Agonist/Antagonist Activity of Oxytocin Variants Obtained from Free Cyclic Peptide Libraries Generated via Amino Acid Substitution.

We established a method for synthesizing a free cyclic peptide library via peptide array synthesis to demonstrate the sequence activity of cyclic peptides. Variants of the cyclic nonapeptide oxytocin (OXT) were synthesized via residue substitution. Natural amino acids (AAs) were classified into eight groups based on their physical properties and the size of their side chains, and a representative AA from each group was selected for residue substitution. All OXT variants were systematically evaluated for agonist/antagonist activity. Consequently, no improvement in agonist activity was observed, although substitution of the P4 and P8 residues resulted in decreased activity due to AA substitution. A few OXT variants exhibited antagonistic activity. In particular, the variants with P2 Leu residue substitution (Y2L) and Phe substitutions at residues 4 (Q4F), 5 (N5F), and 7 (P7F) showed high antagonistic activity. Variant Y2W was found to have the highest inhibitory effect, with a dissociation constant of 44 nM, which was comparable to that of the commercial antagonist atosiban (21 nM). Therefore, a free cyclic peptide library constructed via substitution with a natural AA residue was confirmed to be a powerful tool for bioactive peptide screening.

Increasing the activity of cell adherent cyclic NGR peptides by optimizing the peptide length and amino acid character.

Cyclic peptides are an attractive modality for the development of therapeutics and the identification of functional cyclic peptides that contribute to novel drug development. The peptide array is one of the optimization methods for peptide sequences and also useful to understand sequence-function relationship of peptides. Cell adherent cyclic NGR peptide which selectively binds to the aminopeptidase N (APN or CD13) is known as an attractive tumor marker. In this study, we designed and screened a library of different length and an amino acid substitution library to identify stronger cell adhesion peptides and to reveal that the factor of higher binding between CD13 and optimized cyclic peptides. Additionally, we designed and evaluated 192 peptide libraries using eight representative amino acids to reduce the size of the library. Through these optimization steps of cyclic peptides, we identified 23 peptides that showed significantly higher cell adhesion activity than cKCNGRC, which was previously reported as a cell adhesion cyclic peptide. Among them, cCRHNGRARC showed the highest activity, that is, 1.65 times higher activity than cKCNGRC. An analysis of sequence and functional data showed that the rules which show higher cell adhesion activity for the three basic cyclic peptides (cCX1 HNGRHX2 C, cCX1 HNGRAX2 C, and cCX1 ANGRHX2 C) are related with the position of His residues and cationic amino acids.

Heterologous production of new lasso peptide koreensin based on genome mining.

Lasso peptides are a class of ribosomally biosynthesized and posttranslationally modified peptides with a knot structure as a common motif. Based on a genome search, a new biosynthetic gene cluster of lasso peptide was found in the genome of the proteobacterium Sphingomonas koreensis. Interestingly, the amino acid sequence of the precursor peptide gene includes two cell adhesion motif sequences (KGD and DGR). Heterologous production of the new lasso peptide was performed using the cryptic biosynthetic gene cluster of S. koreensis. As a result, a new lasso peptide named koreensin was produced by the gene expression system in the host strain Sphingomonas subterranea. The structure of koreensin was determined by NMR and ESI-MS analysis. The three-dimensional structure of koreensin was obtained based on an NOE experiment and the coupling constants. A variant peptide (koreensin-RGD), which had RGD instead of KGD, was produced by heterologous production with site-directed mutagenesis experiment. Koreensin and koreensin-RGD did not show cell adhesion inhibitory activity, although the molecules possessed cell adhesion motifs. The possible presence of a salt bridge between the motifs in koreensin was indicated, and it may prevent the cell adhesion motif from functioning.

Controlling distance, size and concentration of nanoconjugates for optimized LSPR based biosensors.

In this report, we have examined the distance- and size-dependent localized surface plasmon resonance (LSPR) between fluorescent quantum dots (QDs) and adjacent gold nanoparticles (AuNPs) to provide a comprehensive evaluation, aiming for practical application in biosensing platform. A series of peptides with different chain lengths, connected between QDs and AuNPs is initially applied to prepare various CdSe QDs-peptide-AuNP systems to optimize LSPR signal. Separation distance between two nanoparticles of these systems before and after conjugation is also confirmed by quantum mechanical modeling and corroborated with their LSPR influenced fluorescence variations. After detailed optimizations, it can be noted that larger sized AuNPs make strong quenching of QDs, which gradually shows enhancement of fluorescence with the increment of distance and the smaller sized AuNPs. Depending on the requirement, it is possible to tune the optimized structure of the CdSe QD-peptide-AuNP nanostructures for the application. In this work, two different structural designs with different peptide chain length are chosen to construct two biosensor systems, observing their fluorescence enhancement and quenching effects, respectively. Using different structural orientation of these biosensors, two nanoconjugates has applied for detection of norovirus and influenza virus, respectively to confirm their application in sensing.

Fluorometric virus detection platform using quantum dots-gold nanocomposites optimizing the linker length variation.

In this study, a tunable biosensor using the localized surface plasmon resonance (LSPR), controlling the distance between fluorescent CdZnSeS/ZnSeS quantum dots (QDs) and gold nanoparticles (AuNPs) has been developed for the detection of virus. The distance between the AuNPs and QDs has been controlled by a linkage with a peptide chain of 18 amino acids. In the optimized condition, the fluorescent properties of the QDs have been enhanced due to the surface plasmon effect of the adjacent AuNPs. Successive virus binding on the peptide chain induces steric hindrance on the LSPR behavior and the fluorescence of QDs has been quenched. After analyzing all the possible aspect of the CdZnSeS/ZnSeS QD-peptide-AuNP nanocomposites, we have detected different concentration of influenza virus in a linear range of 10-14 to 10-9 g mL-1 with detection limit of 17.02 fg mL-1. On the basis of the obtained results, this proposed biosensor can be a good alternative for the detection of infectious viruses in the various range of sensing application.

Disulfide linked hetero dimeric peptide arrays for screening functional peptides inside cells.

Intracellular functional peptides with important roles in cells have been widely studied as regulators of cellular activity. Previously, we proposed a screening system for identifying intracellular functional peptides, which can be utilized to synthesize various cell-penetrating peptide (CPP)-functional peptide complexes, and the intracellular functions of the peptides can then be determined using various cell based assays. We demonstrated that the activity of a cell death-inducing peptide was increased by an amino acid substitution. However, covalent conjugation of CPPs with functional peptides may disrupt the biological characteristics of the functional peptides. In the present study, we developed a novel screening system for intracellular functional peptides combined with a dissociation system after delivery inside cells to eliminate the influence of CPPs. To construct this system, we developed a method for synthesizing CPP-functional peptide hetero-dimers containing a disulfide bond that is cleaved by the intracellular reducing environment. The system used Fmoc-Lys(ivDde)-OH to synthesize CPP and functional peptides in one molecule to selectively form a disulfide bond of hetero-dimeric peptides. Furthermore, we evaluated a single amino acid substitution library of the cell death inducing peptide (WELVVLGKL). We obtained 6 peptides with higher activity than the original peptide. Our results suggest that our new screening system can be eliminate the influence of CPPs and is useful for peptide screening inside cells.

Effective modification of cell death-inducing intracellular peptides by means of a photo-cleavable peptide array-based screening system.

Intracellular functional peptides that play a significant role inside cells have been receiving a lot of attention as regulators of cellular activity. Previously, we proposed a novel screening system for intracellular functional peptides; it combined a photo-cleavable peptide array system with cell-penetrating peptides (CPPs). Various peptides can be delivered into cells and intracellular functions of the peptides can be assayed by means of our system. The aim of the present study was to demonstrate that the proposed screening system can be used for assessing the intracellular activity of peptides. The cell death-inducing peptide (LNLISKLF) identified in a mitochondria-targeting domain (MTD) of the Noxa protein served as an original peptide sequence for screening of peptides with higher activity via modification of the peptide sequence. We obtained 4 peptides with higher activity, in which we substituted serine (S) at the fifth position with phenylalanine (F), valine (V), tryptophan (W), or tyrosine (Y). During analysis of the mechanism of action, the modified peptides induced an increase in intracellular calcium concentration, which was caused by the treatment with the original peptide. Higher capacity for cell death induction by the modified peptides may be caused by increased hydrophobicity or an increased number of aromatic residues. Thus, the present work suggests that the intracellular activity of peptides can be assessed using the proposed screening system. It could be used for identifying intracellular functional peptides with higher activity through comprehensive screening.