Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding

Peptide Dendrimer-Based Antibacterial Agents: Synthesis and Applications

Pathogenic bacteria cause the deaths of millions of people every year. With the development of antibiotics, hundreds and thousands of people's lives have been saved. Nevertheless, bacteria can develop resistance to antibiotics, rendering them insensitive to antibiotics over time. Peptides containing specific amino acids can be used as antibacterial agents; however, they can be easily degraded by proteases in vivo. To address these issues, branched peptide dendrimers are now being considered as good antibacterial agents due to their high efficacy, resistance to protease degradation, and low cytotoxicity. The ease with which peptide dendrimers can be synthesized and modified makes them accessible for use in various biological and nonbiological fields. That is, peptide dendrimers hold a promising future as antibacterial agents with prolonged efficacy without bacterial resistance development. Their in vivo stability and multivalence allow them to effectively target multi-drug-resistant strains and prevent biofilm formation. Thus, it is interesting to have an overview of the development and applications of peptide dendrimers in antibacterial research, including the possibility of employing machine learning approaches for the design of AMPs and dendrimers. This review summarizes the synthesis and applications of peptide dendrimers as antibacterial agents. The challenges and perspectives of using peptide dendrimers as the antibacterial agents are also discussed.

Cyclic cystine knot and its strong implication on the structure and dynamics of cyclotides

The archetypal Viola odorata cyclotide cycloviolacin-O1 and its seven analogs, created by partial or total reduction of the three native S-S linkages belonging to the "cyclic cystine knot" (CCK) motif are studied for their structural and dynamical diversities using molecular dynamics simulations. The results indicate interesting interplay between the constraints imposed by the S-S bonds on the dynamical modes and the corresponding structure of the model peptide. Principal component analysis brings out the variation in the extent of dynamical freedom along the peptide backbone for each model. The motions are characterized by low amplitude diffusive modes in the peptides retaining most of the native S-S linkages in contrast to the large amplitude discrete jumps where at least two or all of the three S-S linkages are reduced. Simulation results further indicate that the disulfide bond between Cys1-18 is formed at a much faster pace compared with its two other peers Cys5-20 and Cys10-25 as found in the native peptide. This gives insight as to why the S-S linkages appear in the native peptide in a particular combination. Model therapeutics and drug delivery engines can potentially utilize this information to customize the engineered S-S bonds and gauge its impact on the dynamic flexibility of a model macrocyclic peptide.

Biotechnological applications of versatile plant lipid transfer proteins (LTPs)

Plant AMPs are usually cysteine-rich, and can be classified in several classes, including lipid transfer proteins (LTPs). LTPs are small plant cationic peptides, and can be classified in two subclasses, LTP₁ (9-10 kDa) and LTP₂ (7 kDa). They have been identified and isolated from various plant species and can be involved in a number of processes, including responses against several phytopathogens. LTP₁ presents 4 parallel α- helices and a 3₁₀-helix fragment. These structures form a tunnel with large and small entrances. LTP₂ presents 3 parallel α- helices, which form a cavity with triangular structure. Both LTP subclasses present a hydrophobic cavity, which makes interaction with different lipids and general hydrophobic molecules possible. Several studies report a broad spectrum of activity of plant LTPs, including antibacterial, antifungal, antiviral, antitumoral, and insecticidal activity. Thus, these molecules can be employed in human and animal health as an alternative to the conventional treatment of disease, well as providing the source of novel drugs. However, employing peptides in human health can present challenges, such as the toxicity of peptides, the difference between the results found in in vitro assays and in pre-clinical or clinical tests and their low efficiency against Gram-negative bacteria. In this context, plant LTPs can be an interesting alternative means by which to bypass such challenges. This review addresses the versatility of plant LTPs, their broad spectrum of activities and their potential applications in human and animal health and in agricultural production, and examines challenges in their biotechnological application.

Head-to-Tail Cyclization after Interaction with Trypsin: A Scorpion Venom Peptide that Resembles Plant Cyclotides

Peptidase inhibitors (PIs) have been broadly studied due to their wide therapeutic potential for human diseases. A potent trypsin inhibitor from Tityus obscurus scorpion venom was characterized and named ToPI1, with 33 amino acid residues and three disulfide bonds. The X-ray structure of the ToPI1:trypsin complex, in association with the mass spectrometry data, indicate a sequential set of events: the complex formation with the inhibitor Lys³² in the trypsin S1 pocket, the inhibitor C-terminal residue Ser³³ cleavage, and the cyclization of ToPI1 via a peptide bond between residues Ile¹ and Lys³². Kinetic and thermodynamic characterization of the complex was obtained. ToPI1 shares no sequence similarity with other PIs characterized to date and is the first PI with CS-α/β motif described from animal venoms. In its cyclic form, it shares structural similarities with plant cyclotides that also inhibit trypsin. These results bring new insights for studies with venom compounds, PIs, and drug design.

Cyclotides: From Structure to Function

This Review explores the class of plant-derived macrocyclic peptides called cyclotides. We include an account of their discovery, characterization, and distribution in the plant kingdom as well as a detailed analysis of their sequences and structures, biosynthesis and chemical synthesis, biological functions, and applications. These macrocyclic peptides are around 30 amino acids in size and are characterized by their head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable, with resistance to thermal or enzymatic degradation. Routes to their chemical synthesis have been developed over the past two decades, and this capability has facilitated a wide range of mutagenesis and structure-activity relationship studies. In turn, these studies have both led to an increased understanding of their mechanisms of action as well as facilitated a range of applications in agriculture and medicine, as ecofriendly crop protection agents, and as drug leads or scaffolds for pharmaceutical design. Our overall objective in this Review is to provide readers with a comprehensive overview of cyclotides that we hope will stimulate further work on this fascinating family of peptides.

In Silico Investigation of the Binding of MCoTI-II Plant Defense Knottin to the γ-NGF Serine Protease of the 7S Nerve Growth Factor Complex and Biological Activity of Its NGF Mimetic Properties

Nerve growth factor (NGF) is an endogenously produced polypeptide that promotes the differentiation, survival, and repair of neurons in the central and peripheral nervous systems. While trophic proteins hold promise for the treatment of neuronal injury and disease, use of NGF is limited by its large molecular weight, lack of permeability through the blood-brain barrier, and peripheral side effects. Previously, we found that an extract of the Momordica cochinchinensis seed stimulated PC-12 neurite outgrowth. Bioactivity-guided fractioning of the seed extract suggested that the NGF mimetic agent was one of few defined proteins from this plant: one group being the defense Knottins and the other group of the lowest mass is the potent trypsin inhibitor MCoTI-II. Here, the NGF mimetic potential of this latter protein was investigated using two concurrent but different approaches. A biological study used recombinant purified MCoTI-II, which when tested in rat PC-12 cells grown on collagen, failed to initiate outgrowth relative to the positive control 7S NGF. In a separate computational study, the possibility was investigated such that MCoTI-II could exert an effect through binding to the serine protease γ-NGF subunit of the 7S NGF complex, analogous to its binding to its native receptor trypsin. Molecular dynamics simulations showed that MCoTI-II can bind stably to γ-NGF for >350 ns. Modeling indicated that this interaction could sterically inhibit 7S NGF complex formation, potentially altering the equilibrium between inactive complexed and free active NFG protein. In conclusion, the biological study now excludes the MCoTI-II protein as the NGF mimetic factor in the Momordica extract, an important and required step to identify the active component in this seed. On the other hand, the theoretical study has revealed a novel observation that may be of use in the development of strategies to affect NGF activity.

Phytochemistry, Pharmacological Activities, Toxicity and Clinical Application of Momordica cochinchinensis

Momordica cochinchinensis (Lour.) Spreng (M. cochinchinensis) is a deciduous vine that grows in Southeast Asia. It is known as gac in Vietnam and as Red Melon in English. Gac is reputed to be extremely benificial for health and has been widely used as food and folk medicine in Southeast Asia. In China, the seed of M. cochinchinensis (Chinese name: Mu biezi) is used as traditional Chinese medicine (TCM) for the treatment of various diseases. More than 60 chemical constituents have been isolated from M. cochinchinensis. Modern pharmacological studies and clinical practice demonstrate that some chemical constituents of M. cochinchinensis possess wide pharmacological activities, such as anti-tumor, anti-oxidation, anti-inflammatory, etc. This paper reviews the phytochemistry, pharmacological activities, toxicity, and clinical application of M. cochinchinensis, aiming to bring new insights into further research and application of this ancient herb.