Cyclotides as a basis for drug design

INTRODUCTION: Cyclotides are plant-made defence proteins with a head-to-tail cyclic backbone combined with a conserved, six cystine knot. They have a range of biological activities, including uterotonic and anti-HIV activity, which have attracted attention to their potential pharmaceutical applications. Furthermore, their unique structures and high stability make them appealing as peptide-based templates for drug design applications. Methods have been developed for their production, including solid phase peptide synthesis as well as recombinant methods. AREAS COVERED: This article reviews the recent literature associated with therapeutic applications of naturally occurring and synthetically modified cyclotides. It includes applications of cyclotides and cyclotide-like molecules as peptide-based drug leads and diagnostic agents. EXPERT OPINION: The ultra-stable cyclotides are promising templates for drug development applications and are currently being assessed for the potential breadth of their applications. For synthetic versions of cyclotides to enter human clinical trials further studies to examine their biopharmaceutical properties and toxicities are required. However, several promising proof-of-concept studies have established that pharmaceutically relevant bioactive peptide sequences can be grafted into cyclotide frameworks and thereby stabilised, while maintaining biological activity. These studies include examples directed at cancer, cardiovascular disease and infectious diseases. Solid phase peptide synthesis has been the preferred approach for making pharmaceutically modified cyclotides so far, but promising progress is being made in biological approaches to cyclotide production.     

Cyclotides as a basis for drug design

Introduction: Cyclotides are plant-made defence proteins with a head-to-tail cyclic backbone combined with a conserved, six cystine knot. They have a range of biological activities, including uterotonic and anti-HIV activity, which have attracted attention to their potential pharmaceutical applications. Furthermore, their unique structures and high stability make them appealing as peptide-based templates for drug design applications. Methods have been developed for their production, including solid phase peptide synthesis as well as recombinant methods.

Areas covered: This article reviews the recent literature associated with therapeutic applications of naturally occurring and synthetically modified cyclotides. It includes applications of cyclotides and cyclotide-like molecules as peptide-based drug leads and diagnostic agents.

Expert opinion: The ultra-stable cyclotides are promising templates for drug development applications and are currently being assessed for the potential breadth of their applications. For synthetic versions of cyclotides to enter human clinical trials further studies to examine their biopharmaceutical properties and toxicities are required. However, several promising proof-of-concept studies have established that pharmaceutically relevant bioactive peptide sequences can be grafted into cyclotide frameworks and thereby stabilised, while maintaining biological activity. These studies include examples directed at cancer, cardiovascular disease and infectious diseases. Solid phase peptide synthesis has been the preferred approach for making pharmaceutically modified cyclotides so far, but promising progress is being made in biological approaches to cyclotide production.     

Potential therapeutic applications of the cyclotides and related cystine knot mini-proteins

Cyclotides are naturally occurring mini-proteins that have a cyclic peptide backbone and a knotted arrangement of three disulfide bonds. They are remarkably stable and have a diverse range of therapeutically useful biological activities, including antimicrobial and anti-HIV activity, although their natural function appears to be as plant defence agents. Cyclotides are amenable to chemical synthesis and the potential exists to graft new bioactivities onto their cyclic cystine knot framework as a way of stabilising peptide drugs. Over the last few years, proof-of-concept that bioactive peptide epitopes can be grafted onto cyclotides and related cystine knot mini-proteins has been obtained. The cystine knot framework is tolerant to a wide range of residue substitutions and is showing great promise as a scaffold in drug design and protein engineering.     

Potential therapeutic applications of the cyclotides and related cystine knot mini-proteins

Cyclotides are naturally occurring mini-proteins that have a cyclic peptide backbone and a knotted arrangement of three disulfide bonds. They are remarkably stable and have a diverse range of therapeutically useful biological activities, including antimicrobial and anti-HIV activity, although their natural function appears to be as plant defence agents. Cyclotides are amenable to chemical synthesis and the potential exists to graft new bioactivities onto their cyclic cystine knot framework as a way of stabilising peptide drugs. Over the last few years, proof-of-concept that bioactive peptide epitopes can be grafted onto cyclotides and related cystine knot mini-proteins has been obtained. The cystine knot framework is tolerant to a wide range of residue substitutions and is showing great promise as a scaffold in drug design and protein engineering.     

Cyclotides, a novel ultrastable polypeptide scaffold for drug discovery

Cyclotides are a unique and growing family of backbone cyclized peptides that also contain a cystine knot motif built from six conserved cysteine residues. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to thermal, chemical, and enzymatic degradation compared to other peptides of similar size. Aside from the conserved residues forming the cystine knot, cyclotides have been shown to have high variability in their sequences. Consisting of over 160 known members, cyclotides have many biological activities, ranging from anti-HIV, antimicrobial, hemolytic, and uterotonic capabilities; additionally, some cyclotides have been shown to have cell penetrating properties. Originally discovered and isolated from plants, cyclotides can also be produced synthetically and recombinantly. The high sequence variability, stability, and cell penetrating properties of cyclotides make them potential scaffolds to be used to graft known active peptides or engineer peptide-based drug design. The present review reports recent findings in the biological diversity and therapeutic potential of natural and engineered cyclotides.     

Discovery, structure and biological activities of cyclotides

Cyclotides are small disulfide-rich peptides that are characterized by a head-to-tail cyclized peptide backbone and a knotted arrangement of three conserved disulfide bonds. They are present in many plants from the Violaceae, Rubiaceae and Cucurbitaceae families, with individual plants expressing a suite of dozens of cyclotides. So far > 140 sequences and 15 three-dimensional structures have been determined but it is estimated that the family probably comprises many thousands of members. Their primary function in plants is thought to be as defense agents, based on their potent insecticidal activity, but they also have a range of other biological activities, including anti-HIV, antimicrobial and cytotoxic activities. Because of their exceptional stability they have attracted interest as templates for protein engineering and drug design applications. This article gives an overview of the discovery of cyclotides, describes their unique structural features and range of bioactivities, and discusses their applications in drug design.     

Insecticidal plant cyclotides and related cystine knot toxins.

Cyclotides are small disulphide-rich peptides found in plants from the violet (Violaceae), coffee (Rubiaceae) and cucurbit (Cucurbitaceae) families. They have the distinguishing structural features of a macrocyclic peptide backbone and a cystine knot made up of six conserved cysteine residues, which makes cyclotides exceptionally stable. Individual plants express a suite of cyclotides in a wide range of tissue types, including leaves, flowers, stems and roots and it is thought that their natural function in plants is as defence agents. This proposal is supported by their high expression levels in plants and their toxic and growth retardant activity in feeding trials against Helicoverpa spp. insect pests. This review describes the structures and activities of cyclotides with specific reference to their insecticidal activity and compares them with structurally similar cystine knot proteins from peas (Pisum sativum) and an amaranthus crop plant (Amaranthus hypocondriancus). More broadly, cystine knot proteins are common in a wide range of organisms from fungi to mammals, and it appears that this interesting structural motif has evolved independently in different organisms as a stable protein framework that has a variety of biological functions.     

Host-defense activities of cyclotides

Cyclotides are plant mini-proteins whose natural function is thought to be to protect plants from pest or pathogens, particularly insect pests. They are approximately 30 amino acids in size and are characterized by a cyclic peptide backbone and a cystine knot arrangement of three conserved disulfide bonds. This article provides an overview of the reported pesticidal or toxic activities of cyclotides, discusses a possible common mechanism of action involving disruption of biological membranes in pest species, and describes methods that can be used to produce cyclotides for potential applications as novel pesticidal agents.     

生物活性环肽及其药学研究进展

环肽是植物来源的超稳定肽,由头至尾环化骨架和形成胱氨酸结的3个二硫键非常稳定。与其他类似大小的肽相比,环肽的这种独特的拓扑学结构使它们对化学、热和生物降解异常稳定,它们出色的稳定性和对序列替换的耐受性可使它们用作药物设计的框架。本文主要介绍了环肽在药学研究领域3个方面的应用,特别是近年来在将生物活性肽序列嫁接到环肽的框架上,以产生新的生物学活性方面的研究进展。     

Discovery and applications of the plant cyclotides

The cyclotides are a family of plant-derived proteins that occur in plants from the Violaceae (violet), Rubiaceae (coffee) and Cucurbitaceae (cucurbit) families and have a diverse range of biological activities, including uterotonic, anti-HIV, antimicrobial, and insecticidal activities; the latter suggests their natural function lies in plant defense. Individual plants express suites of 10-100 cyclotides. Cyclotides comprise ∼30 amino acids, contain a head-to-tail cyclised backbone, and incorporate three disulfide bonds arranged in a cystine knot topology. The combination of a knotted and strongly braced structure with a circular backbone renders the cyclotides impervious to enzymatic breakdown and makes them exceptionally stable. The cyclotides are the largest of several groups of naturally occurring circular proteins that have been discovered in bacteria, plants and animals over recent years. This article describes the discovery of the cyclotides in plants, their structural characterisation, evolutionary relationships and their applications in drug design.     

胱氨酸结模体多肽的特征及其在药物设计和分子工程中的应用

胱氨酸结（cystine knot,CK）模体是由两对二硫键及其相连的肽链骨架形成的一个内部环以及从环中穿过的第三对二硫键组成的球形结构,广泛存在于真菌、植物、海洋软体动物、昆虫以及蜘蛛等生物的毒素多肽和蛋白质中。CK多肽结构非常稳定、生物活性多样,是一类在药物设计和分子工程研究中的理想模型分子。本文综述了抑制剂胱氨酸结（inhibitor cystine knot,ICK）多肽和环形胱氨酸结（cyclic cystine knot,CCK）多肽两类主要CK毒素的氨基酸序列、拓扑结构、排列组合、人工合成以及空间折叠等特征,并进一步阐述了其在药物设计与分子工程中的应用前景。     

The cystine knot motif in toxins and implications for drug design.

The cystine knot structural motif is present in peptides and proteins from a variety of species, including fungi, plants, marine molluscs, insects and spiders. It comprises an embedded ring formed by two disulfide bonds and their connecting backbone segments which is threaded by a third disulfide bond. It is invariably associated with nearby beta-sheet structure and appears to be a highly efficient motif for structure stabilization. Because of this stability it makes an ideal framework for molecular engineering applications. In this review we summarize the main structural features of the cystine knot motif, focussing on toxin molecules containing either the inhibitor cystine knot or the cyclic cystine knot. Peptides containing these motifs are 26-48 residues long and include ion channel blockers, haemolytic agents, as well as molecules having antiviral and antibacterial activities. The stability of peptide toxins containing the cystine knot motif, their range of bioactivities and their unique structural scaffold can be harnessed for molecular engineering applications and in drug design. Applications of cystine knot molecules for the treatment of pain, and their potential use in antiviral and antibacterial applications are described.     

Self-assembling peptides: implications for patenting in drug delivery and tissue engineering

In this paper, a comprehensive review of recent patents concerning the molecular self-assembly of peptides, peptide amphiphiles and peptidomimetics into molecules through nanoarchitectures to hydrogels is provided. Their potential applications in the field of drug delivery and tissue engineering have been highlighted. The design rules of this rapidly growing field are centered mainly on the construction of peptides in the form of peptide amphiphiles, aromatic short peptide derivatives, all-amino acid peptide amphiphiles, lipidated peptides with single and multiple alkyl chains and peptide-based block copolymers and polymer peptide conjugates. The interest in patenting of self-assembling peptides is also driven by their type (I, II, III and IV) and their ability to form well-regulated highly-ordered structures such as β-sheets/β-hairpins, α-helices/coiled coils and to hierarchically self-organize into supra-molecular structures. The applicability of these systems in cell culture scaffolds for tissue engineering, drug and gene delivery and as templates for nanofabrication and biomineralization has inspired various groups over the globe. This resulted in development of self-assembling peptides as synthetic replacements of biological tissues, designing materials for specific medical applications, and materials for new applications such as diagnostic technologies. Furthermore, biologically derived and commercially available systems are also discussed herein along with a brief account of various awarded and pending patents in the past 10 years. An overview of the diversity of the patent applications is also provided for self-assembling systems based on nano- and/or micro-scale such as fibers, fibrils, gels, hydrogels, vesicles, particles, micelles, bilayers and scaffolds.     

The chemistry and biology of cyclotides

Cyclotides are mini-proteins with a macrocyclic peptide backbone and cystine-knot arrangement of disulfide bonds that makes them exceptionally stable to chemical, thermal or enzymatic degradation. They have a diverse range of bioactivities and are amenable to chemical synthesis, making them accessible as molecular templates for protein engineering and drug design applications. In the last two years, methods have been developed for the production of cyclotides using inteins in bacterial expression systems and using plant cell cultures, adding to established methods based on solid-phase peptide synthesis. The availability of an enhanced armory of synthetic methods promises to expand the potential range of cyclotide-based applications.     

Peptide-receptor ligands and multivalent approach

The overexpression of peptide receptors in human tumours makes peptide-ligands attractive agents for the development of specific diagnostic imaging and/or therapy of cancers. Solid-phase peptide synthesis, modern phage display technology and combinatorial peptide chemistry have profoundly affected the pool of available targeting peptides for efficient and specific delivery of imaging or therapeutic label molecules. Additionally, the availability of a wide range of bifunctional chelating agents for the radiolabelling of bioactive peptides with radionuclides has produced a wide variety of useful radiopharmaceutical molecules. This review article examines the principal receptors-binding peptides and their overexpression on tumour cells. We discuss the advantage and the challenges in developing multivalent peptide-based ligands summarising their design strategies and applications.     

Current perspectives on established and putative mammalian oligopeptide transporters

Peptides and peptide-based drugs are increasingly being utilized as therapeutic agents for the treatment of numerous disorders. The increasing development of peptide-based therapeutic agents is largely due to technological advances including the advent of combinatorial peptide libraries, peptide synthesis strategies, and peptidomimetic design. Peptides and peptide-based agents have a broad range of potential clinical applications in the treatment of many disorders including AIDS, hypertension, and cancer. Peptides are generally hydrophilic and often exhibit poor passive transcellular diffusion across biological barriers. Insights into strategies for increasing their intestinal absorption have been derived from the numerous studies demonstrating that the absorption of protein digestion products occurs primarily in the form of small di- and tripeptides. The characterization of the pathways of intestinal, transepithelial transport of peptides and peptide-based drugs have demonstrated that a significant degree of absorption occurs through the role of proteins within the proton-coupled, oligopeptide transporter (POT) family. Considerable focus has been traditionally placed on Peptide Transporter 1 (PepT1) as the main mammalian POT member regulating intestinal peptide absorption. Recently, several new POT members, including Peptide/Histidine Transporter 1 (PHT1) and Peptide/Histidine Transporter 2 (PHT2) and their splice variants have been identified. This has led to an increased need for new experimental methods enabling better characterization of the biophysical and biochemical barriers and the role of these POT isoforms in mediating peptide-based drug transport.     

Discovery and optimization of peptide macrocycles

ABSTRACT

Introduction: Macrocyclic peptides are generally more resistant to proteolysis and often have higher potency than linear peptides and so they are excellent leads in drug design. Their study is significant because they offer potential as a new generation of drugs that are potent and specific, and thus might have fewer side effects than traditional small molecule drugs.

Areas covered: This article covers macrocyclic drug leads based on nature-derived cyclic peptides as well as synthetic cyclic peptides and close derivatives. The natural peptides include cyclotides, sunflower-derived peptides, theta-defensins and orbitides. Technologies to make engineered cyclic peptides covered here include cyclization via amino acid linkers, CLIPS, templates, and stapled peptides.

Expert opinion: Macrocyclic peptides are promising drug leads and several are in clinical trials. The authors believe they offer key advantages over traditional small molecule drugs, as well as some advantages over protein-based ‘biologics’ such as antibodies or growth factors. These include the ability to penetrate cells and attack intracellular targets such as protein-protein interactions as well as to hit extracellular targets. Some macrocyclic peptides such as cyclotides offer the potential for production in plants, thus reducing manufacture costs and potentially increasing opportunities for their distribution to developing countries at low cost.     

The cyclotides and related macrocyclic peptides as scaffolds in drug design

The applicability of linear peptides as drugs is potentially limited by their susceptibility to proteolytic cleavage and poor bioavailability. Cyclotides are macrocyclic cystine-knotted mini-proteins that have a broad range of bioactivities and are exceptionally stable, being resistant to chemical, thermal and enzymatic degradation. The general limitations of peptides as drugs can potentially be overcome by using the cyclotide framework as a scaffold onto which new activities may be engineered. The potential use of cyclotides and related peptide scaffolds for drug design is evaluated herein, with reference to increasing knowledge of the structures and sequence diversity of natural cyclotides and the emergence of new approaches in protein engineering.     

Structure‐Function Studies of the Plant Cyclotides: The Role of a Circular Protein Backbone

The traditional idea of proteins as linear chains of amino acids is being challenged with the discovery of miniproteins that contain a circular backbone. The cyclotide family is the largest group of circular proteins and is characterized by an amide‐circularized protein backbone and six conserved cysteine residues. These conserved cysteines are paired to form a knotted network of disulfide bonds. The combination of the circular backbone and a cystine knot, known as the cyclic cystine knot (CCK) motif, confers exceptional stability upon the cyclotides. This review discusses the role of the circular backbone based on studies of both the oxidative folding of kalata B1, the prototypical cyclotide, and a comparison of the structure and activity of kalata B1 and its acyclic permutants.     

Peptides targeting voltage-gated calcium channels

Many peptides are potent and highly selective blockers or modulators of calcium channel function, and as such are valuable pharmacological tools and potentially valuable leads for the development of human therapeutics. Cone shells and spiders are rich sources of such peptides, although they are also found in scorpions and insects. In this article we compare the amino acid sequences of toxins active against calcium channels and describe their three-dimensional structures and structure-function relationships. Certain structural motifs, in particular the inhibitor cystine knot, prove to be quite common amongst this class of toxins. Aspects of the pharmacology and physiology of these toxins in mammalian systems are also discussed, with an emphasis on their application in the treatment of chronic pain. We then consider the prospects for peptide-based therapeutics targeting calcium channels for this and other indications, including the development of non-peptide (peptidomimetic) compounds based on a detailed understanding of toxin structure-function relationships.