for catalytic activity within the cell wall. The low yields of lignin-derived aromatic monomers, together with the detailed characterization of the pretreatment-soluble and pretreatment-insoluble lignins, indicate that the majority of both lignin pools remained relatively unmodified. As such, the lignins resulting from this process retain features closely resembling native lignins and may, therefore, be amenable to subsequent valorization.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0300-5) contains supplementary material, which is available to authorized users.