Plant cystine-knot peptides: pharmacological perspectives

Plant Protease Inhibitors as Emerging Antimicrobial Peptide Agents: A Comprehensive Review

Antimicrobial peptides (AMPs) are important mediator molecules of the innate defense mechanisms in a wide range of living organisms, including bacteria, mammals, and plants. Among them, peptide protease inhibitors (PPIs) from plants play a central role in their defense mechanisms by directly attacking pathogens or by modulating the plant's defense response. The growing prevalence of microbial resistance to currently available antibiotics has intensified the interest concerning these molecules as novel antimicrobial agents. In this scenario, PPIs isolated from a variety of plants have shown potential in inhibiting the growth of pathogenic bacteria, protozoans, and fungal strains, either by interfering with essential biochemical or physiological processes or by altering the permeability of biological membranes of invading organisms. Moreover, these molecules are active inhibitors of a range of proteases, including aspartic, serine, and cysteine types, with some showing particular efficacy as trypsin and chymotrypsin inhibitors. In this review, we provide a comprehensive analysis of the potential of plant-derived PPIs as novel antimicrobial molecules, highlighting their broad-spectrum antimicrobial efficacy, specificity, and minimal toxicity. These natural compounds exhibit diverse mechanisms of action and often multifunctionality, positioning them as promising molecular scaffolds for developing new therapeutic antibacterial agents.

Carboxypeptidase inhibitors from Solanaceae as a new subclass of pathogenesis related peptide aiming biotechnological targets for plant defense

Background: Plant protease inhibitors play a crucial role in inhibiting proteases produced by phytopathogens and exhibiting inhibitory effects on nematodes, fungi, and insects, making them promising candidates for crop protection. Specifically, carboxypeptidase inhibitors, a subset of proteinase inhibitors, have been extensively studied in potato and tomato of Solanaceae plant family. However, further research is needed to fully understand the functions and biotechnological potential of those inhibitors in plants. This work aimed to in silico characterize carboxypeptidase inhibitors from Solanaceae as potential antimicrobial and defense agents focused on biotechnological targets. Methods: The methodology employed involved search in UniProt, PDB, KNOTTIN, NCBI, and MEROPS databases for solanaceous carboxypeptidase inhibitors, phylogenetic relationships and conservation patterns analyzes using MEGA-X software and Clustal Omega/MView tools, physicochemical properties and antimicrobial potential prediction using ProtParam, ToxinPred, iAMPred, and APD3 tools, and structural features prediction using PSIPRED. Results and discussion: A systematic literature search was conducted to identify relevant studies on Solanaceae carboxypeptidase inhibitors and their activities against pathogens. The selected studies were reviewed and the main findings compiled. The characterization of Solanaceae carboxypeptidase inhibitors proposed for the first time the global sequence consensus motif CXXXCXXXXDCXXXXXCXXC, shedding light on carboxypeptidase inhibitors distribution, sequence variability, and conservation patterns. Phylogenetic analysis showed evolutionary relationships within the Solanaceae family, particularly in Capsicum, Nicotiana, and Solanum genera. Physicochemical characteristics of those peptides indicated their similarity to antimicrobial peptides. Predicted secondary structures exhibited variations, suggesting a broad spectrum of action, and studies had been demonstrated their activities against various pathogens. Conclusion: Carboxypeptidase inhibitors are being proposed here as a new subclass of PR-6 pathogenesis-related proteins, which will aid in a focused understanding of their functional roles in plant defense mechanisms. These findings confirm the Solanaceae carboxypeptidase inhibitors potential as defense agents and highlight opportunities for their biotechnological applications in pathogen control.

Exploring Plants with Flowers: From Therapeutic Nutritional Benefits to Innovative Sustainable Uses

Flowers have played a significant role in society, focusing on their aesthetic value rather than their food potential. This study's goal was to look into flowering plants for everything from health benefits to other possible applications. This review presents detailed information on 119 species of flowers with agri-food and health relevance. Data were collected on their family, species, common name, commonly used plant part, bioremediation applications, main chemical compounds, medicinal and gastronomic uses, and concentration of bioactive compounds such as carotenoids and phenolic compounds. In this respect, 87% of the floral species studied contain some toxic compounds, sometimes making them inedible, but specific molecules from these species have been used in medicine. Seventy-six percent can be consumed in low doses by infusion. In addition, 97% of the species studied are reported to have medicinal uses (32% immune system), and 63% could be used in the bioremediation of contaminated environments. Significantly, more than 50% of the species were only analysed for total concentrations of carotenoids and phenolic compounds, indicating a significant gap in identifying specific molecules of these bioactive compounds. These potential sources of bioactive compounds could transform the health and nutraceutical industries, offering innovative approaches to combat oxidative stress and promote optimal well-being.

Domain Shuffling and Site-Saturation Mutagenesis for the Enhanced Inhibitory Potential of Amaranthaceae α-Amylase Inhibitors

Amaranthaceae α-amylase inhibitors (AAIs) are knottin-type proteins with selective inhibitory potential against coleopteran α-amylases. Their small size and remarkable stability make them exciting molecules for protein engineering to achieve superior selectivity and efficacy. In this report, we have designed a set of AAI pro- and mature peptides chimeras. Based on in silico analysis, stable AAI chimeras having a stronger affinity with target amylases were selected for characterization. In vitro studies validated that chimera of the propeptide from Chenopodium quinoa α-AI and mature peptide from Beta vulgaris α-AI possess 3, 7.6, and 4.26 fold higher inhibition potential than parental counterparts. Importantly, recombinant AAI chimera retained specificity towards target coleopteran α-amylases. In addition, to improve the inhibitory potential of AAI, we performed in silico site-saturation mutagenesis. Computational analysis followed by experimental data showed that substituting Asparagine at the 6th position with Methionine had a remarkable increase in the specific inhibition potential of Amaranthus hypochondriacus α-AI. These results provide structural-functional insights into the vitality of AAI propeptide and a potential hotspot for mutagenesis to enhance the AAI activity. Our investigation will be a toolkit for AAI's optimization and functional differentiation for future biotechnological applications.

CysPresso: a classification model utilizing deep learning protein representations to predict recombinant expression of cysteine-dense peptides

BACKGROUND

Cysteine-dense peptides (CDPs) are an attractive pharmaceutical scaffold that display extreme biochemical properties, low immunogenicity, and the ability to bind targets with high affinity and selectivity. While many CDPs have potential and confirmed therapeutic uses, synthesis of CDPs is a challenge. Recent advances have made the recombinant expression of CDPs a viable alternative to chemical synthesis. Moreover, identifying CDPs that can be expressed in mammalian cells is crucial in predicting their compatibility with gene therapy and mRNA therapy. Currently, we lack the ability to identify CDPs that will express recombinantly in mammalian cells without labour intensive experimentation. To address this, we developed CysPresso, a novel machine learning model that predicts recombinant expression of CDPs based on primary sequence.

RESULTS

We tested various protein representations generated by deep learning algorithms (SeqVec, proteInfer, AlphaFold2) for their suitability in predicting CDP expression and found that AlphaFold2 representations possessed the best predictive features. We then optimized the model by concatenation of AlphaFold2 representations, time series transformation with random convolutional kernels, and dataset partitioning.

CONCLUSION

Our novel model, CysPresso, is the first to successfully predict recombinant CDP expression in mammalian cells and is particularly well suited for predicting recombinant expression of knottin peptides. When preprocessing the deep learning protein representation for supervised machine learning, we found that random convolutional kernel transformation preserves more pertinent information relevant for predicting expressibility than embedding averaging. Our study showcases the applicability of deep learning-based protein representations, such as those provided by AlphaFold2, in tasks beyond structure prediction.

Nutritional and Pharmaceutical Applications of Under-Explored Knottin Peptide-Rich Phytomedicines

Phytomedicines reportedly rich in cystine knot peptides (Knottins) are found in several global diets, food/herbal supplements and functional foods. However, their knottin peptide content has largely been unexplored, notably for their emerging dual potentials at both the food and medicine space. The nutritional roles, biological targets and mechanism(s) of activity of these knotted peptides are largely unknown. Meanwhile, knottins have recently been unveiled as emerging peptide therapeutics and nutraceuticals of primary choice due to their broad spectrum of bioactivity, hyper stability, selective toxicity, impressive selectivity for biomolecular targets, and their bioengineering applications. In addition to their potential dietary benefits, some knottins have displayed desirable limited toxicity to human erythrocytes. In an effort to appraise what has been accomplished, unveil knowledge gaps and explore the future prospects of knottins, an elaborate review of the nutritional and pharmaceutical application of phytomedicines rich in knottins was carried out. Herein, we provide comprehensive data on common dietary and therapeutic knottins, the majority of which are poorly investigated in many food-grade phytomedicines used in different cultures and localities. Findings from this review should stimulate scientific interest to unveil novel dietary knottins and knottin-rich nutraceutical peptide drug candidates/leads with potential for future clinical application.

An Overview of the Potentialities of Antimicrobial Peptides Derived from Natural Sources

Antimicrobial peptides (AMPs) are constituents of the innate immune system in every kind of living organism. They can act by disrupting the microbial membrane or without affecting membrane stability. Interest in these small peptides stems from the fear of antibiotics and the emergence of microorganisms resistant to antibiotics. Through membrane or metabolic disruption, they defend an organism against invading bacteria, viruses, protozoa, and fungi. High efficacy and specificity, low drug interaction and toxicity, thermostability, solubility in water, and biological diversity suggest their applications in food, medicine, agriculture, animal husbandry, and aquaculture. Nanocarriers can be used to protect, deliver, and improve their bioavailability effectiveness. High cost of production could limit their use. This review summarizes the natural sources, structures, modes of action, and applications of microbial peptides in the food and pharmaceutical industries. Any restrictions on AMPs' large-scale production are also taken into consideration.

Plant antimicrobial peptides: An overview about classification, toxicity and clinical applications

Antimicrobial peptides, also known as AMPs, are cationic and amphipathic molecules found in all living organisms, composing part of the defense mechanisms against various pathogens, including fungi, viruses, bacteria, and nematodes. AMPs derived from plants are the focus of this review because they have gained attention as alternative molecules to overcome pathogen resistance as well as new drugs to combat cancer. Plant AMPs are generally classified based on their sequences and structures, as thionins, defensins, hevein-like peptides, knottins, stable-like peptides, lipid transfer proteins, snakins, and cyclotides. Although there are studies reporting the toxicity of plant AMPs to nontarget cells or limitations of oral administration, synthetic AMPs with reduced toxicity or allergenicity, or greater resistance to peptidases can be designed by using different bioinformatics tools. Thus, this review provides information about the classification of plant AMPs, their characteristics, mechanisms of action, hemolytic and cytotoxic potential, possible applications in the medical field, and finally, the use of bioinformatics to help design synthetic AMPs with improved features.

Humanizing plant-derived snakins and their encrypted antimicrobial peptides

Due to safety restrictions, plant-derived antimicrobial peptides (AMPs) need optimization to be consumed beyond preservatives. Herein, 175 GASA-domain-containing snakins were analyzed. Factors including charge, hydrophobicity, helicity, hydrophobic moment (μH), folding enthalpy, folding heat capacity, folding free energy, therapeutic index, allergenicity, and bitterness were considered. The most optimal snakins for oral consumption as preservatives were from Cajanus cajan, Cucumis melo, Durio zibethinus, Glycine soja, Herrania umbratica, and Ziziphus jujuba. Virtual digestion of snakins predicted ACE1 and DPPIV inhibitory as dominant effects upon oral use with antihypertensive and antidiabetic properties. To be applied as a therapeutic in parenteral administration, snakins were browsed for short 20-mer encrypted fragments that were non-toxic or with eliminated toxicity using directed mutagenesis yet retaining the AMP property. The most promising 20-mer AMPs were Mr-SNK2-1a in Morella rubra with BBB permeation, Na-SNK2-2a(C¹⁸W), and Na-SNK2-2b(C¹⁶F) from Nicotiana attenuata. These AMPs were cell-penetrating peptides (CPPs), with a charge of +6, a μH of about 0.40, and a Boman-index higher than 2.48 Kcalmol^-1. Na-SNK2-2a(C¹⁸W) had putative activity against gram-negative bacteria with MIC lower than 25 μgml^-1, and Na-SNK2-2b(C¹⁶F) was a potential anti-HIV with an IC₅₀ of 3.04 μM. Other 20-mer AMPs, such as Cc-SNK1-2a from Cajanus cajan displayed an anti-HCV property with an IC₅₀ of 13.91 μM. While Si-SNK2-3a(C¹⁷P) from Sesamum indicum was a cationic anti-angiogenic CPP targeting the acidic microenvironment of tumors, Cme-SNK2-1a(C¹¹F) from Cucumis melo was an immunomodulator CPP applicable as a vaccine adjuvant. Because of combined mechanisms, investigating cysteine-rich peptides can nominate effective biotherapeutics.

Immunomodulatory peptides-A promising source for novel functional food production and drug discovery

Immunomodulatory peptides are a complex class of bioactive peptides that encompasses substances with different mechanisms of action. Immunomodulatory peptides could also be used in vaccines as adjuvants which would be extremely desirable, especially in response to pandemics. Thus, immunomodulatory peptides in food of plant origin could be regarded both as valuable suplements of novel functional food preparation and/or as precursors or possible active ingredients for drugs design for treatment variety of conditions arising from impaired function of immune system. Given variety of mechanisms, different tests are required to assess effects of immunomodulatory peptides. Some of those effects show good correlation with in vivo results but others, less so. Certain plant peptides, such as defensins, show both immunomodulatory and antimicrobial effect, which makes them interesting candidates for preparation of functional food and feed, as well as templates for design of synthetic peptides.

Protein scaffolds: Antibody alternative for cancer diagnosis and therapy

Although antibodies are well developed and widely used in cancer therapy and diagnostic fields, some defects remain, such as poor tissue penetration, long in vivo metabolic retention, potential cytotoxicity, patent limitation, and high production cost. These issues have led scientists to explore and develop novel antibody alternatives. Protein scaffolds are small monomeric proteins with stable tertiary structures and mutable residues, which emerged in the 1990s. By combining robust gene engineering and phage display techniques, libraries with sufficient diversity could be established for target binding scaffold selection. Given the properties of small size, high affinity, and excellent specificity and stability, protein scaffolds have been applied in basic research, and preclinical and clinical fields over the past two decades. To date, more than 20 types of protein scaffolds have been developed, with the most frequently used being affibody, adnectin, ANTICALIN®, DARPins, and knottin. In this review, we focus on the protein scaffold applications in cancer therapy and diagnosis in the last 5 years, and discuss the pros and cons, and strategies of optimization and design.

Although antibodies are well developed and widely used in cancer therapy and diagnostic fields, some defects remain, such as poor tissue penetration, long in vivo metabolic retention, potential cytotoxicity, patent limitation, and high production cost.

Discovery of a dual pathway aggregation mechanism for a therapeutic constrained peptide

Constrained peptides (CPs) have emerged as attractive candidates for drug discovery and development. To fully unlock the therapeutic potential of CPs, it is crucial to understand their physical stability and minimize the formation of aggregates that could induce immune responses. Although amyloid like aggregates have been researched extensively, few studies have focused on aggregates from other peptide scaffolds (e.g., CPs). In this work, a streamlined approach to effectively profile the nature and formation pathway of CP aggregates was demonstrated. Aggregates of various sizes were detected and shown to be amorphous. Though no major changes were found in peptide structure upon aggregation, these aggregates appeared to have mixed natures, consisting of primarily non-covalent aggregates with a low level of covalent species. This co-existence phenomenon was also supported by two kinetic pathways observed in time- and temperature-dependent aggregation studies. Furthermore, a stability study with 8 additional peptide variants exhibited good correlation between aggregation propensity and peptide hydrophobicity. Therefore, a dual aggregation pathway was proposed, with the non-covalent aggregates driven by hydrophobic interactions, whereas the covalent ones formed through disulfide scrambling. Overall, the workflow presented here provides a powerful strategy for comprehensive characterization of peptide aggregates and understanding their mechanisms of formation.

Linking molecular evolution to molecular grafting

Molecular grafting is a strategy for the engineering of molecular scaffolds into new functional agents, such as next-generation therapeutics. Despite its wide use, studies so far have focused almost exclusively on demonstrating its utility rather than understanding the factors that lead to either poor or successful grafting outcomes. Here, we examine protein evolution and identify parallels between the natural process of protein functional diversification and the artificial process of molecular grafting. We discuss features of natural proteins that are correlated to innovability-the capacity to acquire new functions-and describe their implications to molecular grafting scaffolds. Disulfide-rich peptides are used as exemplars because they are particularly promising scaffolds onto which new functions can be grafted. This article provides a perspective on why some scaffolds are more suitable for grafting than others, identifying opportunities on how molecular grafting might be improved.

Structural and Functional Enrichment Analyses for Antimicrobial Peptides

Whether there is any inclination between structures and functions of antimicrobial peptides (AMPs) is a mystery yet to be unraveled. AMPs have various structures associated with many different antimicrobial functions, including antibacterial, anticancer, antifungal, antiparasitic and antiviral activities. However, none has yet reported any antimicrobial functional tendency within a specific category of protein/peptide structures nor any structural tendency of a specific antimicrobial function with respect to AMPs. Here, we examine the relationships between structures categorized by three structural classification methods (CATH, SCOP, and TM) and seven antimicrobial functions with respect to AMPs using an enrichment analysis. The results show that antifungal activities of AMPs were tightly related to the two-layer sandwich structure of CATH, the knottin fold of SCOP, and the first structural cluster of TM. The associations with knottin and TM Cluster 1 even sustained through the AMPs with a low sequence identity. Moreover, another significant mutual enrichment was observed between the third cluster of TM and anti-Gram-positive-bacterial/anti-Gram-negative-bacterial activities. The findings of the structure-function inclination further our understanding of AMPs and could help us design or discover new therapeutic potential AMPs.

TCMP-2 affects tomato flowering and interacts with BBX16, a homolog of the arabidopsis B-box MiP1b

Flowering and fruiting are processes subject to complex control by environmental and endogenous signals. Endogenous signals comprise, besides classical phytohormones, also signaling peptides and miniproteins. Tomato cystine-knot miniproteins (TCMPs), which belong to a Solanaceous-specific group of Cys-rich protein family, have been recently involved in fruit development. TCMP-1 and TCMP-2 display a highly modulated expression pattern during flower and fruit development. A previous study reported that a change in the ratio of the two TCMPs affects the timing of fruit production. In this work, to investigate TCMP-2 mode of action, we searched for its interacting partners. One of the interactors identified by a yeast two hybrid screen, was the B-box domain-containing protein 16 (SlBBX16), whose closest homolog is the Arabidopsis microProtein 1b implicated in flowering time control. We demonstrated the possibility for the two proteins to interact in vivo in tobacco epidermal cells. Arabidopsis plants ectopically overexpressing the TCMP-2 exhibited an increased level of FLOWERING LOCUS T (FT) mRNA and anticipated flowering. Similarly, in previously generated transgenic tomato plants with increased TCMP-2 expression in flower buds, we observed an augmented expression of SINGLE-FLOWER TRUSS gene, the tomato ortholog of FT, whereas the expression of the antiflorigen SELF-PRUNING was unchanged. Consistently, these transgenic plants showed alterations in the flowering pattern, with an accelerated termination of the sympodial units. Overall, our study reveals a novel function for TCMP-2 as regulatory factor that might integrate, thanks to its capacity to interact with SlBBX16, into the signaling pathways that control flowering, and converge toward florigen regulation.

Connective Tissue Growth Factor: From Molecular Understandings to Drug Discovery

Connective tissue growth factor (CTGF) is a key signaling and regulatory molecule involved in different biological processes, such as cell proliferation, angiogenesis, and wound healing, as well as multiple pathologies, such as tumor development and tissue fibrosis. Although the underlying mechanisms of CTGF remain incompletely understood, a commonly accepted theory is that the interactions between different protein domains in CTGF and other various regulatory proteins and ligands contribute to its variety of functions. Here, we highlight the structure of each domain of CTGF and its biology functions in physiological conditions. We further summarized main diseases that are deeply influenced by CTGF domains and the potential targets of these diseases. Finally, we address the advantages and disadvantages of current drugs targeting CTGF and provide the perspective for the drug discovery of the next generation of CTGF inhibitors based on aptamers.

Isolation of Cysteine-Rich Peptides from Citrullus colocynthis

The plant Citrullus colocynthis, a member of the squash (Cucurbitaceae) family, has a long history in traditional medicine. Based on the ancient knowledge about the healing properties of herbal preparations, plant-derived small molecules, e.g., salicylic acid, or quinine, have been integral to modern drug discovery. Additionally, many plant families, such as Cucurbitaceae, are known as a rich source for cysteine-rich peptides, which are gaining importance as valuable pharmaceuticals. In this study, we characterized the C. colocynthis peptidome using chemical modification of cysteine residues, and mass shift analysis via matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. We identified the presence of at least 23 cysteine-rich peptides in this plant, and eight novel peptides, named citcol-1 to -8, with a molecular weight between ~3650 and 4160 Da, were purified using reversed-phase high performance liquid chromatography (HPLC), and their amino acid sequences were determined by de novo assignment of b- and y-ion series of proteolytic peptide fragments. In silico analysis of citcol peptides revealed a high sequence similarity to trypsin inhibitor peptides from Cucumis sativus, Momordica cochinchinensis, Momordica macrophylla and Momordica sphaeroidea. Using genome/transcriptome mining it was possible to identify precursor sequences of this peptide family in related Cucurbitaceae species that cluster into trypsin inhibitor and antimicrobial peptides. Based on our analysis, the presence or absence of a crucial Arg/Lys residue at the putative P1 position may be used to classify these common cysteine-rich peptides by functional properties. Despite sequence homology and the common classification into the inhibitor cysteine knot family, these peptides appear to have diverse and additional bioactivities yet to be revealed.

Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era

Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.

Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospects

The interaction of fungal pathogens with their host requires a novel invading mechanism and the presence of various virulence-associated components responsible for promoting the infection. The small secretory proteins, explicitly known as effector proteins, are one of the prime mechanisms of host manipulation utilized by the pathogen to disarm the host. Several effector proteins are known to translocate from fungus to the plant cell for host manipulation. Many fungal effectors have been identified using genomic, transcriptomic, and bioinformatics approaches. Most of the effector proteins are devoid of any conserved signatures, and their prediction based on sequence homology is very challenging, therefore by combining the sequence consensus based upon machine learning features, multiple tools have also been developed for predicting apoplastic and cytoplasmic effectors. Various post-genomics approaches like transcriptomics of virulent isolates have also been utilized for identifying active consortia of effectors. Significant progress has been made in understanding biotrophic effectors; however, most of it is underway due to their complex interaction with host and complicated recognition and signaling networks. This review discusses advances, and challenges in effector identification and highlighted various features of the potential effector proteins and approaches for understanding their genetics and strategies for regulation.

The Tomato Metallocarboxypeptidase Inhibitor I, which Interacts with a Heavy Metal-Associated Isoprenylated Protein, Is Implicated in Plant Response to Cadmium

Metallocarboxypeptidases are metal-dependent enzymes, whose biological activity is regulated by inhibitors directed on the metal-containing active site. Some metallocarboxypeptidase inhibitors are induced under stress conditions and have a role in defense against pests. This paper is aimed at investigating the response of the tomato metallocarboxypeptidase inhibitor (TCMP)-1 to Cd and other abiotic stresses. To this aim, the tomato TCMP-1 was ectopically expressed in the model species Arabidopsis thaliana, and a yeast two-hybrid analysis was performed to identify interacting proteins. We demonstrate that TCMP-1 is responsive to Cd, NaCl, and abscisic acid (ABA) and interacts with the tomato heavy metal-associated isoprenylated plant protein (HIPP)26. A. thaliana plants overexpressing TCMP-1 accumulate lower amount of Cd in shoots, display an increased expression of AtHIPP26 in comparison with wild-type plants, and are characterized by a modulation in the expression of antioxidant enzymes. Overall, these results suggest a possible role for the TCMP-1/HIPP26 complex in Cd response and compartmentalization.

Roseltide rT7 is a disulfide-rich, anionic, and cell-penetrating peptide that inhibits proteasomal degradation

Disulfide-rich plant peptides with molecular masses of 2-6 kDa represent an expanding class of peptidyl-type natural products with diverse functions. They are structurally compact, hyperstable, and underexplored as cell-penetrating agents that inhibit intracellular functions. Here, we report the discovery of an anionic, 34-residue peptide, the disulfide-rich roseltide rT7 from Hibiscus sabdariffa (of the Malvaceae family) that penetrates cells and inhibits their proteasomal activities. Combined proteomics and NMR spectroscopy revealed that roseltide rT7 is a cystine-knotted, six-cysteine hevein-like cysteine-rich peptide. A pair-wise comparison indicated that roseltide rT7 is >100-fold more stable against protease degradation than its S-alkylated analog. Confocal microscopy studies and cell-based assays disclosed that after roseltide rT7 penetrates cells, it causes accumulation of ubiquitinated proteins, inhibits human 20S proteasomes, reduces tumor necrosis factor-induced IκBα degradation, and decreases expression levels of intercellular adhesion molecule-1. Structure-activity studies revealed that roseltide rT7 uses a canonical substrate-binding mechanism for proteasomal inhibition enabled by an IIML motif embedded in its proline-rich and exceptionally long intercysteine loop 4. Taken together, our results provide mechanistic insights into a novel disulfide-rich, anionic, and cell-penetrating peptide, representing a potential lead for further development as a proteasomal inhibitor in anti-cancer or anti-inflammatory therapies.

Building upon Nature's Framework: Overview of Key Strategies Toward Increasing Drug-Like Properties of Natural Product Cyclopeptides and Macrocycles

The pharmaceutical industry has focused mainly in the development of small-molecule entities intended for oral administration for the past decades. As a result, the majority of existing drugs address only a narrow range of biological targets. In the era of post-genomics, transcriptomics, and proteomics, there is an increasing interest on larger modulators of proteins that can span larger surfaces, access new therapeutic mechanisms of action, and provide greater target specificity. Traditional drug-like molecules developed using "rule-of-five" (Ro5) guidelines have been proven ineffective against a variety of challenging targets, such as protein-protein interactions, nucleic acid complexes, and antibacterial modalities. However, natural products are known to be effective at modulating such targets, leading to a renewed focus by medicinal chemists on investigating underrepresented chemical scaffolds associated with natural products. Here we describe recent efforts toward identification of novel natural cyclopeptides and macrocycles as well as selected medicinal chemistry strategies to increase drug-like properties or further exploration of their activity.

The role of antimicrobial peptides in plant immunity

Selective pressure imposed by millions of years of relentless biological attack has led to the development of an extraordinary array of defense strategies in plants. Among these, antimicrobial peptides (AMPs) stand out as one of the most prominent components of the plant immune system. These small and usually basic peptides are deployed as a generalist defense strategy that grants direct and durable resistance against biotic stress. Even though their name implies a function against microbes, the range of plant-associated organisms affected by these peptides is much broader. In this review, we highlight the advances in our understanding on the role of AMPs in plant immunity. We demonstrate that the capacity of plant AMPs to act against a large spectrum of enemies relies on their diverse mechanism of action and remarkable structural stability. The efficacy of AMPs as a defense strategy is evidenced by their widespread occurrence in the plant kingdom, an astonishing heterogeneity in host peptide composition, and the extent to which plant enemies have evolved effective counter-measures to evade AMP action. Plant AMPs are becoming an important topic of research due to their significance in allowing plants to thrive and for their enormous potential in agronomical and pharmaceutical fields.

Bioinspired Designs, Molecular Premise and Tools for Evaluating the Ecological Importance of Antimicrobial Peptides

This review article provides an overview of recent developments in antimicrobial peptides (AMPs), summarizing structural diversity, potential new applications, activity targets and microbial killing responses in general. The use of artificial and natural AMPs as templates for rational design of peptidomimetics are also discussed and some strategies are put forward to curtail cytotoxic effects against eukaryotic cells. Considering the heat-resistant nature, chemical and proteolytic stability of AMPs, we attempt to summarize their molecular targets, examine how these macromolecules may contribute to potential environmental risks vis-à-vis the activities of the peptides. We further point out the evolutional characteristics of the macromolecules and indicate how they can be useful in designing target-specific peptides. Methods are suggested that may help to assess toxic mechanisms of AMPs and possible solutions are discussed to promote the development and application of AMPs in medicine. Even if there is wide exposure to the environment like in the hospital settings, AMPs may instead contribute to prevent healthcare-associated infections so long as ecotoxicological aspects are considered.

Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field

Plant-microbe associations are thought to be beneficial for plant growth and resistance against biotic or abiotic stresses, but for natural ecosystems, the ecological analysis of microbiome function remains in its infancy. We used transformed wild tobacco plants (Nicotiana attenuata) which constitutively express an antimicrobial peptide (Mc-AMP1) of the common ice plant, to establish an ecological tool for plant-microbe studies in the field. Transgenic plants showed in planta activity against plant-beneficial bacteria and were phenotyped within the plants´ natural habitat regarding growth, fitness and the resistance against herbivores. Multiple field experiments, conducted over 3 years, indicated no differences compared to isogenic controls. Pyrosequencing analysis of the root-associated microbial communities showed no major alterations but marginal effects at the genus level. Experimental infiltrations revealed a high heterogeneity in peptide tolerance among native isolates and suggests that the diversity of natural microbial communities can be a major obstacle for microbiome manipulations in nature.

Screening, large-scale production and structure-based classification of cystine-dense peptides

Peptides folded through interwoven disulfides display extreme biochemical properties and unique medicinal potential. However, their exploitation has been hampered by the limited amounts isolatable from natural sources and the expense of chemical synthesis. We developed reliable biological methods for high-throughput expression, screening and large-scale production of these peptides: 46 were successfully produced in multimilligram quantities, and >600 more were deemed expressible through stringent screening criteria. Many showed extreme resistance to temperature, proteolysis and/or reduction, and all displayed inhibitory activity against at least 1 of 20 ion channels tested, thus confirming their biological functionality. Crystal structures of 12 confirmed proper cystine topology and the utility of crystallography to study these molecules but also highlighted the need for rational classification. Previous categorization attempts have focused on limited subsets featuring distinct motifs. Here we present a global definition, classification and analysis of >700 structures of cystine-dense peptides, providing a unifying framework for these molecules.

Two metallocarboxypeptidase inhibitors are implicated in tomato fruit development and regulated by the Inner No Outer transcription factor

The TCMP-1 and TCMP-2 genes of tomato code for metallocarboxypeptidase inhibitors and show sequential, tightly regulated expression patterns during flower and fruit development. In particular, TCMP-1 is highly expressed in flower buds before anthesis, while TCMP-2 in ripe fruits. Their expression pattern suggests that they might play a role in fruit development. Here, to investigate their function, we altered their endogenous levels by generating transgenic plants harbouring a chimeric gene expressing the TCMP-1 coding sequence under the control of the TCMP-2 promoter. The expression of the transgene caused an earlier fruit setting with no visible phenotypic effects on plant and fruit growth. The altered TCMP-1 regulation determines an increased level of TCMP-1 in the fruit and unexpected changes in the levels of both TCMPs in flower buds before anthesis, suggesting a mechanism of transcriptional cross-regulation. We in silico analysed TCMPs promoter regions for the presence of common cis acting elements related to ovary/fruit development and we found that both promoters contain putative binding sites for INNER NO OUTER (INO), a transcription factor implicated in ovule development. By chromatin immunoprecipitation, we proved that INO binds to TCMP-1 and TCMP-2 promoters, thereby representing a candidate regulatory factor for coordinated control of TCMPs.

Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets

Protein:protein interactions are among the most difficult to treat molecular mechanisms of disease pathology. Cystine-dense peptides have the potential to disrupt such interactions, and are used in drug-like roles by every clade of life, but their study has been hampered by a reputation for being difficult to produce, owing to their complex disulfide connectivity. Here we describe a platform for identifying target-binding cystine-dense peptides using mammalian surface display, capable of interrogating high quality and diverse scaffold libraries with verifiable folding and stability. We demonstrate the platform’s capabilities by identifying a cystine-dense peptide capable of inhibiting the YAP:TEAD interaction at the heart of the oncogenic Hippo pathway, and possessing the potency and stability necessary for consideration as a drug development candidate. This platform provides the opportunity to screen cystine-dense peptides with drug-like qualities against targets that are implicated for the treatment of diseases, but are poorly suited for conventional approaches.

Pathologies related to protein:protein interaction are hard to treat but cystine-dense peptides have the potential to disrupt such interactions. Here the authors develop a high-diversity mammalian cell screen for cystine-dense peptides with drug potential and use it to identify a YAP:TEAD inhibitor.

Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold

Cysteine-rich peptides (CRPs) of 2–6 kDa are generally thermally and proteolytically stable because of their multiple cross-bracing disulfide bonds. Here, we report the discovery and characterization of two novel cystine-stapled CRPs, designated lybatide 1 and 2 (lyba1 and lyba2), from the cortex of Lycium barbarum root. Lybatides, 32 to 33 amino acids in length, are hyperstable and display a novel disulfide connectivity with a cysteine motif of C-C-C-C-CC-CC which contains two pairs of adjacent cysteines (-CC-CC). X-ray structure analysis revealed the presence of a single cystine-stabilized (α + π)-helix in lyba2, a rare feature of CRPs. Together, our results suggest that lybatides, one of the smallest four-disulfide-constrained plant CRPs, is a new family of CRPs. Additionally, this study provides new insights into the molecular diversity of plant cysteine-rich peptides and the unusual lybatide scaffold could be developed as a useful template for peptide engineering and therapeutic development.

The interaction of the bioinsecticide PA1b (Pea Albumin 1 subunit b) with the insect V-ATPase triggers apoptosis

PA1b (Pea Albumin 1, subunit b) peptide is an entomotoxin, extracted from Legume seeds, with a lethal activity towards several insect pests, such as mosquitoes, some aphids and cereal weevils. This toxin acts by binding to the subunits c and e of the plasma membrane H+-ATPase (V-ATPase) in the insect midgut. In this study, two cereal weevils, the sensitive Sitophilus oryzae strain WAA42, the resistance Sitophilus oryzae strain ISOR3 and the insensitive red flour beetle Tribolium castaneum, were used in biochemical and histological experiments to demonstrate that a PA1b/V-ATPase interaction triggers the apoptosis mechanism, resulting in insect death. Upon intoxication with PA1b, apoptotic bodies are formed in the cells of the insect midgut. In addition, caspase-3 enzyme activity occurs in the midgut of sensitive weevils after intoxication with active PA1b, but not in the midgut of resistant weevils. These biochemical data were confirmed by immuno-histochemical detection of the caspase-3 active form in the midgut of sensitive weevils. Immuno-labelling experiments also revealed that the caspase-3 active form and V-ATPase are close-localized in the insect midgut. The results concerning this unique peptidic V-ATPase inhibitor pave the way for the utilization of PA1b as a promising, more selective and eco-friendly insecticide.

Venom-derived peptide inhibitors of voltage-gated potassium channels

Voltage-gated potassium channels play a key role in human physiology and pathology. Reflecting their importance, numerous channelopathies have been characterised that arise from mutations in these channels or from autoimmune attack on the channels. Voltage-gated potassium channels are also the target of a broad range of peptide toxins from venomous organisms, including sea anemones, scorpions, spiders, snakes and cone snails; many of these peptides bind to the channels with high potency and selectivity. In this review we describe the various classes of peptide toxins that block these channels and illustrate the broad range of three-dimensional structures that support channel blockade. The therapeutic opportunities afforded by these peptides are also highlighted. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'

The Mammalian Peptide Adrenomedullin Acts as a Growth Factor in Tobacco Plants

Growth factors are extracellular signals that regulate cell proliferation and total body mass. Some animal growth factors can work on plant tissues and vice versa. Here we show that the mammalian growth factor adrenomedullin (AM) induces growth in tobacco plants. Addition of synthetic AM resulted in a dose-dependent growth of tobacco calluses. Furthermore, AM transgenic plants showed enhanced survival and significant increases in stem diameter, plant height, leaf length, weight of all organs, and a reduction in the time to flowering when compared to plants transformed with the control vector. These differences were maintained when organs were dried, resulting in a mean total biomass increase of 21.3%. The levels of soluble sugars and proteins in the leaves were unchanged between genotypes. AM transgenic plants had a significantly higher expression of cyclin D3 and the transcription factor E2FB than controls, suggesting that cell cycle regulation may be part of the intracellular signaling of AM in plants. In summary, mammalian AM increases vascular plants' survival and biomass with no apparent detriment of plant's morphological and/or biochemical properties, thus this strategy could be useful for crop productivity improvement.

Plant cystine-knot peptides: pharmacological perspectives

Cystine-knot miniproteins are a class of 30-50 amino acid long peptides widespread in eukaryotic organisms. Due to their very peculiar three-dimensional structure, they exhibit high resistance to heat and peptidase attack. The cystine-knot peptides are well represented in several plant species including medicinal herbs and crops. The pharmacological interest in plant cystine-knot peptides derives from their broad biological activities, mainly cytotoxic, antimicrobial and peptidase inhibitory and in the possibility to engineer them to incorporate pharmacophoric information for oral delivery or disease biomonitoring. The mechanisms of action of plant cystine-knot peptides are still largely unknown, although the capacity to interfere with plasma membranes seems a feature common to several cystine-knot peptides. In some cases, such as potato carboxypetidase inhibitor (PCI) and tomato cystine-knot miniproteins (TCMPs), the cystine-knot peptides target human growth factor receptors either by acting as growth factor antagonist or by altering their signal transduction pathway. The possibility to identify specific molecular targets of plant cystine-knot peptides in human cells opens novel possibilities for the pharmacological use of these peptides besides their use as scaffold to develop stable disease molecular markers and therapeutic agents.