Alpha-helical cationic antimicrobial peptides: relationships of structure and function

Antimicrobial peptides (AMPs), with their extraordinary properties, such as broad-spectrum activity, rapid action and difficult development of resistance, have become promising molecules as new antibiotics. Despite their various mechanisms of action, the interaction of AMPs with the bacterial cell membrane is the key step for their mode of action. Moreover, it is generally accepted that the membrane is the primary target of most AMPs, and the interaction between AMPs and eukaryotic cell membranes (causing toxicity to host cells) limits their clinical application. Therefore, researchers are engaged in reforming or de novo designing AMPs as a ‘single-edged sword’ that contains high antimicrobial activity yet low cytotoxicity against eukaryotic cells. To improve the antimicrobial activity of AMPs, the relationship between the structure and function of AMPs has been rigorously pursued. In this review, we focus on the current knowledge of α-helical cationic antimicrobial peptides, one of the most common types of AMPs in nature.     

抗菌肽RIKL的分子设计及生物学活性分析

天然抗菌肽具有较强的杀菌能力,但高生物相容性抗菌肽的构建一直阻碍着该领域的发展.为了提高抗菌肽的选择特异性,通过分子动力学分析探讨了抗菌肽的结构特性,并检测其生物学活性.首先以(RXKY)2(YRY)2 (X代表Ile,Y代表Leu)为模板设计新型抗菌肽分子RIKL.通过圆二色谱(circular dichroism,...     

Biological consequences of improving the structural stability of hairpins that have antimicrobial activity

Designing new antimicrobial peptides (AMPs) focuses heavily on the activity of the peptide and less on the elements that stabilize the secondary structure of these peptides. Studies have shown that improving the structure of naturally occurring AMPs can affect activity and so here we explore the relationship between structure and activity of two non‐naturally occurring AMPs. We have used a backbone‐cyclized peptide as a template and designed an uncyclized analogue of this peptide that has antimicrobial activity. We focused on beta‐hairpin‐like structuring features. Improvements to the structure of this peptide reduced the activity of the peptide against gram‐negative, Escherichia coli but improved the activity against gram‐positive, Corynebacterium glutamicum. Distinctions in structuring effects on gram‐negative versus gram‐positive activity were also seen in a second peptide system. Structural improvements resulted in a peptide that was more active than the native against gram‐positive bacterium but less active against gram‐negative bacterium. Our results show that there is not always a correlation between improved hairpin‐structuring and activity. Other factors such as the type of bacteria being targeted as well as net positive charge can play a role in the potency of AMPs. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Design of novel analogues of short antimicrobial peptide anoplin with improved antimicrobial activity

Currently, novel antibiotics are urgently required to combat the emergence of drug‐resistant bacteria. Antimicrobial peptides with membrane‐lytic mechanism of action have attracted considerable interest. Anoplin, a natural α‐helical amphiphilic antimicrobial peptide, is an ideal research template because of its short sequence. In this study, we designed and synthesized a group of analogues of anoplin. Among these analogues, anoplin‐4 composed of d ‐amino acids displayed the highest antimicrobial activity due to increased charge, hydrophobicity and amphiphilicity. Gratifyingly, anoplin‐4 showed low toxicity to host cells, indicating high bacterial selectivity. Furthermore, the mortality rate of mice infected with Escherichia coli was significantly reduced by anoplin‐4 treatment relative to anoplin. In conclusion, anoplin‐4 is a novel anoplin analogue with high antimicrobial activity and enzymatic stability, which may represent a potent agent for the treatment of infection. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

A review on anti‐tuberculosis peptides: Impact of peptide structure on anti‐tuberculosis activity

Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug‐resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug‐resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug‐resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non‐TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti‐TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti‐mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.     

Antimicrobial activity of the indolicidin‐derived novel synthetic peptide In‐58

Natural peptides with antimicrobial activity are extremely diverse, and peptide synthesis technologies make it possible to significantly improve their properties for specific tasks. Here, we investigate the biological properties of the natural peptide indolicidin and the indolicidin‐derived novel synthetic peptide In‐58. In‐58 was generated by replacing all tryptophan residues on phenylalanine in D‐configuration; the α‐amino group in the main chain also was modified by unsaturated fatty acid. Compared with indolicidin, In‐58 is more bactericidal, more resistant to proteinase K, and less toxic to mammalian cells. Using molecular physics approaches, we characterized the action of In‐58 on bacterial cells at the cellular level. Also, we have found that studied peptides damage bacterial membranes. Using the Escherichia coli luminescent biosensor strain MG1655 (pcolD’::lux), we investigated the action of indolicidin and In‐58 at the subcellular level. At subinhibitory concentrations, indolicidin and In‐58 induced an SOS response. Our data suggest that indolicidin damages the DNA, but bacterial membrane perturbation is its principal mode of action. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

蜜蜂抗菌肽研究及其应用进展

抗菌肽是一类由特定基因编码的小分子多肽,广泛分布于各种生物中,是生物天然免疫的重要效应分子,其对缺乏获得性免疫系统的昆虫尤为重要。蜜蜂是一种对环境极其重要的社会性模式昆虫,又有着极高的经济价值,因此蜜蜂抗菌肽有着较大的研究意义。本文对蜜蜂4种天然免疫抗菌肽(Apidaecin、Abaecin、Hymenoptaecin和Defensin)和蜂产品中的抗菌肽(Jelleines、Melittin和Apamin)研究进展进行了综述,介绍了它们的功能、作用机制及其应用,提出了蜜蜂抗菌肽未来可行的研究方向,旨在推动蜜蜂抗菌肽的研究。     

High‐yield recombinant expression of the chicken antimicrobial peptide fowlicidin‐2 in Escherichia coli

The antimicrobial peptide fowlicidin‐2 identified in chicken is a member of the cathelicidins family. The mature fowlicidin‐2 possesses high antibacterial efficacy and lipopolysaccharide (LPS) neutralizing activity, and also represents an excellent candidate as an antimicrobial agent. In the present study, the recombinant fowlicidin‐2 was successfully produced by Escherichia coli (E. coli) recombinant expression system. The gene encoding fowlicidin‐2 with the codon preference of E. coli was designed through codon optimization and synthesized in vitro. The gene was then ligated into the plasmid pET‐32a(+), which features fusion protein thioredoxin at the N‐terminal. The recombinant plasmid was transformed into E. coli BL21(DE3) and cultured in Luria‐Bertani (LB) medium. After isopropyl‐β‐D‐thiogalactopyranoside (IPTG) induction, the fowlicidin‐2 fusion protein was successfully expressed as inclusion bodies. The inclusion bodies were dissolved and successfully released the peptide in 70% formic acid solution containing cyanogen bromide (CNBr) in a single step. After purification by reverse‐phase high‐performance liquid chromatography (RP‐HPLC), ～6.0 mg of fowlicidin‐2 with purity more than 97% was obtained from 1 litre of bacteria culture. The recombinant peptide exhibited high antibacterial activity against the Gram‐positive and Gram‐negative bacteria, and even drug‐resistant strains. This system could be used to rapidly and efficiently produce milligram quantities of a battery of recombinant antimicrobial peptides as well as for large‐scale production. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:369–374, 2015     

昆虫抗菌肽结构与功能关系及其在分子设计中的应用

昆虫抗菌肽在自然分布广泛,结构多样,其作用机制尚未确切阐明,但其结构上的某些共同特征与其功能密切相关,同时,对其结构与功能间关系的研究有利于设计合成新的抗菌肽,为以后发现活性更强,毒性更低且作用广谱的抗菌素奠定基础。     

Design of novel antimicrobial peptide dimer analogues with enhanced antimicrobial activity in vitro and in vivo by intermolecular triazole bridge strategy

Currently, antimicrobial peptides have attracted considerable attention because of their broad-sprectum activity and low prognostic to induce antibiotic resistance. In our study, for the first time, a series of side-chain hybrid dimer peptides J-AA (Anoplin-Anoplin), J-RR (RW-RW), and J-AR (Anoplin-RW) based on the wasp peptide Anoplin and the arginine- and tryptophan-rich hexapeptide RW were designed and synthesized by click chemistry, with the intent to improve the antimicrobial efficacy of peptides against bacterial pathogens. The results showed that all dimer analogues exhibited up to a 4–16 fold increase in antimicrobial activity compared to the parental peptides against bacterial strains. Furthermore, the antimicrobial activity was confirmed by time-killing kinetics assay with two strains which showed that these dimer analogues at 1, 2 × MIC were rapidly bactericidal and reduced the initial inoculum significantly during the first 2–6 h. Notably, dimer peptides showed synergy and additivity effects when used in combination with conventional antibiotics rifampin or penicillin respectively against the multidrug-resistant strains. In the Escherichia coli-infected mouse model, all of hybrid dimer analogues had significantly lower degree of bacterial load than the untreated control group when injected once i.p. at 5 mg/kg. In addition, the infected mice by methicillin-resistant (MRSA) strain could be effectively treated with J-RR. All of dimer analogues had membrane-active action mode. And the membrane-dependent mode of action signifies that peptides functions freely and without regard to conventional resistant mechanisms. Circular dichroism analyses of all dimer analogues showed a general predominance of α-helix conformation in 50% trifluoroethanol (TFE). Additionally, the acute toxicities study indicated that J-RR or J-AR did not show the signs of toxicity when adult mice exposed to concentration up to 120 mg/kg. The 50% lethal dose (LD₅₀) of J-AA was 53.6 mg/kg. In conclusion, to design and synthesize side chain-hybrid dimer analogues via click chemistry may offer a new strategy for antibacterial therapeutic option.     

Mammalian antimicrobial peptide protegrin‐4 self assembles and forms amyloid‐like aggregates: Assessment of its functional relevance

Protegrin‐4 (PG‐4) is a member of the porcine leukocyte protegrins family of cysteine‐rich antimicrobial peptides (AMPs) isolated from Sus scrofa. It consists of 18 amino acid residues and works as a part of innate immune system. In this study, we examined the intrinsic aggregation propensity of this AMP using multiple computational algorithms, namely, TANGO, AGGRESCAN, FOLDAMYLOID, AMYLPRED, and ZYGGREGATOR, and found that the peptide is predicted to have a high propensity for the β sheet formation that disposes this peptide to be amyloidogenic. Under in vitro conditions, PG‐4 formed visible aggregates and displayed the hallmark properties of typical amyloids such as enhanced binding of Congo red, increased fluorescence with Thioflavin‐T, and fibrillar morphology under transmission electron microscopy. Then we examined its antimicrobial activity against Bacillus subtilis and found that the aggregated peptide retained its antimicrobial activity. Additionally, the aggregates remain non‐toxic to the HEK293 and Caco2 cells. Our study suggests that the inherent aggregation properties of AMP can rationally be explored as a potential source of peptide‐based antimicrobials with enhanced stability.     

抗菌肽的结构分析、抗菌机制及改造应用的研究进展

细菌感染已成为威胁人类健康的重要公共卫生问题之一,而抗生素的滥用又加快了细菌耐药性的进程。抗菌肽因其广谱抗菌活性、快速杀菌作用、低毒性和不易产生耐药性等特点受到了广泛关注。然而,抗菌肽的天然结构也预示了其应用存在一些限制,如易降解、不稳定、低渗透和高成本等。如何改良抗菌肽仍是需要解决的难题。本文从抗菌肽的来源和结构特征出发,分析了与抗菌相关的空间结构及其所对应的抗菌机制,总结了现有抗菌肽的改良策略,为寻求新型改良方案奠定基础。希望为今后抗菌肽的改造与临床应用提供新的思路和方向。     

Immobilization and orientation‐dependent activity of a naturally occurring antimicrobial peptide

A naturally occurring antimicrobial peptide, SMAP‐29, was synthesized with an n‐terminal or c‐terminal cysteine, termed c_SMAP and SMAP_c, respectively, for site‐directed immobilization to superparamagnetic beads. Immobilized SMAP orientation‐dependent activity was probed against multiple bacteria of clinical interest including Acinetobacter baumannii, Pseudomonas aeruginosa, Bacillus anthracis sterne and Staphylococcus aureus. A kinetic microplate assay was employed to reveal both concentration and time‐dependent activity for elucidation of minimum bactericidal concentration (MBC) and sub‐lethal effects. Immobilized SMAP activity was equivalent or reduced compared with soluble SMAP_c and c_SMAP regardless of immobilization orientation, with only one exception. A comparison of immobilized SMAP_c and c_SMAP activity revealed a bacteria‐specific potency dependent on immobilization orientation, which was contrary to that seen in solution, wherein SMAP_c was more potent against all bacteria than c_SMAP. Sub‐MBC kinetic studies displayed the influence of peptide exposure to the cells with multiple bacteria exhibiting increased susceptibility and efficacy at lower concentrations upon extended exposure (i.e. MBC enhancement). For instances in which complete killing was not achieved, two predominant effects were evident: retardation of growth rate and an increased lag phase. Both effects, seen independently and concomitantly, indicate some degree of induced cellular damage that can serve as a predictor toward eventual cell death. SMAP_c immobilized on glass through standard silanization chemistry was also investigated to ascertain the influence of substrate on activity against select bacteria. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.     

Antimicrobial activity and stability of protonectin with D‐amino acid substitutions

The misuse and overuse of antibiotics result in the emergence of resistant bacteria and fungi, which make an urgent need of the new antimicrobial agents. Nowadays, antimicrobial peptides have attracted great attention of researchers. However, the low physiological stability in biological system limits the application of naturally occurring antimicrobial peptides as novel therapeutics. In the present study, we synthesized derivatives of protonectin by substituting all the amino acid residues or the cationic lysine residue with the corresponding D ‐amino acids. Both the D ‐enantiomer of protonectin (D ‐prt) and D ‐Lys‐protonectin (D ‐Lys‐prt) exhibited strong antimicrobial activity against bacteria and fungi. Moreover, D ‐prt showed strong stability against trypsin, chymotrypsin and the human serum, while D ‐Lys‐prt only showed strong stability against trypsin. Circular dichroism analysis revealed that D ‐Lys‐prt still kept typical α‐helical structure in the membrane mimicking environment, while D ‐prt showed left hand α‐helical structure. In addition, propidium iodide uptake assay and bacteria and fungi killing experiments indicated that all D ‐amino acid substitution or partially D ‐amino acid substitution analogs could disrupt the integrity of membrane and lead the cell death. In summary, these findings suggested that D ‐prt and D ‐Lys‐prt might be promising candidate antibiotic agents for therapeutic application against resistant bacteria and fungi infection. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Design,expression, and characterization of the hybrid antimicrobial peptide T‐catesbeianin‐1 based on FyuA

The overuse of antibiotics has resulted in the emergence of antibiotic‐resistant bacteria, which presents an urgent need for new antimicrobial agents. At present, antimicrobial peptides have attracted a great deal of attention from researchers. However, antimicrobial peptides often affect a broad range of microorganisms, including the normal flora in a host organism. In the present study, we designed a novel hybrid antimicrobial peptide, expressed the hybrid peptide, and studied its specific target. The hybrid peptide, named T‐catesbeianin‐1, which includes the FyuA‐binding domain of pesticin and the peptide catesbeianin‐1, was designed and expressed in Pichia pastoris X‐33. Then, we determined the antimicrobial activity, cytotoxicity, and specific target of the peptide. T‐catesbeianin‐1 has strong antimicrobial activity and binds to FyuA to inhibit or kill Escherichia coli present in clinical specimens and mixed‐species culture. In summary, these findings suggested that T‐catesbeianin‐1 might be promising and specific antibiotic agent for therapeutic application against fyuA⁺ E. coli.     

Deletion of the carboxyl‐terminal residue disrupts the amino‐terminal folding,self‐association,and thermal stability of an amphipathic antimicrobial peptide

Understanding the complex relationship between amino acid sequence and protein behaviors, such as folding and self‐association, is a major goal of protein research. In the present work, we examined the effects of deleting a C‐terminal residue on the intrinsic properties of an amphapathic α‐helix of mastoparan‐B (MP‐B), an antimicrobial peptide with the sequence LKLKSIVSWAKKVL‐NH2. We used circular dichroism and nuclear magnetic resonance to demonstrate that the peptide MP‐B^[1‐13] displayed significant unwinding at the N‐terminal helix compared with the parent peptide of MP‐B, as the temperature increased when the residue at position 14 was deleted. Pulsed‐field gradient nuclear magnetic resonance data revealed that MP‐B forms a larger diffusion unit than MP‐B^[1‐13] at all experimental temperatures and continuously dissociates as the temperature increases. In contrast, the size of the diffusion unit of MP‐B^[1‐13] is almost independent of temperature. These findings suggest that deleting the flexible, hydrophobic amino acid from the C‐terminus of MP‐B is sufficient to change the intrinsic helical thermal stability and self‐association. This effect is most likely because of the modulation of enthalpic interactions and conformational freedom that are specified by this residue. Our results implicate terminal residues in the biological function of an antimicrobial peptide. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

Antimicrobial activities and membrane‐active mechanism of CPF‐C1 against multidrug‐resistant bacteria,a novel antimicrobial peptide derived from skin secretions of the tetraploid frog Xenopus clivii

Hospital‐acquired infections caused by multidrug‐resistant bacteria pose significant challenges for treatment, which necessitate the development of new antibiotics. Antimicrobial peptides are considered potential alternatives to conventional antibiotics. The skin of Anurans (frogs and toads) amphibians is an extraordinarily rich source of antimicrobial peptides. CPF‐C1 is a typical cationic antimicrobial peptide that was originally isolated from the tetraploid frog Xenopus clivii. Our results showed that CPF‐C1 has potent antimicrobial activity against both sensitive and multidrug‐resistant bacteria. It disrupted the outer and inner membranes of bacterial cells. CPF‐C1 induced both propidium iodide uptake into the bacterial cell and the leakage of calcein from large liposome vesicles, which suggests a mode of action that involves membrane disturbance. Scanning electron microscopy and transmission electron microscopy verified the morphologic changes of CPF‐C1‐treated bacterial cells and large liposome vesicles. The membrane‐dependent mode of action signifies that the CPF‐C1 peptide functions freely and without regard to conventional resistant mechanisms. Additionally, it is difficult for bacteria to develop resistance against CPF‐C1 under this action mode. Other studies indicated that CPF‐C1 had low cytotoxicity against mammalian cell. In conclusion, considering the increase in multidrug‐resistant bacterial infections, CPF‐C1 may offer a new strategy that can be considered a potential therapeutic agent for the treatment of diseases caused by multidrug‐resistant bacteria. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

Effects of dimerization of the cell‐penetrating peptide Tat analog on antimicrobial activity and mechanism of bactericidal action

The cell‐penetrating peptide Tat (48–60) (GRKKRRQRRRPPQ) derived from HIV‐1 Tat protein showed potent antibacterial activity (MIC: 2–8 µM ). To investigate the effect of dimerization of Tat (48–60) analog, [Tat(W): GRKKRRQRRRPWQ‐NH₂], on antimicrobial activity and mechanism of bactericidal action, its dimeric peptides, di‐Tat(W)‐C and di‐Tat(W)‐K, were synthesized by a disulfide bond linkage and lysine linkage of monomeric Tat(W), respectively. From the viewpoint of a weight basis and the monomer concentration, these dimeric peptides displayed almost similar antimicrobial activity against six bacterial strains tested but acted more rapidly against Staphylococcus aureus on kinetics of bactericidal activity, compared with monomeric Tat(W). Unlike monomeric Tat(W), these dimeric peptides significantly depolarized the cytoplasmic membrane of intact S. aureus cells at MIC and induced dye leakage from bacterial‐membrane‐mimicking egg yolk L ‐α‐phosphatidylethanolamine/egg yolk L ‐α‐phosphatidyl‐DL ‐glycerol (7:3, w/w) vesicles. Furthermore, these dimeric peptides were less effective to translocate across lipid bilayers than monomeric Tat(W). These results indicated that the dimerization of Tat analog induces a partial change in the mode of its bactericidal action from intracellular target mechanism to membrane‐targeting mechanism. Collectively, our designed dimeric Tat peptides with high antimicrobial activity and rapid bactericidal activity appear to be excellent candidates for future development as novel antimicrobial agents. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

铰链结构对抗菌肽生物活性的影响及在分子设计中的应用研究进展

铰链结构,又称铰链区或转角,是部分抗菌肽序列中存在的一种特殊结构。但目前抗菌肽结构的研究多集中于标准的α-螺旋和β-折叠二级结构,对于铰链结构及其作用总结较少。铰链结构对抗菌肽生物活性有重要影响,主要原因是铰链结构能够提高抗菌肽的结构灵活性,促进其对细菌细胞膜的破坏作用或与胞内作用靶点的结合效率,进而提高抗菌肽的抗菌活性。同时,降低的抗菌肽结构刚性,消减了抗菌肽对真核细胞的毒性。文中结合了笔者课题组相关工作,就铰链结构特点、对抗菌肽生物活性的影响以及在抗菌肽分子设计方面的应用进行了综述,以期为新型抗菌肽的设计和开发提供参考。     

抗菌肽结构改造与人工智能研发策略

抗菌肽是一类广泛存在于生物体内的小分子肽,参与构成生物体先天免疫,可以有效抵抗病原微生物的入侵。抗菌肽具有广谱抗菌活性,且不易产生耐药性等特点,在治疗感染性疾病方面具有独特的优势,有望成为理想的抗感染药物。然而,由于部分抗菌肽尚存在稳定性差、毒性高等问题,限制了抗菌肽的广泛应用。由于人工智能算法能有效合成具有高稳定性、低毒性的抗菌肽,在探索天然抗菌肽中展现了巨大的潜力,因此本文简述了抗菌肽的抗菌机制、结构改造以及利用机器学习和深度学习等人工智能算法进行新型抗菌肽研发的优化策略,以期为抗菌肽结构优化及研发提供新思路。