Rattusin structure reveals a novel defensin scaffold formed by intermolecular disulfide exchanges

A Novel Dimeric Short Peptide Derived from α-Defensin-Related Rattusin with Improved Antimicrobial and DNA-Binding Activities

Rattusin, an α-defensin-related antimicrobial peptide isolated from the small intestine of rats, has been previously characterized through NMR spectroscopy to elucidate its three-dimensional structure, revealing a C2 homodimeric scaffold stabilized by five disulfide bonds. This study aimed to identify the functional region of rattusin by designing and synthesizing various short analogs, subsequently leading to the development of novel peptide-based antibiotics. The analogs, designated as F1, F2, F3, and F4, were constructed based on the three-dimensional configuration of rattusin, among which F2 is the shortest peptide and exhibited superior antimicrobial efficacy compared to the wild-type peptide. The central cysteine residue of F2 prompted an investigation into its potential to form a dimer at neutral pH, which is critical for its antimicrobial function. This activity was abolished upon the substitution of the cysteine residue with serine, indicating the necessity of dimerization for antimicrobial action. Further, we synthesized β-hairpin-like analogs, both parallel and antiparallel, based on the dimeric structure of F2, which maintained comparable antimicrobial potency. In contrast to rattusin, which acts by disrupting bacterial membranes, the F2 dimer binds directly to DNA, as evidenced by fluorescence assays and DNA retardation experiments. Importantly, F2 exhibited negligible cytotoxicity up to 515 μg/mL, assessed via hemolysis and MTT assays, underscoring its potential as a lead compound for novel peptide-based antibiotic development.

Development strategies and application of antimicrobial peptides as future alternatives to in-feed antibiotics

The use of in-feed antibiotics has been widely restricted due to the significant environmental pollution and food safety concerns they have caused. Antimicrobial peptides (AMPs) have attracted widespread attention as potential future alternatives to in-feed antibiotics owing to their demonstrated antimicrobial activity and environment friendly characteristics. However, the challenges of weak bioactivity, immature stability, and low production yields of natural AMPs impede practical application in the feed industry. To address these problems, efforts have been made to develop strategies for approaching the AMPs with enhanced properties. Herein, we summarize approaches to improving the properties of AMPs as potential alternatives to in-feed antibiotics, mainly including optimization of structural parameters, sequence modification, selection of microbial hosts, fusion expression, and industrially fermentation control. Additionally, the potential for application of AMPs in animal husbandry is discussed. This comprehensive review lays a strong theoretical foundation for the development of in-feed AMPs to achieve the public health globally.

Advancements, challenges and future perspectives on peptide-based drugs: Focus on antimicrobial peptides

Among other health related issues, the rising concerns on drug resistance led to look for alternative pharmaceutical drugs that are effective both against infectious and noninfectious diseases. Antimicrobial peptides (AMPs) emerged as potential therapeutic molecule with wide range of applications. With their limitations, AMPs have gained reputable attentions in research as well as in the pharmaceutical industry. This review highlighted the historical background, research trends, technological advancements, challenges, and future perspectives in the development and applications of peptide drugs. Some vital questions related with the need for pharmaceutical production, factors for the slow and steady journey, the importance of oral bioavailability, and the drug resistance possibilities of AMPs were raised and addressed accordingly. Therefore, the current study is believed to provide a profound understanding in the past and current scenarios and future directions on the therapeutic impacts of peptide drugs.

Identification and Functional Characterization of Peptides With Antimicrobial Activity From the Syphilis Spirochete, Treponema pallidum

The etiological agent of syphilis, Treponema pallidum ssp. pallidum, is a highly invasive “stealth” pathogen that can evade the host immune response and persist within the host for decades. This obligate human pathogen is adept at establishing infection and surviving at sites within the host that have a multitude of competing microbes, sometimes including pathogens. One survival strategy employed by bacteria found at polymicrobial sites is elimination of competing microorganisms by production of antimicrobial peptides (AMPs). Antimicrobial peptides are low molecular weight proteins (miniproteins) that function directly via inhibition and killing of microbes and/or indirectly via modulation of the host immune response, which can facilitate immune evasion. In the current study, we used bioinformatics to show that approximately 7% of the T. pallidum proteome is comprised of miniproteins of 150 amino acids or less with unknown functions. To investigate the possibility that AMP production is an unrecognized defense strategy used by T. pallidum during infection, we developed a bioinformatics pipeline to analyze the complement of T. pallidum miniproteins of unknown function for the identification of potential AMPs. This analysis identified 45 T. pallidum AMP candidates; of these, Tp0451a and Tp0749 were subjected to further bioinformatic analyses to identify AMP critical core regions (AMPCCRs). Four potential AMPCCRs from the two predicted AMPs were identified and peptides corresponding to these AMPCCRs were experimentally confirmed to exhibit bacteriostatic and bactericidal activity against a panel of biologically relevant Gram-positive and Gram-negative bacteria. Immunomodulation assays performed under inflammatory conditions demonstrated that one of the AMPCCRs was also capable of differentially regulating expression of two pro-inflammatory chemokines [monocyte chemoattractant protein-1 (MCP-1) and interleukin-8 (IL-8)]. These findings demonstrate proof-of-concept for our developed AMP identification pipeline and are consistent with the novel concept that T. pallidum expresses AMPs to defend against competing microbes and modulate the host immune response.

Mammals' humoral immune proteins and peptides targeting the bacterial envelope: from natural protection to therapeutic applications against multidrug‐resistant Gram ‐negatives

Mammalian innate immunity employs several humoral ‘weapons’ that target the bacterial envelope. The threats posed by the multidrug‐resistant ‘ESKAPE’ Gram‐negative pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are forcing researchers to explore new therapeutic options, including the use of these immune elements. Here we review bacterial envelope‐targeting (peptidoglycan and/or membrane‐targeting) proteins/peptides of the mammalian immune system that are most likely to have therapeutic applications. Firstly we discuss their general features and protective activity against ESKAPE Gram‐negatives in the host. We then gather, integrate, and discuss recent research on experimental therapeutics harnessing their bactericidal power, based on their exogenous administration and also on the discovery of bacterial and/or host targets that improve the performance of this endogenous immunity, as a novel therapeutic concept. We identify weak points and knowledge gaps in current research in this field and suggest areas for future work to obtain successful envelope‐targeting therapeutic options to tackle the challenge of antimicrobial resistance.

Unifying the classification of antimicrobial peptides in the antimicrobial peptide database

Natural products offer an important avenue to novel therapeutics against drug-resistant bacteria, viruses, fungi, parasites, and cancer. However, there are numerous hurdles and challenges in discovering such molecules, including antimicrobial peptides (AMPs). While a thorough characterization of AMPs is limited by the amount of material, existing technology, and researcher's expertise, peptide classification is complicated by incomplete information as well as different methods proposed for AMPs from bacteria, plants, and animals. This article describes unified classification schemes for natural AMPs on a common platform: the Antimicrobial Peptide Database (APD; https://aps.unmc.edu). The various criteria for these unified classifications include peptide biological source, biosynthesis machinery, biological activity, amino acid sequence, mechanism of action, and three-dimensional structure. To overcome the problem with a limited number of known 3D structures, a universal peptide classification has also been refined and executed in the APD database. This universal method, based on the spatial connection patterns of polypeptide chains, is independent of peptide source, size, activity, 3D structure, or mechanism of action. It facilitates information registration, naming, exchange, decoding, prediction, and design of novel antimicrobial peptides.

Apolipoproteins L1-6 share key cation channel-regulating residues but have different membrane insertion and ion conductance properties

The human apolipoprotein L gene family encodes the apolipoprotein L1–6 (APOL1–6) proteins, which are effectors of the innate immune response to viruses, bacteria and protozoan parasites. Due to a high degree of similarity between APOL proteins, it is often assumed that they have similar functions to APOL1, which forms cation channels in planar lipid bilayers and membranes resulting in cytolytic activity. However, the channel properties of the remaining APOL proteins have not been reported. Here, we used transient overexpression and a planar lipid bilayer system to study the function of APOL proteins. By measuring lactate dehydrogenase release, we found that APOL1, APOL3, and APOL6 were cytolytic, whereas APOL2, APOL4, and APOL5 were not. Cells expressing APOL1 or APOL3, but not APOL6, developed a distinctive swollen morphology. In planar lipid bilayers, recombinant APOL1 and APOL2 required an acidic environment for the insertion of each protein into the membrane bilayer to form an ion conductance channel. In contrast, recombinant APOL3, APOL4, and APOL5 readily inserted into bilayers to form ion conductance at neutral pH, but required a positive voltage on the side of insertion. Despite these differences in membrane insertion properties, the ion conductances formed by APOL1-4 were similarly pH-dependent and cation-selective, consistent with conservation of the pore-lining region in each protein. Thus, despite structural conservation, the APOL proteins are functionally different. We propose that these proteins interact with different membranes and under different voltage and pH conditions within a cell to effect innate immunity to different microbial pathogens.

Spotlight on the Selected New Antimicrobial Innate Immune Peptides Discovered During 2015-2019

BACKGROUND

Antibiotic resistance is a global issue and new anti-microbials are required.

INTRODUCTION

Anti-microbial peptides are important players of host innate immune systems that prevent infections. Due to their ability to eliminate drug-resistant pathogens, AMPs are promising candidates for developing the next generation of anti-microbials.

METHODS

The anti-microbial peptide database provides a useful tool for searching, predicting, and designing new AMPs. In the period from 2015-2019, ~500 new natural peptides have been registered.

RESULTS

This article highlights a selected set of new AMP members with interesting properties. Teixobactin is a cell wall inhibiting peptide antibiotic, while darobactin inhibits a chaperone and translocator for outer membrane proteins. Remarkably, cOB1, a sex pheromone from commensal enterococci, restricts the growth of multidrug-resistant Enterococcus faecalis in the gut at a picomolar concentration. A novel proline-rich AMP has been found in the plant Brassica napus. A shrimp peptide MjPen- II comprises three different sequence domains: serine-rich, proline-rich, and cysteine-rich regions. Surprisingly, an amphibian peptide urumin specifically inhibits H1 hemagglutinin-bearing influenza A virus. Defensins are abundant and typically consist of three pairs of intramolecular disulfide bonds. However, rat rattusin dimerizes via forming five pairs of intermolecular disulfide bonds. While human LL-37 can be induced by vitamin D, vitamin A induces the expression of resistin-like molecule alpha (RELMα) in mice. The isolation and characterization of an alternative human cathelicidin peptide, TLN-58, substantiates the concept of one gene multiple peptides. The involvement of a fly AMP nemuri in sleep induction may promote the research on the relationship between sleep and infection control.

CONCLUSION

The functional roles of AMPs continue to grow and the general term "innate immune peptides" becomes useful. These discoveries widen our view on the anti-microbial peptides and may open new opportunities for developing novel peptide therapeutics for different applications.

Syncollin is an antibacterial polypeptide

Syncollin is a 16-kDa protein found predominantly in the zymogen granules of pancreatic acinar cells, with expression at lower levels in intestinal epithelial cells and neutrophils. Here, we used Strep-tagged syncollin isolated from the supernatant of transiently transfected mammalian cells to test the hypothesis that syncollin has antibacterial properties, which might enable it to play a role in host defence in the gut and possibly elsewhere. We show that syncollin is an exceptionally thermostable protein with a circular dichroism spectrum consistent with a predominantly beta-sheet structure. Syncollin binds to bacterial peptidoglycan and restricts the growth of representative Gram-positive (Lactococcus lactis) and Gram-negative (Escherichia coli) bacteria. Syncollin induces propidium iodide uptake into E. coli (but not L. lactis), indicating permeabilisation of the bacterial membrane. It also causes surface structural damage in both L. lactis and E. coli, as visualised by scanning electron microscopy. We propose that syncollin is a previously unidentified member of a large group of antimicrobial polypeptides that control the gut microbiome. TAKE AWAYS: Syncollin is a 16-kDa protein found in pancreatic zymogen granules. Syncollin is highly thermostable and has a predominantly beta-sheet structure. Syncollin binds peptidoglycan and restricts the growth of L. lactis and E. coli. Syncollin causes propidium iodide uptake into E. coli (but not L. lactis). Syncollin causes surface structural damage in both L. lactis and E. coli.

Cysteines and Disulfide Bonds as Structure-Forming Units: Insights From Different Domains of Life and the Potential for Characterization by NMR

Disulfide bridges establish a fundamental element in the molecular architecture of proteins and peptides which are involved e.g., in basic biological processes or acting as toxins. NMR spectroscopy is one method to characterize the structure of bioactive compounds including cystine-containing molecules. Although the disulfide bridge itself is invisible in NMR, constraints obtained via the neighboring NMR-active nuclei allow to define the underlying conformation and thereby to resolve their functional background. In this mini-review we present shortly the impact of cysteine and disulfide bonds in the proteasome from different domains of life and give a condensed overview of recent NMR applications for the characterization of disulfide-bond containing biomolecules including advantages and limitations of the different approaches.

Molecular Diversity of Mytilin-Like Defense Peptides in Mytilidae (Mollusca, Bivalvia)

The CS-αβ architecture is a structural scaffold shared by a high number of small, cationic, cysteine-rich defense peptides, found in nearly all the major branches of the tree of life. Although several CS-αβ peptides involved in innate immune response have been described so far in bivalve mollusks, a clear-cut definition of their molecular diversity is still lacking, leaving the evolutionary relationship among defensins, mytilins, myticins and other structurally similar antimicrobial peptides still unclear. In this study, we performed a comprehensive bioinformatic screening of the genomes and transcriptomes available for marine mussels (Mytilida), redefining the distribution of mytilin-like CS-αβ peptides, which in spite of limited primary sequence similarity maintain in all cases a well-conserved backbone, stabilized by four disulfide bonds. Variations in the size of the alpha-helix and the two antiparallel beta strand region, as well as the positioning of the cysteine residues involved in the formation of the C1-C5 disulfide bond might allow a certain degree of structural flexibility, whose functional implications remain to be investigated. The identification of mytilins in Trichomya and Perna spp. revealed that many additional CS-αβ AMPs remain to be formally described and functionally characterized in Mytilidae, and suggest that a more robust scheme should be used for the future classification of such peptides with respect with their evolutionary origin.

The antimicrobial peptide database provides a platform for decoding the design principles of naturally occurring antimicrobial peptides

This article is written for the 2020 tool issue of Protein Science. It briefly introduces the widely used antimicrobial peptide database, initially online in 2003. After a description of the main features of each database version and some recent additions, the focus is on the peptide design parameters for each of the four unified classes of natural antimicrobial peptides (AMPs). The amino acid signature in AMPs varies substantially, leading to a variety of structures for functional and mechanistic diversity. Also, Nature is a master of combinatorial chemistry by deploying different amino acids onto the same structural scaffold to tune peptide functions. In addition, the single-domain AMPs may be posttranslationally modified, self-assembled, or combined with other AMPs for function. Elucidation of the design principles of natural AMPs will facilitate future development of novel molecules for various applications.