Flexibility is a mechanical determinant of antimicrobial activity for amphipathic cationic α-helical antimicrobial peptides

Unraveling the molecular drivers of antibacterial prenylated (iso)flavonoids and chalcones against Streptococcus mutans

Given the negative side effects and increased resistance associated with conventional oral antimicrobials, prenylated phenolics are promising alternatives to combat the oral pathogen Streptococcus mutans. A total of 40 prenylated phenolics were evaluated for their antibacterial activity against S. mutans. Eleven prenylated phenolics were purified from licorice (Glycyrrhiza spp.) spent, including the newly discovered double prenylated 2-arylbenzofuran, isokanzonol V. Twenty-eight compounds showed similar potency as chlorhexidine. Activity was correlated with structural properties and novel structure-activity relationships were established: (i) Hydrophobic volume was the main driver associated to activity (double prenylated phenolics were consistently more active than single prenylated phenolics); (ii) the conversion of flavanones to chalcones by C-ring opening increases molecular length and planarity as well as antibacterial activity, and (iii) active single prenylated isoflavones have balanced molecular hydrophilicity. Hence, double or single prenylated phenolics featuring planarity, an extended configuration, and balanced hydrophilicity hold promise for S. mutans control.

The Role of Flexibility in the Bioactivity of Short α-Helical Antimicrobial Peptides

The formation of aqueous pores through the interaction of amphipathic peptides is a process facilitated by the conformational dynamics typical of these biomolecules. Prior to their insertion with the membrane, these peptides go through several conformational states until they finally reach a stable α-helical structure. The conformational dynamics of these pore-forming peptides, α-PFP, is, thus, encoded in their amino acid sequence, which also predetermines their intrinsic flexibility. However, although the role of flexibility is widely recognized as fundamental in their bioactivity, it is still unclear whether this parameter is indeed decisive, as there are reports favoring the view of highly disruptive flexible peptides and others where relative rigidity also predetermines high rates of permeability across membranes. In this review we discuss in depth all those aspects linked to the conformational dynamics of these small biomolecules and which depend on the composition, sequence and dynamic performance both in aqueous phase and in close interaction with phospholipids. In addition, evidence is provided for the contribution of the known carboxyamidation in some well-studied α-PFPs, which are preferentially associated with sequences intrinsically more rigid than those not amidated and generally more flexible than the former. Taken together, this information is of great relevance for the optimization of new antibiotic peptides.

Achatina fulica haemocyanin-derived peptides as novel antimicrobial agents

Haemocyanin-derived peptides were previously found in semi-purified fractions of mucus secretion from the snail Achatina fulica, which exhibited an inhibitory effect on Staphylococcus aureus strains. Here, an in silico rational design strategy was employed to generate new antimicrobial peptides (AMPs) from A. fulica haemocyanin-derived peptides (AfH). The designed peptides were chemically synthetized using the Fmoc strategy, and their antimicrobial activity against Escherichia coli and S. aureus strains was evaluated using the broth microdilution method. In addition, the cytotoxic activity on Vero, HaCat, and human erythrocyte cells was also determined. The results demonstrated that 15-residue alpha-helical and cationic synthetic peptides exhibited the highest biological activity against Gram-positive strains, with minimum inhibitory concentrations (MIC) in the range from 7.5 to 30 μM. The positive selectivity index suggests a higher selectivity, primarily on the microorganisms evaluated, but not on eukaryotic cells. In this study, A. fulica hemocyanin was identified as an appropriate protein model for the rational design of AMPs against bacteria of public health significance. Further studies are required to evaluate the activity of the peptides on Gram-negative bacteria other than E. coli.

Molecular Dynamics Simulations of Structurally Nanoengineered Antimicrobial Peptide Polymers Interacting with Bacterial Cell Membranes

Multidrug resistance (MDR) to conventional antibiotics is one of the most urgent global health threats, necessitating the development of effective and biocompatible antimicrobial agents that are less inclined to provoke resistance. Structurally nanoengineered antimicrobial peptide polymers (SNAPPs) are a novel and promising class of such alternatives. These star-shaped polymers are made of a dendritic core with multiple arms made of copeptides with varying amino acid sequences. Through a comprehensive set of in vivo experiments, we previously showed that SNAPPs with arms made of random blocks of lysine (K) and valine (V) residues exhibit sub-μM efficacy against Gram-negative and Gram-positive bacteria tested. Cryo-TEM images suggested pore formation by a SNAPP with random block copeptide arms as one of their modes of actions. However, the molecular mechanisms responsible for this mode of action of SNAPPs are not fully understood. To address this gap, we employed an atomistic molecular dynamics simulation technique to investigate the influence of three different sequences of amino acids, namely (1) alt-block KKV, (2) ran-block, and (3) diblock motifs on the secondary structure of their arms and SNAPP's overall configuration as well as their interactions with lipid bilayer. We, for the first time, identified a step-by-step mechanism through which alt-block and random SNAPPs interact with lipid bilayer and lead to "pore formation", hence, cell death. These insights provide a strong foundation for further optimization of the chemical structure of SNAPPs for maximum performance against MDR bacteria, therefore offering a promising avenue for addressing antibiotic resistance and the development of effective antibacterial agents.

A Critical Review of Short Antimicrobial Peptides from Scorpion Venoms, Their Physicochemical Attributes, and Potential for the Development of New Drugs

Scorpion venoms have proven to be excellent sources of antimicrobial agents. However, although many of them have been functionally characterized, they remain underutilized as pharmacological agents, despite their evident therapeutic potential. In this review, we discuss the physicochemical properties of short scorpion venom antimicrobial peptides (ssAMPs). Being generally short (13-25 aa) and amidated, their proven antimicrobial activity is generally explained by parameters such as their net charge, the hydrophobic moment, or the degree of helicity. However, for a complete understanding of their biological activities, also considering the properties of the target membranes is of great relevance. Here, with an extensive analysis of the physicochemical, structural, and thermodynamic parameters associated with these biomolecules, we propose a theoretical framework for the rational design of new antimicrobial drugs. Through a comparison of these physicochemical properties with the bioactivity of ssAMPs in pathogenic bacteria such as Staphylococcus aureus or Acinetobacter baumannii, it is evident that in addition to the net charge, the hydrophobic moment, electrostatic energy, or intrinsic flexibility are determining parameters to understand their performance. Although the correlation between these parameters is very complex, the consensus of our analysis suggests that there is a delicate balance between them and that modifying one affects the rest. Understanding the contribution of lipid composition to their bioactivities is also underestimated, which suggests that for each peptide, there is a physiological context to consider for the rational design of new drugs.

Unwrapping the structural and functional features of antimicrobial peptides from wasp venoms

The study of wasp venoms has captured attention due to the presence of a wide variety of active compounds, revealing a diverse array of biological effects. Among these compounds, certain antimicrobial peptides (AMPs) such as mastoparans and chemotactic peptides have emerged as significant players, characterized by their unique amphipathic short linear alpha-helical structure. These peptides exhibit not only antibiotic properties but also a range of other biological activities, which are related to their ability to interact with biological membranes to varying degrees. This review article aims to provide updated insights into the structure/function relationships of AMPs derived from wasp venoms, linking this knowledge to the potential development of innovative treatments against infections.

A Deep Learning Model for Accurate Diagnosis of Infection Using Antibody Repertoires

The adaptive immune receptor repertoire consists of the entire set of an individual's BCRs and TCRs and is believed to contain a record of prior immune responses and the potential for future immunity. Analyses of TCR repertoires via deep learning (DL) methods have successfully diagnosed cancers and infectious diseases, including coronavirus disease 2019. However, few studies have used DL to analyze BCR repertoires. In this study, we collected IgG H chain Ab repertoires from 276 healthy control subjects and 326 patients with various infections. We then extracted a comprehensive feature set consisting of 10 subsets of repertoire-level features and 160 sequence-level features and tested whether these features can distinguish between infected individuals and healthy control subjects. Finally, we developed an ensemble DL model, namely, DL method for infection diagnosis (https://github.com/chenyuan0510/DeepID), and used this model to differentiate between the infected and healthy individuals. Four subsets of repertoire-level features and four sequence-level features were selected because of their excellent predictive performance. The DL method for infection diagnosis outperformed traditional machine learning methods in distinguishing between healthy and infected samples (area under the curve = 0.9883) and achieved a multiclassification accuracy of 0.9104. We also observed differences between the healthy and infected groups in V genes usage, clonal expansion, the complexity of reads within clone, the physical properties in the α region, and the local flexibility of the CDR3 amino acid sequence. Our results suggest that the Ab repertoire is a promising biomarker for the diagnosis of various infections.

Stapling of Peptides Potentiates: The Antibiotic Treatment of Acinetobacter baumannii In Vivo

The rising incidence of multidrug resistance in Gram-negative bacteria underlines the urgency for novel treatment options. One promising new approach is the synergistic combination of antibiotics with antimicrobial peptides. However, the use of such peptides is not straightforward; they are often sensitive to proteolytic degradation, which greatly limits their clinical potential. One approach to increase stability is to apply a hydrocarbon staple to the antimicrobial peptide, thereby fixing them in an α-helical conformation, which renders them less exposed to proteolytic activity. In this work we applied several different hydrocarbon staples to two previously described peptides shown to act on the outer membrane, L6 and L8, and tested their activity in a zebrafish embryo infection model using a clinical isolate of Acinetobacter baumannii as a pathogen. We show that the introduction of such a hydrocarbon staple to the peptide L8 improves its in vivo potentiating activity on antibiotic treatment, without increasing its in vivo antimicrobial activity, toxicity or hemolytic activity.

The Potential of Modified and Multimeric Antimicrobial Peptide Materials as Superbug Killers

Antimicrobial peptides (AMPs) are found in nearly all living organisms, show broad spectrum antibacterial activity, and can modulate the immune system. Furthermore, they have a very low level of resistance induction in bacteria, which makes them an ideal target for drug development and for targeting multi-drug resistant bacteria 'Superbugs'. Despite this promise, AMP therapeutic use is hampered as typically they are toxic to mammalian cells, less active under physiological conditions and are susceptible to proteolytic degradation. Research has focused on addressing these limitations by modifying natural AMP sequences by including e.g., d-amino acids and N-terminal and amino acid side chain modifications to alter structure, hydrophobicity, amphipathicity, and charge of the AMP to improve antimicrobial activity and specificity and at the same time reduce mammalian cell toxicity. Recently, multimerisation (dimers, oligomer conjugates, dendrimers, polymers and self-assembly) of natural and modified AMPs has further been used to address these limitations and has created compounds that have improved activity and biocompatibility compared to their linear counterparts. This review investigates how modifying and multimerising AMPs impacts their activity against bacteria in planktonic and biofilm states of growth.

Main-chain flexibility and hydrophobicity of ionenes strongly impact their antimicrobial activity: an extended study on drug resistance strains and Mycobacterium

The spread of antibiotic-resistant pathogens and the resurgence of tuberculosis disease are major motivations to search for novel antimicrobial agents. Some promising candidates in this respect are cationic polymers, also known as synthetic mimics of antimicrobial peptides (SMAMPs), which act through the membrane-lytic mechanism. Development of resistance toward SMAMPs is less likely than toward currently employed antibiotics; however, further studies are needed to better understand their structure–activity relationship. The main objective of this work is to understand the cross-influence of hydrophobicity, main-chain flexibility, and the topology of ionenes (polycations containing a cationic moiety within the main-chain) on activity. To fulfill this goal, a library of ionenes was developed and compared with previously investigated molecules. The obtained compounds display promising activity against the model microorganisms and drug-resistance clinical isolates, including Mycobacterium tuberculosis. The killing efficiency was also investigated, and results confirm a strong effect of hydrophobicity, revealing higher activity for molecules possessing the flexible linker within the polymer main-chain.

A high significance of the main chain flexibility and an unexpected effect of hydrophobicity on the biological activity in series of ionenes was observed. The most potent among the tested polycations showed high activity toward clinical bacterial isolates.

Epimers l- and d-Phenylseptin: How the relative stereochemistry affects the peptide-membrane interactions

In recent decades, several epimers of peptides containing d-amino acids have been identified in antimicrobial sequences, a feature which has been associated with post-translational modification. Generally, d-isomers present similar or inferior antimicrobial activity, only surpassing their epimers in resistance to peptidases. The naturally occurring l-Phenylseptin (l-Phes) and d-Phenylseptin (d-Phes) peptides (FFFDTLKNLAGKVIGALT-nh₂) were reported with d-epimer showing higher activity against Staphylococcus aureus and Xanthomonas axonopodis in comparison with the l-epimer. In this study, we combine structural (CD, solution NMR), orientational (solid-state NMR) and biophysical (ITC, DSC and DLS) studies to understand the role of the d-phenylalanine in the increase of the antimicrobial activity. Although both peptides are structurally similar in the helical region ranging from D4 to the C-terminus, significant structural differences were observed near the peptides' N-termini (which encompasses the FFF motif). Specific aromatic interactions involving the phenylalanine side chains of d-Phes is responsible to maintaining the F1-F3 residues on the hydrophobic face of the peptide, increasing its amphipathicity when compared to the l-epimer. The higher capability of d-Phes to exert an efficient anchoring in the hydrophobic core of the phospholipid bilayer indicates a pivotal role of the N-terminus in enhancing the interaction between the d-peptide and the membrane interface in relation to its epimer.

Helicity Modulation Improves the Selectivity of Antimicrobial Peptoids

The modulation of conformational flexibility in antimicrobial peptides (AMPs) has been investigated as a strategy to improve their efficacy against bacterial pathogens while reducing their toxicity. Here, we synthesized a library of helicity-modulated antimicrobial peptoids by the position-specific incorporation of helix-inducing monomers. The peptoids displayed minimal variations in hydrophobicity, which permitted the specific assessment of the effect of conformational differences on antimicrobial activity and selectivity. Among the moderately helical peptoids, the most dramatic increase in selectivity was observed in peptoid 17, providing more than a 20-fold increase compared to fully helical peptoid 1. Peptoid 17 had potent broad-spectrum antimicrobial activity that included clinically isolated multi-drug-resistant pathogens. Compared to pexiganan AMP, 17 showed superior metabolic stability, which could potentially reduce the dosage needed, alleviating toxicity. Dye-uptake assays and high-resolution imaging revealed that the antimicrobial activity of 17 was, as with many AMPs, mainly due to membrane disruption. However, the high selectivity of 17 reflected its unique conformational characteristics, with differential interactions between bacterial and erythrocyte membranes. Our results suggest a way to distinguish different membrane compositions solely by helicity modulation, thereby improving the selectivity toward bacterial cells with the maintenance of potent and broad-spectrum activity.

Peptides with Dual Antimicrobial-Anticancer Activity: Strategies to Overcome Peptide Limitations and Rational Design of Anticancer Peptides

Peptides are naturally produced by all organisms and exhibit a wide range of physiological, immunomodulatory, and wound healing functions. Furthermore, they can provide with protection against microorganisms and tumor cells. Their multifaceted performance, high selectivity, and reduced toxicity have positioned them as effective therapeutic agents, representing a positive economic impact for pharmaceutical companies. Currently, efforts have been made to invest in the development of new peptides with antimicrobial and anticancer properties, but the poor stability of these molecules in physiological environments has triggered a bottleneck. Therefore, some tools, such as nanotechnology and in silico approaches can be applied as alternatives to try to overcome these obstacles. In silico studies provide a priori knowledge that can lead to the development of new anticancer peptides with enhanced biological activity and improved stability. This review focuses on the current status of research in peptides with dual antimicrobial-anticancer activity, including advances in computational biology using in silico analyses as a powerful tool for the study and rational design of these types of peptides.

The effect of lipidation and glycosylation on short cationic antimicrobial peptides

The global health threat surrounding bacterial resistance has resulted in antibiotic researchers shifting their focus away from 'traditional' antibiotics and concentrating on other antimicrobial agents, including antimicrobial peptides. These low molecular weight "mini-proteins" exhibit broad-spectrum activity against bacteria, including multi-drug resistant strains, viruses, fungi and protozoa and constitute a major element of the innate-immune system of many multicellular organisms. Some naturally occurring antimicrobial peptides are lipidated and/or glycosylated and almost all antimicrobial peptides in clinical use are either lipopeptides (Daptomycin and Polymyxin E and B) or glycopeptides (Vancomycin). Lipidation, glycosylation and PEGylation are an option for improving stability and activity in serum and for reducing the rapid clearing via the kidneys and liver. Two broad-spectrum antimicrobial peptides NH₂-RIRIRWIIR-CONH₂ (A1) and NH₂-KRRVRWIIW-CONH₂ (B1) were conjugated via a linker, producing A2 and B2, to individual fatty acids of C₈, C₁₀, C₁₂ and C₁₄ and in addition, A2 was conjugated to either glucose, N-acetyl glucosamine, galactose, mannose, lactose or polyethylene glycol (PEG). Antimicrobial activity against two Gram-positive strains (methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus faecalis (VRE)) and three Gram-negative strains (Salmonella typhimurium, E. coli and Pseudomonas aeruginosa) were determined. Activity patterns for the lipidated versions are very complex, dependent on sequence, bacteria and fatty acid. Two reciprocal effects were measured; compared to the parental peptides, some combinations led to a 16-fold improvement whereas other combinations let to a 32-fold reduction in antimicrobial activity. Glycosylation decreased antimicrobial activity by 2 to 16-fold in comparison to A1, respectively on the sugar-peptide combination. PEGylation rendered the peptide inactive. Antimicrobial activity in the presence of 25% human serum of A1 and B1 was reduced 32-fold and 8-fold, respectively. The longer chain fatty acids almost completely restored this activity; however, these fatty acids increased hemolytic activity. B1 modified with C8 increased the therapeutic index by 2-fold for four bacterial strains. Our results suggest that finding the right lipid-peptide combination can lead to improved activity in the presence of serum and potentially more effective drug candidates for animal studies. Glycosylation with the optimal sugar and numbers of sugars at the right peptide position could be an alternative route or could be used in addition to lipidation to counteract solubility and toxicity issues.

Therapeutic Potential of Trp-Rich Engineered Amphiphiles by Single Hydrophobic Amino Acid End-Tagging

End-tagging with a single hydrophobic residue contributes to improve the cell selectivity of antimicrobial peptides (AMPs), but systematic studies have been lacking. Thus, this study aimed to systematically investigate how end-tagging with hydrophobic residues at the C-terminus and Gly capped at the N-terminus of W4 (RWRWWWRWR) affects the bioactivity of W4 variants. Among all the hydrophobic residues, only Ala end-tagging improved the antibacterial activity of W4. Meanwhile, Gly capped at the N-terminus could promote the helical propensity of the end-tagged peptides in dodecylphosphocholine micelles, increasing their antimicrobial activities. Of these peptides, GW4A (GRWRWWWRWRA) showed the best antibacterial activity against the 19 species of bacteria tested (GM_MIC = 1.86 μM) with low toxicity, thus possessing the highest cell selectivity (TI_all = 137.63). It also had rapid sterilization, good salt and serum resistance, and LPS-neutralizing activity. Antibacterial mechanism studies showed that the short peptide GW4A killed bacteria by destroying cell membrane integrity and causing cytoplasmic leakage. Overall, these findings suggested that systematic studies on terminal modifications promoted the development of peptide design theory and provided a potential method for optimization of effective AMPs.

Increases in Hydrophilicity and Charge on the Polar Face of Alyteserin 1c Helix Change its Selectivity towards Gram-Positive Bacteria

Recently, resistance of pathogens towards conventional antibiotics has increased, representing a threat to public health globally. As part of the fight against this, studies on alternative antibiotics such as antimicrobial peptides have been performed, and it has been shown that their sequence and structure are closely related to their antimicrobial activity. Against this background, we here evaluated the antibacterial activity of two peptides developed by solid-phase synthesis, Alyteserin 1c (WT) and its mutant derivative (ΔM), which shows increased net charge and reduced hydrophobicity. These structural characteristics were modified as a result of amino acid substitutions on the polar face of the WT helix. The minimum inhibitory concentration (MIC) of both peptides was obtained in Gram-positive and Gram-negative bacteria. The results showed that the rational substitutions of the amino acids increased the activity in Gram-positive bacteria, especially against Staphylococcus aureus, for which the MIC was one-third of that for the WT analog. In contrast to the case for Gram-positive bacteria, these substitutions decreased activity against Gram-negative bacteria, especially in Escherichia coli, for which the MIC was eight-fold higher than that exhibited by the WT peptide. To understand this, models of the peptide behavior upon interacting with membranes of E. coli and S. aureus created using molecular dynamics were studied and it was determined that the helical stability of the peptide is indispensable for antimicrobial activity. The hydrogen bonds between the His20 of the peptides and the phospholipids of the membranes should modulate the selectivity associated with structural stability at the carboxy-terminal region of the peptides.

Star-shaped polypeptides exhibit potent antibacterial activities

Peptide-based biomaterials are a promising class of antimicrobial agents that work by physically damaging bacterial cell membranes rather than targeting intracellular factors, resulting in less susceptibility to drug resistance. Herein we report the synthesis of cationic, star-shaped polypeptides with 3 to 8 arms and their evaluation as antimicrobial agents against different types of bacteria. The effects of the arm number and side chain group on their antimicrobial activities were systematically investigated. Compared to their linear counterparts, these star-shaped polypeptides exhibited potent antibacterial activity (which may involve adhesion and disruption processes). The increase of the arm number can efficiently increase the antibacterial activities up until 8 arms, which did not exhibit further improvement of antibacterial activities. Poly(l-lysine) (PLL) modified with an indole group (PLL-g-indo) exhibited the best antibacterial activity among all grafted copolypeptides and improved cytotoxic selectivity towards pathogens over mammalian cells without compromising their hemolytic activities. In vivo studies showed that the star-shaped PLL-g-indo can effectively suppress Enterohaemorrhagic E. coli (EHEC) infection and attenuate the clinical symptoms in mice, suggesting that they are promising antimicrobial agents.

Inhibitory effect of four novel synthetic peptides on food spoilage yeasts

The spoilage of foods caused by the growth of undesirable yeast species is a problem in the food industry. Yeast species such as Zygosaccharomyces bailii, Zygosaccharomyces rouxii, Debaryomyces hansenii, Kluyveromyces lactis and Saccharomyces cerevisiae have been encountered in foods such as high sugar products, fruit juices, wine, mayonnaise, chocolate and soft drinks. The demand for new methods of preservations has increased because of the negative association attached to chemical preservatives. The sequence of a novel short peptide (KKFFRAWWAPRFLK-NH2) was modified to generate three versions of this original peptide. These peptides were tested for the inhibition of the yeasts mentioned above, allowing for the better understanding of their residue modifications. The range of the minimum inhibitory concentration was between 25 and 200 μg/mL. Zygosaccharomyces bailii was the most sensitive strain to the peptides, while Zygosaccharomyces rouxii was the most resistant. Membrane permeabilisation was found to be responsible for yeast inhibition at a level which was a two-fold increase of the MIC (400 μg/mL). The possibility of the production of reactive oxygen species was also assessed but was not recognised as a factor involved for the peptides' mode of action. Their stability in different environments was also tested, focusing on high salt, pH and thermal stability. The newly designed peptides showed good antifungal activity against some common food spoilage yeasts and has been proven effective in the application in Fanta Orange. These efficient novel peptides represent a new source of food preservation that can be used as an alternative for current controversial preservatives used in the food industry.

Discovery and identification of antimicrobial peptides in Sichuan pepper (Zanthoxylum bungeanum Maxim) seeds by peptidomics and bioinformatics

Antimicrobial peptides (AMPs) have generated growing attention because of the increasing bacterial resistance. However, the discovery and identification of AMPs have proven to be challenging due to the complex purification procedure associated with conventional methods. For the reasons given above, it is necessary to explore more efficient ways to obtain AMPs. We established a new method for discovery and identification of novel AMPs by proteomics and bioinformatics from Zanthoxylum bungeanum Maxim seeds protein hydrolysate directly. This process was initially achieved by employing ultra-performance liquid chromatography-electrospray ionization-mass spectrometry/mass (UPLC-ESI-MS/MS) spectrometry to identify peptides derived from Z. bungeanum Maxim seed protein hydrolysates. Three online servers were introduced to predict potential AMPs. Sixteen potential AMPs ranging from 1.5 to 2.7 kDa were predicted and chemically synthesized, one of which, designated NP-6, inhibited activity against all the tested strains according to antimicrobial assay. Time-killing assay indicated that NP-6 could quickly kill almost all the Escherichia coli within 180 min and Staphylococcus aureus at 360 min. Moreover, the simulation 3D structure of NP-6 was consisted of α-helix and random coil, and this was verified by circular dichroism (CD) spectra. At last, the scanning electron microscope (SEM) images of E. coli and S. aureus treated by NP-6 demonstrated that NP-6 had a significant effect on bacteria cell morphology. Our findings provide an efficient approach for discovery of AMPs, and Z. bungeanum Maxim seeds may be a nature resource to extract antimicrobial agents.

The Evolutionary Conserved γ-Core Motif Influences the Anti-Candida Activity of the Penicillium chrysogenum Antifungal Protein PAF

Small, cysteine-rich and cationic antimicrobial proteins (AMPs) from filamentous ascomycetes represent ideal bio-molecules for the development of next-generation antifungal therapeutics. They are promising candidates to counteract resistance development and may complement or even replace current small molecule-based antibiotics in the future. In this study, we show that a 14 amino acid (aa) long peptide (Pγ) spanning the highly conserved γ-core motif of the Penicillium chrysogenum antifungal protein (PAF) has antifungal activity against the opportunistic human pathogenic yeast Candida albicans. By substituting specific aa we elevated the positive net charge and the hydrophilicity of Pγ and created the peptide variants Pγvar and Pγopt with 10-fold higher antifungal activity than Pγ. Similarly, the antifungal efficacy of the PAF protein could be significantly improved by exchanging the respective aa in the γ-core of the protein by creating the protein variants PAFγvar and PAFγopt. The designed peptides and proteins were investigated in detail for their physicochemical features and mode of action, and were tested for cytotoxicity on mammalian cells. This study proves for the first time the important role of the γ-core motif in the biological function of an AMP from ascomycetes. Furthermore, we provide a detailed phylogenetic analysis that proves the presence and conservation of the γ-core motif in all AMP classes from Eurotiomycetes. We emphasize the potential of this common protein motif for the design of short antifungal peptides and as a protein motif in which targeted aa substitutions enhance antimicrobial activity.

QSAR-based molecular signatures of prenylated (iso)flavonoids underlying antimicrobial potency against and membrane-disruption in Gram positive and Gram negative bacteria

Prenylated flavonoids and isoflavonoids are phytochemicals with remarkable antibacterial activity. In this study, 30 prenylated (iso)flavonoids were tested against Listeria monocytogenes and Escherichia coli (the latter in combination with an efflux pump inhibitor). Minimum inhibitory concentrations of the most active compounds ranged between 6.3–15.0 µg/mL. Quantitative structure-activity relationships (QSAR) analysis was performed and linear regression models were proposed with R² between 0.77–0.80, average R²_m between 0.70–0.75, Q²_LOO between 0.66–0.69, and relatively low amount of descriptors. Shape descriptors (related to flexibility and globularity), together with hydrophilic/hydrophobic volume and surface area descriptors, were identified as important molecular characteristics related to activity. A 3D pharmacophore model explaining the effect of the prenyl position on the activity of compounds was developed for each bacterium. These models predicted active compounds with an accuracy of 71–88%. With regard to the mode of action, good antibacterial prenylated (iso)flavonoids with low relative hydrophobic surface area caused remarkable membrane permeabilization, whereas those with higher relative hydrophobic surface area did not. Based on the QSAR and membrane permeabilization studies, the mode of action of antibacterial prenylated (iso)flavonoids was putatively rationalized.

Antimicrobial action of the cationic peptide, chrysophsin-3: a coarse-grained molecular dynamics study

Antimicrobial peptides (AMPs) are small cationic proteins that are able to destabilize a lipid bilayer structure through one or more modes of action. In this study, we investigate the processes of peptide aggregation and pore formation in lipid bilayers and vesicles by the highly cationic AMP, Chrysophsin-3 (chrys-3), using coarse-grained molecular dynamics (CG-MD) simulations and potential of mean force calculations. We study long 50 μs simulations of chrys-3 at different concentrations, both at the surface of dipalmitoylphosphatidylcholine (DPPC) and palmitoyloleoylphosphatidylcholine (POPC) bilayers, and also interacting within the interior of the lipid membrane. We show that aggregation of peptides at the surface, leads to pronounced deformation of lipid bilayers, leading in turn to lipid protrusions for peptide : ligand ratios > 1 : 12. In addition, aggregation of chrys-3 peptides within the centre of a lipid bilayer leads to spontaneous formation of pores and aggregates. Both mechanisms of interaction are consistent with previously reported experimental data for chrys-3. Similar results are observed also in POPC vesicles and mixed lipid bilayers composed of the zwitterionic lipid palmitoyloleoylphosphatidylethanolamine (POPE) and the negatively charged lipid palmitoyloleoylphosphatidylglycerol (POPG). The latter are employed as models of the bacterial membrane of Escherichia coli.

Flexibility vs rigidity of amphipathic peptide conjugates when interacting with lipid bilayers

For the first time, the photoisomerization of a diarylethene moiety (DAET) in peptide conjugates was used to probe the effects of molecular rigidity/flexibility on the structure and behavior of model peptides bound to lipid membranes. The DAET unit was incorporated into the backbones of linear peptide-based constructs, connecting two amphipathic sequences (derived from the β-stranded peptide (KIGAKI)₃ and/or the α-helical peptide BP100). A β-strand-DAET-α-helix and an α-helix-DAET-α-helix models were synthesized and studied in phospholipid membranes. Light-induced photoisomerization of the linker allowed the generation of two forms of each conjugate, which differed in the conformational mobility of the junction between the α-helical and/or the β-stranded part of these peptidomimetic molecules. A detailed study of their structural, orientational and conformational behavior, both in isotropic solution and in phospholipid model membranes, was carried out using circular dichroism and solid-state ¹⁹F-NMR spectroscopy. The study showed that the rigid and flexible forms of the two conjugates had appreciably different structures only when embedded in an anisotropic lipid environment and only in the gel phase. The influence of the rigidity/flexibility of the studied conjugates on the lipid thermotropic phase transition was also investigated by differential scanning calorimetry. Both models were found to destabilize the lamellar gel phases.

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DAET building blocks can be used to study rigidity/flexibility effects in supramolecular model systems.

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Photoswitchable DAET linkers perturb only up to 3–4 adjacent amino acid residues.

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Membrane-bound amphiphilic secondary structure elements exert a negligible influence on each other when linked by DAET.

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The rigidity of peptide conjugates affected their structural behavior only in the lipid gel phase.

Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study

A large number of antimicrobial peptides (AMPs) acts with high selectivity and specificity through interactions with membrane lipid components. These peptides undergo complex conformational changes in solution; upon binding to an interface, one major conformation is stabilized. Here we describe a study of the interaction between tritrpticin (TRP3), a cathelicidin AMP, and micelles of different chemical composition. The peptide's structure and dynamics were examined using one-dimensional and two-dimensional NMR. Our data showed that the interaction occurred by conformational selection and the peptide acquired similar structures in all systems studied, despite differences in detergent headgroup charge or dipole orientation. Fluorescence and paramagnetic relaxation enhancement experiments showed that the peptide is located in the interface region and is slightly more deeply inserted in 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-1'-rac-glycerol (LMPG, anionic) than in 1-lauroyl-2-hydroxy-sn-glycero-3-phosphocholine (LLPC, zwitterionic) micelles. Moreover, the tilt angle of an assumed helical portion of the peptide is similar in both systems. In previous work we proposed that TRP3 acts by a toroidal pore mechanism. In view of the high hydrophobic core exposure, hydration, and curvature presented by micelles, the conformation of TRP3 in these systems could be related to the peptide's conformation in the toroidal pore.

Computer prediction of paratope on antithrombotic antibody 10B12 and epitope on platelet glycoprotein VI via molecular dynamics simulation

BACKGROUND

Interaction between immunoglobulin-like receptor glycoprotein VI (GPVI) and collagen plays a central role in platelet activation and sequent firm adhesion. Of various antithrombotic agents targeting GPVI, antibody 10B12 is of great potential to block the GPVI-collagen interaction, but less is known about 10B12 paratope and GPVI epitope.

METHODS

Along the pathway in the computer strategy presented in our previous work, the 10B12/GPVI complex model was constructed through homology modeling and rigid-body docking, and the molecular dynamics (MD) simulation was used to detect the paratope residues on 10B12 and their partners on GPVI. Quantified by free and steered MD simulations, the stabilities of hydrogen bonds and salt bridges were used to rank the contributions of interface residues to binding of 10B12 and GPVI.

RESULTS

We predicted 12 key and seven dispensable residues in interaction of 10B12 to GPVI with present computational procedure. Besides of the 12 key residues, two are epitope residues (LYS⁴¹ and LYS⁵⁹) which had been identified by previous mutation experiments, and others, including four epitope residues (ARG³⁸, SER⁴⁴, ARG⁴⁶ and TYR⁴⁷ on GPVI) and six paratope residues (GLU¹, ASP⁹⁸, GLU¹⁰², ASP¹⁰⁷, ASP¹⁰⁸ and ASP¹¹¹ on 10B12), were newly found and also might be important for the 10B12-GPVI binding. The seven predicted dispensable residues on GPVI were had been illustrated in previous mutation experiments.

CONCLUSIONS

The present computer strategy combining homology modeling, rigid body docking and MD simulation was illustrated to be effective in mapping paratope on antithrombotic antibody 10B12 to epitope on GPVI, and have large potential in drug discovery and antibody research.

Modulation of Backbone Flexibility for Effective Dissociation of Antibacterial and Hemolytic Activity in Cyclic Peptides

Bacterial resistance to antibiotic therapy is on the rise and threatens to evolve into a worldwide emergency: alternative solutions to current therapies are urgently needed. Cationic amphipathic peptides are potent membrane-active agents that hold promise as the next-generation therapy for multidrug-resistant infections. The peptides' behavior upon encountering the bacterial cell wall is crucial, and much effort has been dedicated to the investigation and optimization of this amphipathicity-driven interaction. In this study we examined the interaction of a novel series of nine-membered flexible cyclic AMPs with liposomes mimicking the characteristics of bacterial membranes. Employed techniques included circular dichroism and marker release assays, as well as microbiological experiments. Our analysis was aimed at correlating ring flexibility with their antimicrobial, hemolytic, and membrane activity. By doing so, we obtained useful insights to guide the optimization of cyclic antimicrobial peptides via modulation of their backbone flexibility without loss of activity.

Activity of Synthetic Antimicrobial Peptide GH12 against Oral Streptococci

Controlling the growth of cariogenic microorganisms such as oral streptococci is an adjunct therapy for caries-active individuals to prevent and treat caries. Here we investigated the antimicrobial activity of the synthetic amphipathic α- helical antimicrobial peptide GH12 (GLLWHLLHHLLH-NH2) against oral streptococci in vitro. Circular dichroism studies showed that GH12 takes on an α-helical conformation in the presence of membrane-mimicking solvents, and reversed-phase high-performance liquid chromatography studies showed that GH12 remains stable in saliva. The peptide showed bactericidal activity against oral streptococci, with minimum inhibitory concentrations ranging from 6.7 to 32.0 μg/ml. GH12 concentrations 4-fold higher than the minimum bactericidal concentration completely killed oral streptococci within 20 min. Treating oral streptococci with GH12 caused noticeable changes in bacterial viability and morphology based on confocal laser scanning microscopy and scanning electron microscopy. Effects of GH12 on biofilm formation and on viability of mature biofilm were quantified by crystal violet staining and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. GH12 effectively inhibited biofilm formation and metabolic activity in biofilms of oral streptococci, especially S. mutans, S. sobrinus and S. salivarius. These results suggest that GH12 shows rapid and strong antimicrobial activity against oral streptococci in vitro, opening the door to preclinical and clinical studies to explore its potential for caries prevention and treatment.

Short, multiple-stranded β-hairpin peptides have antimicrobial potency with high selectivity and salt resistance

The β-hairpin structure has been proposed to exhibit potent antimicrobial properties with low cytotoxicity, thus, multiple β-hairpin structures have been proved to be highly stable in structures containing tightly packed hydrophobic cores. The aim of this study was to develop peptide-based synthetic strategies for generating short, but effective AMPs as inexpensive antimicrobial agents. Multiple-stranded β-hairpin peptides with the same β-hairpin unit, (WRXxRW)n where n=1, 2, 3, or 4 and Xx represent the turn sequence, were synthesized, and their potential as antimicrobial agents was evaluated. Owning to the tightly packed hydrophobic core and paired Trp of this multiple-stranded β-hairpin structure, all the 12-residues peptides exhibited high cell selectivity towards bacterial cells over human red blood cells (hRBCs), and the peptide W2 exhibited stronger antimicrobial activities with the MIC values of 2-8μM against various tested bacteria. Not only that, but W2 also showed obvious synergy with streptomycin and chloramphenicol against Escherichia coli, and displayed synergy with ciprofloxacin against Staphylococcus aureus with the FICI values ⩽0.5. Fluorescence spectroscopy and electron microscopy analyses indicated that W2 kills microbial cells by permeabilizing the cell membrane and damaging membrane integrity. Collectively, based on the multiple β-hairpin peptides, the ability to develop libraries of short and effective peptides will be a powerful approach to the discovery of novel antimicrobial agents.

STATEMENT OF SIGNIFICANCE

We successfully screened a peptide W2 ((WRPGRW)2) from a series of multiple-stranded β-hairpin antimicrobial peptides based on the "S-shaped" motif that induced the formation of a globular structure, and Trp zipper was used to replace the disulfide bonds to reduce the cost of production. This novel structure applied to AMPs improved cell selectivity and salt stability. The findings of this study will promote the development of peptide-based antimicrobial biomaterials. Further exploration of these AMPs will allow for diverse biotechnological and clinical applications such as biomedical coating, food storaging, and animal feeding.

An Amphipathic Undecapeptide with All d-Amino Acids Shows Promising Activity against Colistin-Resistant Strains of Acinetobacter baumannii and a Dual Mode of Action

Multiple strains of Acinetobacter baumannii have developed multidrug resistance (MDR), leaving colistin as the only effective treatment. The cecropin-α-melittin hybrid BP100 (KKLFKKILKYL-NH2) and its analogs have previously shown activity against a wide array of plant and human pathogens. In this study, we investigated the in vitro antibacterial activities of 18 BP100 analogs (four known and 14 new) against the MDR A. baumannii strain ATCC BAA-1605, as well as against a number of other clinically relevant human pathogens. Selected peptides were further evaluated against strains of A. baumannii that acquired resistance to colistin due to mutations of the lpxC, lpxD, pmrA, and pmrB genes. The novel analogue BP214 showed antimicrobial activity at 1 to 2 μM and a hemolytic 50% effective concentration (EC50) of >150 μM. The lower activity of its enantiomer suggests a dual, specific and nonspecific mode of action. Interestingly, colistin behaved antagonistically to BP214 when pmrAB and lpxC mutants were challenged.

High specific selectivity and Membrane-Active Mechanism of the synthetic centrosymmetric α-helical peptides with Gly-Gly pairs

We used a template-assisted approach to develop synthetic antimicrobial peptides, which differ from naturally occurring antimicrobial peptides that can compromise host natural defenses. Previous researches have demonstrated that symmetrical distribution patterns of amino acids contribute to the antimicrobial activity of natural peptides. However, there is little research describing such design ideas for synthetic α-helical peptides. Therefore, here, we established a centrosymmetric α-helical sequence template (y + hhh + y)_n (h, hydrophobic amino acid; +, cationic amino acid; y, Gly or hydrophobic amino acid), which contributed to amphipathicity, and a series of centrosymmetric peptides was designed with pairs of small amino acids (Ala and Gly), which were utilized to modulate the biological activity. The centrosymmetric peptides with 3 repeat units exhibited strong antimicrobial activity; in particular, the Gly-rich centrosymmetric peptide GG3 showed stronger selectivity for gram-negative bacteria without hemolysis. Furthermore, beyond our expectation, fluorescence spectroscopy and electron microscopy analyses indicated that the GG3, which possessed poor α-helix conformation, dramatically exhibited marked membrane destruction via inducing bacterial membrane permeabilization, pore formation and disruption, even bound DNA to further exert antimicrobial activity. Collectively, the Gly-rich centrosymmetric peptide GG3 was an ideal candidate for commercialization as a clinical therapeutic to treat gram-negative bacterial infections.