Molecular details on the intermediate states of melittin action on a cell membrane

Helicity-directed recognition of bacterial phospholipid via radially amphiphilic antimicrobial peptides

The fundamental differences in phospholipids between bacterial and mammalian cell membranes present remarkable opportunities for antimicrobial design. However, it is challenging to distinguish bacterial anionic phospholipid phosphatidylglycerol (PG) from mammalian anionic phosphatidylserine (PS) with the same net charge. Here, we report a class of radially amphiphilic α helix antimicrobial peptides (RAPs) that can selectively discriminate PG from PS, relying on the helix structure. The representative RAP, L10-MMBen, can direct the rearrangement of PG vesicles into a lamellar structure with its helix axis parallel to the PG membrane surface. The helical structure imparts both the thermodynamic and kinetic advantages of L10-MMBen/PG assembly, and the hiding of hydrophobic regions in RAPs is crucial for PG recognition. L10-MMBen exhibits high selectivity against bacteria depending on PG recognition, showing low in vivo toxicity and significant treatment efficacy in mice infection models. Our study introduces a helicity-direct bacterial phospholipid recognition paradigm for designing highly selective antimicrobial peptides.

Assembly-Induced Membrane Selectivity of Artificial Model Peptides through Entropy-Enthalpy Competition

Peptide design and drug development offer a promising solution for combating serious diseases or infections. In this study, using an AI-human negotiation approach, we have designed a class of minimal model peptides against tuberculosis (TB), among which K7W6 exhibits potent efficacy attributed to its assembly-induced function. Comprising lysine and tryptophan with an amphiphilic α-helical structure, the K7W6 sequence exhibits robust activity against various infectious bacteria causing TB (including clinically isolated and drug-resistant strains) both in vitro and in vivo. Moreover, it synergistically enhances the effectiveness of the first-line antibiotic rifampicin while displaying low potential for inducing drug resistance and minimal toxicity toward mammalian cells. Biophysical experiments and simulations elucidate that K7W6's exceptional performance can be ascribed to its highly selective and efficient membrane permeabilization activity induced by its distinctive self-assembly behavior. Additionally, these assemblies regulate the interplay between enthalpy and entropy during K7W6-membrane interaction, leading to the peptide's two-step mechanism of membrane interaction. These findings provide valuable insights into rational design principles for developing advanced peptide-based drugs while uncovering the functional role played by assembly.

Cell Membrane Perforation: Patterns, Mechanisms and Functions

Cell membrane is crucial for the cellular activities, and any disruption to it may affect the cells. It is demonstrated that cell membrane perforation is associated with some biological processes like programmed cell death (PCD) and infection of pathogens. Specific developments make it a promising technique to perforate the cell membrane controllably and precisely. The pores on the cell membrane provide direct pathways for the entry and exit of substances, and can also cause cell death, which means reasonable utilization of cell membrane perforation is able to assist intracellular delivery, eliminate diseased or cancerous cells, and bring about other benefits. This review classifies the patterns of cell membrane perforation based on the mechanisms into 1) physical patterns, 2) biological patterns, and 3) chemical patterns, introduces the characterization methods and then summarizes the functions according to the characteristics of reversible and irreversible pores, with the aim of providing a comprehensive summary of the knowledge related to cell membrane perforation and enlightening broad applications in biomedical science.

Transition between Different Diffusion Modes of Individual Lipids during the Membrane-Specific Action of As-CATH4 Peptides

The cell membrane permeabilization ability of immune defense antimicrobial peptides (AMPs) is widely applied in biomedicine. Although the mechanisms of peptide-membrane interactions have been widely investigated, analyses at the molecular level are still lacking. Herein, the membrane-specific action of a native AMP, As-CATH4, is investigated using a single-lipid tracking method in combination with live cell and model membrane assays conducted at different scales. The peptide-membrane interaction process is characterized by analyzing single-lipid diffusion behaviors. As-CATH4 exhibits potent antimicrobial activity through bacterial membrane permeabilization, with moderate cytotoxicity against mammalian cells. In-plane diffusion analyses of individual lipids show that the lipid molecules exhibit non-Gaussian and heterogeneous diffusion behaviors in both pristine and peptide-treated membranes, which can be decomposed into two Gaussian subgroups corresponding to normal- and slow-diffusive lipids. Assessment of the temporal evolution of these two diffusion modes of lipids reveal that the peptide action states of As-CATH4 include surface binding, transmembrane defect formation, and dynamic equilibrium. The action mechanisms of As-CATH4 at varying concentrations and against different membranes are distinguished. This work resolves the simultaneous mixed diffusion mechanisms of single lipids in biomimetic cell membranes, especially during dynamic membrane permeabilization by AMPs.

Fluorinated dendritic amphiphiles, their stomatosome aggregates and application in enzyme encapsulation

Enzymes are more selective and efficient than synthetic catalysts but are limited by difficult recycling. This is overcome by immobilisation, namely through encapsulation, with the main drawback of this method being slow diffusion of products and reactants, resulting in effectively lowered enzyme activity. Fluorinated dendritic amphiphiles were reported to self-assemble into regularly perforated bilayer vesicles, so-called "stomatosomes". It was proposed that they could be promising novel reaction vessels due to their increased porosity while retaining larger biomolecules at the same time. Amphiphiles were synthesised and their aggregation was analysed by cryogenic transmission electron microscopy (cryo-TEM) and dynamic light scattering (DLS) in buffered conditions necessary for enzyme encapsulation. Urease and albumin were encapsulated using the thin-film hydration method and investigated by confocal and time-gated stimulated emission depletion microscopy (gSTED). Their release was then used to probe the selective retention of cargo by stomatosomes. Free and encapsulated enzyme activity were compared and their capacity to be reused was evaluated using the Berthelot method. Urease was successfully encapsulated, did not leak out at room temperature, and showed better activity in perforated vesicles than in closed vesicles without perforations. Encapsulated enzyme could be reused with retained activity over 8 cycles using centrifugation, while free enzyme had to be filtrated. These results show that stomatosomes may be used in enzyme immobilisation applications and present advantages over closed vesicles or free enzyme.

Strategies for Improving Transdermal Administration: New Approaches to Controlled Drug Release

In this work, we aim to address several strategies to improve transdermal drug delivery, such as iontophoresis, sonophoresis, electroporation and micron. We also propose a review of some transdermal patches and their applications in medicine. TDDs (transdermal patches with delayed active substances) are multilayered pharmaceutical preparations that may contain one or more active substances, of which, systemic absorption is achieved through intact skin. The paper also presents new approaches to the controlled release of drugs: niosomes, microemulsions, transfersomes, ethosomes, but also hybrid approaches nanoemulsions and microns. The novelty of this review lies in the presentation of strategies to improve the transdermal administration of drugs, combined with their applications in medicine, in light of pharmaceutical technological developments.

Therapeutic Use of Bee Venom and Potential Applications in Veterinary Medicine

Apitherapy is a branch of alternative medicine that consists of the treatment of diseases through products collected, processed, and secreted by bees, specifically pollen, propolis, honey, royal jelly, and bee venom. In traditional medicine, the virtues of honey and propolis have been well-known for centuries. The same, however, cannot be said for venom. The use of bee venom is particularly relevant for many therapeutic aspects. In recent decades, scientific studies have confirmed and enabled us to understand its properties. Bee venom has anti-inflammatory, antioxidant, central nervous system inhibiting, radioprotective, antibacterial, antiviral, and antifungal properties, among others. Numerous studies have often been summarised in reviews of the scientific literature that have focused on the results obtained with mouse models and their subsequent transposition to the human patient. In contrast, few reviews of scientific work on the use of bee venom in veterinary medicine exist. This review aims to take stock of the research achievements in this particular discipline, with a view to a recapitulation and stabilisation in the different research fields.

Non-Gaussian Diffusion of Individual Lipids Unveils the Unique Peptide-Membrane Interaction Dynamics

The dynamics of protein (or peptide)-membrane interactions plays a central role in cellular functions; however, the underlying mechanisms remain unclear. Herein, through analyzing the diffusion of individual lipids in a bilayer membrane during the membrane actions of typical peptides (e.g., pore-forming peptide melittin and cell-penetrating peptide TAT) at varying concentrations, the spatial heterogeneity as well as temporal dynamics of lipid motions were investigated which showed close correlation with the peptide action mechanism. Specifically, the spatial heterogeneity of lipid diffusion was characterized by the non-Gaussianity of lipid trajectories, which was further decomposed into two basic diffusion modes; moreover, the temporal evolution of the Gaussian fitting parameters provided quantitative information on the varying metastable interaction states between peptides and the membrane (e.g., peptide landing, membrane insertion, and equilibrium). Generally, this work gives an insight into the correlation between single-lipid diffusion and function-realization of membrane-active peptides.

Enhanced Therapeutic Effect of Optimized Melittin-dKLA, a Peptide Agent Targeting M2-like Tumor-Associated Macrophages in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is characterized by a high possibility of metastasis. M2-like tumor-associated macrophages (TAMs) are the main components of the tumor microenvironment (TME) and play a key role in TNBC metastasis. Therefore, TAMs may be a potential target for reducing TNBC metastasis. Melittin-dKLA, a peptide composed of fused melittin and pro-apoptotic peptide d(KLAKLAK)2 (dKLA), showed a potent therapeutic effect against cancers by depleting TAMs. However, melittin has a strong adverse hemolytic effect. Hence, we attempted to improve the therapeutic potential of melittin-dKLA by reducing toxicity and increasing stability. Nine truncated melittin fragments were synthesized and examined. Of the nine peptides, the melittin-dKLA8-26 showed the best binding properties to M2 macrophages and discriminated M0/M1/M2. All fragments, except melittin, lost their hemolytic effects. To increase the stability of the peptide, melittin-dKLA8-26 fragment was conjugated with PEGylation at the amino terminus and was named PEG-melittin-dKLA8-26. This final drug candidate was assessed in vivo in a murine TNBC model and showed superior effects on tumor growth, survival rates, and lung metastasis compared with the previously used melittin-dKLA. Taken together, our study showed that the novel PEG-melittin-dKLA8-26 possesses potential as a new drug for treating TNBC and TNBC-mediated metastasis by targeting TAMs.

Heterogeneous Structural Disturbance of Cell Membrane by Peptides with Modulated Hydrophobic Properties

Extensive effort has been devoted to developing new clinical therapies based on membrane-active peptides (MAPs). Previous models on the membrane action mechanisms of these peptides mostly focused on the MAP−membrane interactions in a local region, while the influence of the spatial heterogeneity of the MAP distribution on the membrane was much ignored. Herein, three types of natural peptide variants, AS4-1, AS4-5, and AS4-9, with similar amphiphilic α-helical structures but distinct hydrophobic degrees (AS4-1 < AS4-5 < AS4-9) and net charges (+9 vs. +7 vs. +5), were used to interact with a mixed phosphatidylcholine (PC) and phosphatidylglycerol (PG) membrane. A combination of giant unilamellar vesicle (GUV) leakage assays, atomic force microscopy (AFM) characterizations, and molecular dynamics (MD) simulations demonstrated the coexistence of multiple action mechanisms of peptides on a membrane, probably due to the spatially heterogeneous distribution of peptides on the membrane surface. Specifically, the most hydrophobic peptide (i.e., AS4-9) had the strongest membrane binding, perturbation, and permeabilization effects, leading to the formation of large peptide−lipid aggregates (10 ± 5 nm in height and 150 ± 50 nm in size), as well as continuous fragments and ridges on the supported membrane surface. The AS4-5 peptides, with a half-hydrophilic and half-hydrophobic structure, induced membrane lysis in addition to reconstruction. The most hydrophilic peptide AS4-1 only exhibited unstable binding on the supported membrane surface. These results demonstrate the heterogeneous structural disturbance of model cell membranes by amphiphilic α-helical peptides, which could be significantly strengthened by increasing the degree of hydrophobicity and/or local number density of peptides. This work provides support for the modulation of the membrane activity of MAPs by adjusting their hydrophobicity and local concentration.

Organizations of melittin peptides after spontaneous penetration into cell membranes

The antimicrobial peptide, melittin, is a potential next-generation antibiotic because melittin can spontaneously form pores in bacterial cell membranes and cause cytoplasm leakage. However, the organizations of melittin peptides in cell membranes remain elusive, which impedes the understanding of the poration mechanism. In this work, we use coarse-grained and all-atom molecular dynamics (MD) simulations to investigate the organizations of melittin peptides during and after spontaneous penetration into DPPC/POPG lipid bilayers. We find that the peptides in lipid bilayers adopt either a transmembrane conformation or a U-shaped conformation, which are referred to as T- and U-peptides, respectively. Several U-peptides and/or T-peptides aggregate to form stable pores. We analyze a T-pore consisting of four T-peptides and a U-pore consisting of three U-peptides and one T-peptide. In both pores, peptides are organized in a manner such that polar residues face inward and hydrophobic residues face outward, which stabilizes the pores and produces water channels. Compared with the U-pore, the T-pore has lower energy, larger pore diameter, and higher permeability. However, the T-pore occurs less frequently than the U-pore in our simulations, probably because the formation of the T-pore is kinetically slower than the U-pore. The stability and permeability of both pores are confirmed by 300 ns all-atom MD simulations. The peptide organizations obtained in this work should deepen the understanding of the stability, poration mechanism, and permeability of melittin, and facilitate the optimization of melittin to enhance the antibacterial ability.

Inhibitory activities of propolis, nisin, melittin and essential oil compounds on Paenibacillus alvei and Bacillus subtilis

Background

Natural products represent important sources of antimicrobial compounds. Propolis and compounds from essential oils comprise good examples of such substances because of their inhibitory effects on bacterial spores, including bee pathogens.

Methods

Ethanol extracts of propolis (EEP) from Apis mellifera were prepared using different methods: double ultrasonication, double maceration and maceration associated with ultrasonication. Together with the antimicrobial peptides nisin and melittin, and compounds present in the essential oils of clove (Syzygium aromaticum) and cinnamon (Cinnamomum zeylanicum), assays were carried out on one Bacillus subtilis isolate and Paenibacillus alvei (ATCC 6344) against vegetative and sporulated forms, using the resazurin microtiter assay. Synergism with all the antimicrobials in association with tetracycline was verified by the time-kill curve method. Potassium and phosphate efflux, release of proteins and nucleic acids were investigated.

Results

EEPs showed the same MIC, 156.25 µg/mL against B. subtilis and 78.12 µg/mL against P. alvei. The peptides showed better activities against B. subtilis (MIC of 12 µg/mL for melittin and 37.50 µg/mL for nisin). Antimicrobials showed similar inhibitory effects, but cinnamaldehyde (39.06 µg/mL) showed the best action against P. alvei. Melittin and nisin showed the greatest capacity to reduce spores, regarding B. subtilis there was a 100% reduction at 6.25 and 0.78 µg/mL, respectively. Concerning P. alvei, the reduction was 93 and 98% at concentrations of 80 µg/mL of melittin and 15 µg/mL of nisin. EEPs showed the highest effects on the protein release against B. subtilis and P. alvei. Nucleic acid release, phosphate and potassium efflux assays indicated bacterial cell membrane damage. Synergism between antimicrobials and tetracycline was demonstrated against both bacteria.

Conclusion

All antimicrobials tested showed antibacterial activities against vegetative and sporulated forms of P. alvei and B. subtilis, especially nisin and melittin. Synergism with tetracycline and damage on bacterial cell membrane also occurred.

Biophysical Characterization of LTX-315 Anticancer Peptide Interactions with Model Membrane Platforms: Effect of Membrane Surface Charge

LTX-315 is a clinical-stage, anticancer peptide therapeutic that disrupts cancer cell membranes. Existing mechanistic knowledge about LTX-315 has been obtained from cell-based biological assays, and there is an outstanding need to directly characterize the corresponding membrane-peptide interactions from a biophysical perspective. Herein, we investigated the membrane-disruptive properties of the LTX-315 peptide using three cell-membrane-mimicking membrane platforms on solid supports, namely the supported lipid bilayer, intact vesicle adlayer, and tethered lipid bilayer, in combination with quartz crystal microbalance-dissipation (QCM-D) and electrochemical impedance spectroscopy (EIS) measurements. The results showed that the cationic LTX-315 peptide selectively disrupted negatively charged phospholipid membranes to a greater extent than zwitterionic or positively charged phospholipid membranes, whereby electrostatic interactions were the main factor to influence peptide attachment and membrane curvature was a secondary factor. Of note, the EIS measurements showed that the LTX-315 peptide extensively and irreversibly permeabilized negatively charged, tethered lipid bilayers that contained high phosphatidylserine lipid levels representative of the outer leaflet of cancer cell membranes, while circular dichroism (CD) spectroscopy experiments indicated that the LTX-315 peptide was structureless and the corresponding membrane-disruptive interactions did not involve peptide conformational changes. Dynamic light scattering (DLS) measurements further verified that the LTX-315 peptide selectively caused irreversible disruption of negatively charged lipid vesicles. Together, our findings demonstrate that the LTX-315 peptide preferentially disrupts negatively charged phospholipid membranes in an irreversible manner, which reinforces its potential as an emerging cancer immunotherapy and offers a biophysical framework to guide future peptide engineering efforts.

Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study

We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.

Anisaxins, helical antimicrobial peptides from marine parasites, kill resistant bacteria by lipid extraction and membrane disruption

An infecting and propagating parasite relies on its innate defense system to evade the host's immune response and to survive challenges from commensal bacteria. More so for the nematode Anisakis, a marine parasite that during its life cycle encounters both vertebrate and invertebrate hosts and their highly diverse microbiotas. Although much is still unknown about how the nematode mitigates the effects of these microbiota, its antimicrobial peptides likely play an important role in its survival. We identified anisaxins, the first cecropin-like helical antimicrobial peptides originating from a marine parasite, by mining available genomic and transcriptomic data for Anisakis spp. These peptides are potent bactericidal agents in vitro, selectively active against Gram-negative bacteria, including multi-drug resistant strains, at sub-micromolar concentrations. Their interaction with bacterial membranes was confirmed by solid state NMR (ssNMR) and is highly dependent on the peptide concentration as well as peptide to lipid ratio, as evidenced by molecular dynamics (MD) simulations. MD results indicated that an initial step in the membranolytic mode of action involves membrane bulging and lipid extraction; a novel mechanism which may underline the peptides' potency. Subsequent steps include membrane permeabilization leading to leakage of molecules and eventually cell death, but without visible macroscopic damage, as shown by atomic force microscopy and flow cytometry. This membranolytic antibacterial activity does not translate to cytotoxicity towards human peripheral blood mononuclear cells (HPBMCs), which was minimal at well above bactericidal concentrations, making anisaxins promising candidates for further drug development. STATEMENT OF SIGNIFICANCE: Witnessing the rapid spread of antibiotic resistance resulting in millions of infected and dozens of thousands dying worldwide every year, we identified anisaxins, antimicrobial peptides (AMPs) from marine parasites, Anisakis spp., with potent bactericidal activity and selectivity towards multi-drug resistant Gram-negative bacteria. Anisaxins are membrane-active peptides, whose activity, very sensitive to local peptide concentrations, involves membrane bulging and lipid extraction, leading to membrane permeabilization and bacterial cell death. At the same time, their toxicity towards host cells is negligible, which is often not the case for membrane-active AMPs, therefore making them suitable drug candidates. Membrane bulging and lipid extraction are novel concepts that broaden our understanding of peptide interactions with bacterial functional structures, essential for future design of such biomaterials.

Studying the Mechanics of Membrane Permeabilization through Mechanoelectricity

In this research, real-time monitoring of lipid membrane disruption is made possible by exploiting the dynamic properties of model lipid bilayers formed at oil-water interfaces. This involves tracking an electrical signal generated through rhythmic membrane perturbation translated into the adsorption and penetration of charged species within the membrane. Importantly, this allows for the detection of membrane surface interactions that occur prior to pore formation that may be otherwise undetected. The requisite dynamic membranes for this approach are made possible through the droplet interface bilayer (DIB) technique. Membranes are formed at the interface of lipid monolayer-coated aqueous droplets submerged in oil. We present how cyclically alternating the membrane area leads to the generation of mechanoelectric current. This current is negligible without a transmembrane voltage until a composition mismatch between the membrane monolayers is produced, such as a one-sided accumulation of disruptive agents. The generated mechanoelectric current is then eliminated when an applied electric field compensates for this asymmetry, enabling measurement of the transmembrane potential offset. Tracking the compensating voltage with respect to time then reveals the gradual accumulation of disruptive agents prior to membrane permeabilization. The innovation of this work is emphasized in its ability to continuously track membrane surface activity, highlighting the initial interaction steps of membrane disruption. In this paper, we begin by validating our proposed approach against measurements taken for fixed composition membranes using standard electrophysiological techniques. Next, we investigate surfactant adsorption, including hexadecyltrimethylammonium bromide (CTAB, cationic) and sodium decyl sulfate (SDS, anionic), demonstrating the ability to track adsorption prior to disruption. Finally, we investigate the penetration of lipid membranes by melittin, confirming that the peptide insertion and disruption mechanics are, in part, modulated by membrane composition.

Real-time monitoring the interfacial dynamic processes at model cell membranes: Taking cell penetrating peptide TAT as an example

A real-time and molecule-level monitoring of the interfacial dynamic interactions between molecules and a cell membrane is of vital importance. Herein, taking TAT, one of the most representative cell penetrating peptides, as an example, a photo-voltage transient technique and a dynamic giant bistratal vesicle (GBV) leakage method were combined with the traditional giant unilamellar vesicle (GUV) leakage assays, to provide a molecule-level understanding of the dynamic membrane interaction process performed in a low ionic strength and neutral pH condition. The photo-voltage test based on supported phospholipid bilayers showed a quick disturbance (<1 min) followed by a continuous reconstruction of the membrane by peptides, leading to a slight destruction (at TAT concentrations lower than 1 μg mL^-1, i.e., 0.64 μM) or strong damage (e.g. at 10 μg mL^-1, i.e., 6.4 μM) of the bilayer structure. The GUV/GBV leakage assays further demonstrated the TAT-induced membrane deformation and transmembrane diffusion of dyes, which occurred in an immediate, linear, and TAT-concentration dependent manner. Moreover, the flux of dye across the substrate-immobilized membranes was approximately three times of that across the substrate-free ones. This work gives information on time and molecular mechanism of the TAT-membrane interactions, demonstrates the different permeabilizing effects of TAT on immobilized and free membranes. Overall, it provides useful strategies to investigate the nano-bio interfacial interactions in a simple, global and real-time way.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

Molecular Cloning, Functional and Biophysical Characterization of an Antimicrobial Peptide from Rhizosphere Soil

AIM

This study was designed to screen and identify an antimicrobial peptide from rhizosphere soil. The study was further focused towards overexpression, purification and characterization of this antimicrobial peptide, and to functionally validate its efficiency and efficacy as an antimicrobial agent. Yet the study was further aimed at corroborating structural and functional studies using biophysical tools.

BACKGROUND

Antimicrobial resistance is emerging as one of the top 10 global health crisis, it is multifaceted and is the second largest cause of mortality. According to the World Health Organization (WHO), around the world, an estimated 700,000 people die each year from infection caused by antibiotic-resistant microbes. Antimicrobial peptides offers best alternative to combat and overcome this crisis. In this manuscript, we report cloning, expression, purification and characterization of an antimicrobial peptide discovered from rhizosphere soil.

OBJECTIVE

Objectives of this study includes construction, screening and identification of antimicrobial peptide from metagenome followed by its expression, purification and functional and biophysical investigation. Yet another objective of the study was to determine antimicrobial efficacy and efficiency as an antimicrobial peptide towards MRSA strains.

METHODS

In this study, we used array of molecular biology tools that include genetic engineering, PCR amplification, construction of an expression construct and NI-NTA based purification of the recombinant peptide. We have also carried out antimicrobial activity assay to determine MIC and IC50 values of antimicrobial peptide. To establish structural and functional relationship, circular dichroism, and both extrinsic and intrinsic fluorescence spectroscopy studies were carried out.

RESULTS

Screening of metagenomic library resulted in identification of gene (~500bp) harbouring an open reading frame (ORF) consisting of 282 bp. Open reading frame identified in gene encodes an antimicrobial peptide which had shared ~95% sequence similarity with the antimicrobial peptide of Bacillus origin. Purification of recombinant protein using Ni-NTA column chromatography demonstrated a purified protein band of ~11 kDa on 14% SDS-PAGE which is well corroborated to theoretical deduced molecular weight of peptide from its amino acids sequence. Interestingly, the peptide exhibited antimicrobial activity in broad range of pH and temperature. MIC (minimum inhibitory concentration) determined against gram positive Bacillus sp. was found to be 0.015mg/ml, whereas in case of gram negative E. coli, it was calculated to be 0.062mg/ml. The peptide exhibited IC50 values corresponding to ~0.25mg/ml against Bacillus and ~0.5 mg/ml against E. coli. Antimicrobial susceptibility assay performed against methicillin resistant Staphylococcus aureus strain ATCC 3412 and standard strain of Staphylococcus aureus ATCC 9144 revealed its strong inhibitory activity against MRSA, whereby we observed a ~16mm clearance zone at higher peptide concentrations ~2mg/ml (~181.8µM). Biophysical investigation carried out using Trp fluorescence, ANS fluorescence and circular dichroism spectroscopy further revealed conformational stability in its secondary and tertiary structure at wide range of temperature and pH.

CONCLUSION

Altogether, the peptide discovered from rhizosphere metagenome hold potential in inhibiting the growth of both the gram positive and gram negative bacteria, and was equally effective in inhibiting the multidrug resistant pathogenic strains (MRSA).

Computational Methods and Tools in Antimicrobial Peptide Research

The evolution of antibiotic-resistant bacteria is an ongoing and troubling development that has increased the number of diseases and infections that risk going untreated. There is an urgent need to develop alternative strategies and treatments to address this issue. One class of molecules that is attracting significant interest is that of antimicrobial peptides (AMPs). Their design and development has been aided considerably by the applications of molecular models, and we review these here. These methods include the use of tools to explore the relationships between their structures, dynamics, and functions and the increasing application of machine learning and molecular dynamics simulations. This review compiles resources such as AMP databases, AMP-related web servers, and commonly used techniques, together aimed at aiding researchers in the area toward complementing experimental studies with computational approaches.

Lipid Phase Influences the Dynamic Interactions between Graphene Oxide Nanosheets and a Phospholipid Membrane

To understand the possible perturbations of graphene oxide (GO) nanosheets on cell membranes is the first step to evaluate their cytotoxicity, while the membrane heterogeneity such like lipid phase separation complicates such interactions. Using the dynamic giant unilamellar vesicle leakage assays, atomic force microscopy characterizations, and molecular dynamics simulations, we demonstrated the structural and property disturbance of GO on a lipid bilayer membrane in a low ionic strength and neutral pH condition, specifically the influence of lipid phase on this process. GO tends to obliquely insert into and even be sandwiched between leaflets of a liquid-phase membrane, inducing formidable flaw in lipid packing states and fast transmembrane leakage. However, GO adopts parallel adsorption or vertical insertion on/into a gel-phase bilayer, while permeabilization occurs only when the disturbance is strong enough. Our results are helpful to understand the fundamental interaction mechanism between GO nanosheets and cells.

Cholesterols Work as a Molecular Regulator of the Antimicrobial Peptide-Membrane Interactions

The existing cholesterols (Chols) in animal cell membranes play key roles in many fundamental cellular processes, which also promise the possibility to modulate the bioactivity of various membrane-active biomacromolecules. Here, combining dynamic giant unilamellar vesicle leakage experiments and molecular dynamics simulations, the inhibitory effect of Chols on the membrane poration activity of melittin (Mel), a typical natural antimicrobial peptide, is demonstrated. Molecular details of the Mel-Chol interactions in membrane show that, for a Chol-contained lipid membrane, Mel exposure would perturb the symmetric bilayer structure of the membrane and specifically influence the location and orientation distributions of Chol molecules to an asymmetric state between the two leaflets; moreover, the Mel-Chol interactions are significantly influenced by the membrane environment such as unsaturation degree of the lipid components. Such inhibitory effect is normally ascribed to an accumulation of Chol molecules around the membrane-bound peptide chains and formation of Chol-Mel complexes in the membrane, which hinder the further insertion of peptides into the membrane. This work clarifies the molecular interactions between membrane-active peptides and Chol-contained membranes, and suggest the possibility to develop targeted drugs due to the membrane component specificity between bacterial and animal cells.

Bee Venom: An Updating Review of Its Bioactive Molecules and Its Health Applications

Bee venom (BV) is usually associated with pain since, when humans are stung by bees, local inflammation and even an allergic reaction can be produced. BV has been traditionally used in ancient medicine and in acupuncture. It consists of a mixture of substances, principally of proteins and peptides, including enzymes as well as other types of molecules in a very low concentration. Melittin and phospholipase A2 (PLA2) are the most abundant and studied compounds of BV. Literature of the main biological activities exerted by BV shows that most studies focuses on the comprehension and test of anti-inflammatory effects and its mechanisms of action. Other properties such as antioxidant, antimicrobial, neuroprotective or antitumor effects have also been assessed, both in vitro and in vivo. Moreover, human trials are necessary to confirm those clinical applications. However, notwithstanding the therapeutic potential of BV, there are certain problems regarding its safety and the possible appearance of adverse effects. On this perspective, new approaches have been developed to avoid these complications. This manuscript is aimed at reviewing the actual knowledge on BV components and its associated biological activities as well as the latest advances on this subject.

Individual Roles of Peptides PGLa and Magainin 2 in Synergistic Membrane Poration

Synergy between antimicrobial peptides PGLa and Magainin 2 (MAG2) provides an efficient way to enhance their antimicrobial ability. However, the underlying molecular mechanism of such synergy, especially the individual roles of each peptide, remains poorly understood. We combined a giant unilamellar vesicle leakage assay, in situ interfacial photovoltage testing, and molecular dynamics to investigate membrane poration under the action of PGLa, MAG2, or a PGLa/MAG2 mixture. Our results clearly show the different membrane action modes of the three systems and demonstrate the importance of forming PGLa-MAG2 heterodimers in the membrane poration process. PGLa inserted into and extracted from a membrane rapidly and continually with minimal aggregation and produced only transient, small pores. In contrast, MAG2 peptides tended to aggregate together on the membrane surface or only shallowly embed in the membrane. Additionally, the PGLa and MAG2 residues were well integrated into the membrane via the formation of PGLa-MAG2 heterodimers. The membrane defect produced by the rapid insertion of PGLa was stabilized by MAG2, which further recruited other peptides for the formation of PGLa-MAG2 heterodimers and even heterodimer clusters. Growth in pore size then occurred in a step-by-step process involving the formation and assembly of heterodimer clusters within the membrane. Our results provide insight into the complicated synergy that occurs between PGLa and MAG2 during membrane poration and will assist in the design of new antimicrobial peptides.

Correlation between Single-Molecule Dynamics and Biological Functions of Antimicrobial Peptide Melittin

Many fundamental biological processes occur on cell membranes, and a typical example is the membrane permeabilization by peptides for an antimicrobial purpose. Previous studies of the underlying mechanism mostly focus on structural changes of membranes and peptides during their interactions. Herein, from a new perspective of single-molecule dynamics, the real-time three-dimensional motions of individual phospholipid and peptide molecules were monitored, and specifically, their correlation with the membrane poration function of melittin, a most representative natural antimicrobial peptide, was studied. We found that the adsorption and accumulation of melittin on the membrane surface significantly sped up the lateral diffusion of lipids surrounding the peptides, which in turn facilitated the peptide insertion at such heterogeneous regions. A unique "U"-bending pathway of melittin during membrane insertion and the ultimate formation of toroidal pores with dynamical translocations of peptides and lipids with several metastable states between the two leaflets of bilayer were observed.

Lipid-specific interactions determine the organization and dynamics of membrane-active peptide melittin

The cell membranes of different cells deviate significantly in lipid compositions and thus provide varying biological environments to modulate the diffusion, organization and the resultant function of biomacromolecules. However, the detailed modulation mechanism remains elusive especially in consideration of the current overuse of the simplified membrane models such as the pure phosphatidylcholine (PC) membrane. In this work, with the typical membrane-active peptide melittin, we demonstrated that a more complicated membrane environment, such as the bacterial (IME) or plasma membrane (PM), would significantly change the organization and dynamics of melittin, by using molecular dynamics simulations as a "computational microscope". It was found that in these membrane systems, adding melittin would cause a varying degree of reduction in the lateral diffusion of lipids due to the different assembly states of peptides. Melittin tended to aggregate to oligomers in the pure PC membrane, mostly as a tetramer or trimer, while in IME or PM, its degree of oligomerization was significantly reduced. More surprisingly, melittin displayed a strong affinity with ganglioside GM3 in PM, leading to the formation of melittin-GM3 nanoclusters, which hindered its diffusion and further oligomerization. Additionally, small changes in the residue sequence of melittin could modulate the degree or structure of the peptide oligomer. Our work provides a typical example of a study on the organization and dynamics of pore-forming peptides in specific membrane environments and has great significance on the optimization of peptide sequences and the design of helix bundles in the membrane for target biological function.

Little Antimicrobial Peptides with Big Therapeutic Roles

Antimicrobial Peptides (AMPs) are short amphipathic biological molecules generally with less than 100 amino acids. AMPs not only present high bioactivities against bacteria, fungi or protists-induced infections, but also play important roles in anticancer activity, immune response and inflammation regulation. AMPs are classified as ribosomally synthesized, non-ribosomally synthesized and post-translationally modified, non-ribosomally synthesized ones and several synthetic or semisynthetic peptides according to their synthesis with or without the involvement of ribosomes. The molecular characterization and bioactivity action mechanisms are summarized for several ribosomally synthesized AMPs and main non-ribosomally synthesized members (cyclopeptides, lipopeptides, glycopeptides, lipoglycopeptides). We also analyze challenges and new strategies to overcome drug resistance and application limitations for AMP discovery. In conclusion, the growing novel small molecular AMPs have huge therapeutic potentials of antibacterial, antiviral, anticancer and immunoregulatory bioactivities through new techniquesdriven drug discovery strategy including bioinformatics prediction, de novo rational design and biosynthesis.

The membrane effects of melittin on gastric and colorectal cancer

The cytotoxic effects of melittin, a bee-venom peptide, have been widely studied towards cancer cells. Typically, these studies have examined the effect of melittin over extended-time courses (6-24 hours), meaning that immediate cellular interactions have been overlooked. In this work, we demonstrate the rapid effects of melittin on both gastric and colorectal cancer, specifically AGS, COLO205 and HCT-15 cell lines, over a period of 15 minutes. Melittin exhibited a dose dependent effect at 4 hours of treatment, with complete cellular death occurring at the highest dose of 20 μg/mL. Interestingly, when observed at shorter time points, melittin induced cellular changes within seconds; membrane damage was observed as swelling, breakage or blebbing. High-resolution imaging revealed treated cells to be compromised, showing clear change in cellular morphology. After 1 minute of melittin treatment, membrane changes were observed, and intracellular material could be seen expelled from the cells. Overall, these results enhance our understanding of the fast acting anti-cancer effects of melittin.

How Melittin Inserts into Cell Membrane: Conformational Changes, Inter-Peptide Cooperation, and Disturbance on the Membrane

Antimicrobial peptides (AMPs), as a key component of the immune defense systems of organisms, are a promising solution to the serious threat of drug-resistant bacteria to public health. As one of the most representative and extensively studied AMPs, melittin has exceptional broad-spectrum activities against microorganisms, including both Gram-positive and Gram-negative bacteria. Unfortunately, the action mechanism of melittin with bacterial membranes, especially the underlying physics of peptide-induced membrane poration behaviors, is still poorly understood, which hampers efforts to develop melittin-based drugs or agents for clinical applications. In this mini-review, we focus on recent advances with respect to the membrane insertion behavior of melittin mostly from a computational aspect. Membrane insertion is a prerequisite and key step for forming transmembrane pores and bacterial killing by melittin, whose occurrence is based on overcoming a high free-energy barrier during the transition of melittin molecules from a membrane surface-binding state to a transmembrane-inserting state. Here, intriguing simulation results on such transition are highlighted from both kinetic and thermodynamic aspects. The conformational changes and inter-peptide cooperation of melittin molecules, as well as melittin-induced disturbances to membrane structure, such as deformation and lipid extraction, are regarded as key factors influencing the insertion of peptides into membranes. The associated intermediate states in peptide conformations, lipid arrangements, membrane structure, and mechanical properties during this process are specifically discussed. Finally, potential strategies for enhancing the poration ability and improving the antimicrobial performance of AMPs are included as well.

Designing Melittin-Graphene Hybrid Complexes for Enhanced Antibacterial Activity

Antimicrobial peptides (AMPs) promise a fundamental solution to the devastating threat of drug-resistant bacteria. However, drawbacks of AMPs (e.g., poor cell membrane penetration efficiency) seriously block their clinical use. In this work, rational design of a hybrid complex of melittin (as a representative AMP) and graphene or graphene oxide (Gra or GO) nanosheets for enhanced antibacterial ability is achieved, via combining in-silico prediction and in-tube test. In comparison to pristine melittin, the specifically designed AMP-Gra (/GO) complex exhibits remarkable efficiency in transmembrane perforation with an over tenfold decrease in the threshold working concentration of peptide; moreover, it has an up to 20-fold enhancement in antibacterial activity against both Gram-negative and Gram-positive bacteria. Such improvement is ascribed to the synergetic insertion of nanosheets and melittin due to similarity in antibacterial mechanism between them and is further regulated by the structural factors of the complex, including the intersheet spacing and surface functionalization of the Gra/GO sheets, etc. These results provide practical guidelines to engineer AMPs with nanotechnology for improved antimicrobial performances, especially based on targeted functionalization of the Gra/GO nanosheets.