Synthesis of a stimulus-responsive processing device and its application to a nucleocytoplasmic shuttle Peptide

Trimethyl Lock Based Tools for Drug Delivery and Cell Imaging - Synthesis and Properties

Trimethyl lock (TML) systems have become increasingly important in medicinal and bioorganic chemistry, particularly for their roles in the targeted delivery of therapeutic agents and as integral components in fluorogenic probes for cellular imaging. The simplicity and efficiency of their synthesis have established TML systems as versatile platforms for the controlled release of active molecules under particular physiological conditions. This review consolidates recent advancements in the application of TML systems, with a focus on their use in drug delivery, cellular imaging, and other areas where precise molecular release is crucial. Additionally, we discuss the synthetic strategies employed to construct TML-based conjugates, underscoring their potential to enhance the specificity and efficacy of bioactive compounds in various biomedical applications.

Photoresponsive peptide materials: Spatiotemporal control of self-assembly and biological functions

Peptides work as both functional molecules to modulate various biological phenomena and self-assembling artificial materials. The introduction of photoresponsive units to peptides allows the spatiotemporal remote control of their structure and function upon light irradiation. This article overviews the photoresponsive peptide design, interaction with biomolecules, and applications in self-assembling materials over the last 30 years. Peptides modified with photochromic (photoisomerizable) molecules, such as azobenzene and spiropyran, reversibly photo-controlled the binding to biomolecules and nanostructure formation through self-assembly. Photocleavable molecular units irreversibly control the functions of peptides through cleavage of the main chain and deprotection by light. Photocrosslinking between peptides or between peptides and other biomolecules enhances the structural stability of peptide assemblies and complexes. These photoresponsive peptides spatiotemporally controlled the formation and dissociation of peptide assemblies, gene expressions, protein-drug interactions, protein-protein interactions, liposome deformation and motility, cytoskeleton structure and stability, and cell functions by appropriate light irradiation. These molecular systems can be applied to photo-control biological functions, molecular robots, artificial cells, and next-generation smart drug delivery materials.

Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials

Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.

Development of Chemical Biology Tools Focusing on Peptide/Amide Bond Cleavage Reaction

Peptides and proteins are involved in almost all biological events. In this review, three chemical biology tools, which were developed for peptide/protein sciences from a viewpoint of peptide/amide bond cleavage, are overviewed. First, study on an artificial amino acid that enables stimulus-responsive functional control of peptides/proteins is briefly described. Two N-S acyl transfer reaction-based tools, one a linker molecule for facile identification of target proteins of bioactive compounds and the other a reagent for selective labeling of proteins of interest, are then discussed.

UV-responsive cyclic peptide progelator bioinks

We describe cyclic peptide progelators which cleave in response to UV light to generate linearized peptides which then self-assemble into gel networks. Cyclic peptide progelators were synthesized, where the peptides were sterically constrained, but upon UV irradiation, predictable cleavage products were generated. Amino acid sequences and formulation conditions were altered to tune the mechanical properties of the resulting gels. Characterization of the resulting morphologies and chemistry was achieved through liquid phase and standard TEM methods, combined with matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS).

[Looking Back on Study Abroad at The Scripps Research Institute]

Just after receiving my Ph.D. degree in 2004 from Tokushima University, under the supervision of Professor Masayuki Shibuya, I had the opportunity to work as a Research Associate in the laboratory of Professor Kim D. Janda at The Scripps Research Institute in the U.S., for about a year. Since it has already been more than 10 years since my time at Scripps, the specific research performed at that time may no longer be of interest to readers, but the benefit of working in a different research environment is timeless. Therefore, this paper describes not only details of the research conducted, but also the significance of working in a foreign country as a postdoc, and the subsequent influence those experiences at The Scripps Research Institute have had on my career.

Amide Bond Activation of Biological Molecules

Amide bonds are the most prevalent structures found in organic molecules and various biomolecules such as peptides, proteins, DNA, and RNA. The unique feature of amide bonds is their ability to form resonating structures, thus, they are highly stable and adopt particular three-dimensional structures, which, in turn, are responsible for their functions. The main focus of this review article is to report the methodologies for the activation of the unactivated amide bonds present in biomolecules, which includes the enzymatic approach, metal complexes, and non-metal based methods. This article also discusses some of the applications of amide bond activation approaches in the sequencing of proteins and the synthesis of peptide acids, esters, amides, and thioesters.

Trimethyl Lock: A Multifunctional Molecular Tool for Drug Delivery, Cellular Imaging, and Stimuli-Responsive Materials

Trimethyl lock (TML) systems are based on ortho-hydroxydihydrocinnamic acid derivatives displaying increased lactonization reactivity owing to unfavorable steric interactions of three pendant methyl groups, and this leads to the formation of hydrocoumarins. Protection of the phenolic hydroxy function or masking of the reactivity as benzoquinone derivatives prevents lactonization and provides a trigger for controlled release of molecules attached to the carboxylic acid function through amides, esters, or thioesters. Their easy synthesis and possible chemical adaption to several different triggers make TML a highly versatile module for the development of drug-delivery systems, prodrug approaches, cell-imaging tools, molecular tools for supramolecular chemistry, as well as smart stimuliresponsive materials.

Invention of stimulus-responsive peptide-bond-cleaving residue (Spr) and its application to chemical biology tools

Elucidation of biological functions of peptides and proteins is essential for understanding peptide/protein-related biological events and developing drugs. Caged peptides and proteins that release a parent active peptide/protein by photo-irradiation have successfully been employed to elucidate the functions. Whereas the usual caged peptide/protein enables conversion of an inactive form to an active form (OFF-to-ON conversion) by photo-induced deprotection, photo-triggered main chain cleavage is reported to be applicable to ON-to-OFF conversion. These peptides and proteins are photo-responsive; however, if peptides and proteins could respond to other stimuli such as disease-related environment or enzymes, their range of application should be widened. To convert the photo-responsive peptide/protein into other stimulus-responsive peptide/protein, quite laborious de novo design and synthesis of the stimulus-responsive unit are required. In this context, we designed a stimulus-responsive peptide-bond-cleaving residue (Spr) in which the stimuli available for the main chain cleavage vary according to the choice of protecting groups on the residue. In this review, design and synthesis of Spr are introduced, and challenges to apply Spr to other fields to enable, for example, functional control, localization control, delivery of cargos, labeling of a protein of interest in living cells, and identification of target proteins of bioactive ligands are discussed. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Visible-light-mediated cleavage of polymer chains under physiological conditions via quinone photoreduction and trimethyl lock

We introduce a click and visible-light triggered unclick approach via thio-bromo reaction and hydroquinone photoreduction/trimethyl lock cleavage for polymer modifications.

Medicinal Chemistry Focusing on Aggregation of Amyloid-β

The aggregation of peptides/proteins is intimately related to a number of human diseases. More than 20 have been identified which aggregate into fibrils containing extensive β-sheet structures, and species generated in the aggregation processes (i.e., oligomers and fibrils) contribute to disease development. Amyloid-β peptide (designated Aβ), related to Alzheimer's disease (AD), is the representative example. The intensive aggregation property of Aβ also leads to difficulty in its synthesis. To improve the synthetic problem, we developed an O-acyl isopeptide of Aβ1-42, in which the N-acyl linkage (amide bond) of Ser(26) was replaced with an O-acyl linkage (ester bond) at the side chain. The O-acyl isopeptide demonstrated markedly higher water-solubility than that of Aβ1-42, while it quickly converted to intact monomer Aβ1-42 via an O-to-N acyl rearrangement under physiological conditions. Inhibition of the pathogenic aggregation of Aβ1-42 might be a therapeutic strategy for curing AD. We succeeded in the rational design and identification of a small molecule aggregation inhibitor based on a pharmacophore motif obtained from cyclo[-Lys-Leu-Val-Phe-Phe-]. Moreover, the inhibition of Aβ aggregation was achieved via oxygenation (i.e., incorporation of oxygen atoms to Aβ) using an artificial catalyst. We identified a selective, cell-compatible photo-oxygenation catalyst of Aβ, a flavin catalyst attached to an Aβ-binding peptide, which markedly decreased the aggregation potency and neurotoxicity of Aβ.

Photo-triggered fluorescent labelling of recombinant proteins in live cells

A method to photo-chemically trigger fluorescent labelling of proteins in live cells is developed. The approach is based on photo-caged split-intein mediated conditional protein trans-splicing reaction and enabled background-free fluorescent labelling of target proteins with the necessary spatiotemporal control.

Development of a traceable linker containing a thiol-responsive amino acid for the enrichment and selective labelling of target proteins

A traceable linker that is potentially applicable to identification of a target protein of bioactive compounds was developed. It enabled not only thiol-induced cleavage of the linker for enrichment of the target protein but also selective labelling to pick out the target from contaminated non-target proteins for facile identification.

A photoinduced growth system of peptide nanofibres addressed by DNA hybridization

Spatiotemporal control of peptide nanofibre growth was achieved by photocleavage of a DNA-conjugated β-sheet-forming peptide with a photoresponsive amino acid.

Synthesis, characterization, and X-ray attenuation properties of ultrasmall BiOI nanoparticles: toward renal clearable particulate CT contrast agents

A unique decelerated hydrolytic procedure is developed and reported here for the preparation of ultrasmall nanoparticles (NPs) of PVP-coated BiOI with a narrow size distribution, i.e., 2.8 ± 0.5 nm. The crystal structure of this compound is determined by X-ray powder diffraction using the bulk materials. The stability, cytotoxicity, and potential use of the PVP-coated ultrasmall BiOI NPs as a CT contrast agent are investigated. Because of the combined X-ray attenuation effect of bismuth and iodine, such NPs exhibit a CT value that is among the best of those of the inorganic nanoparticle-based CT contrast agents reported in the literature.

Synthesis of O-acyl isopeptides

O-Acyl isopeptides, in which the N-acyl linkage on the hydroxyamino acid residue (e.g., Ser and Thr) is replaced with an O-acyl linkage, generally possess superior water-solubility to their corresponding native peptides, as well as other distinct physicochemical properties. In addition, O-acyl isopeptides can be rapidly converted into their corresponding native peptide under neutral aqueous conditions through an O-to-N acyl migration. By exploiting these characteristics, researchers have applied the O-acyl isopeptide method to various peptide-synthesis fields, such as the synthesis of aggregative peptides and convergent peptide synthesis. This O-acyl-isopeptide approach also serves as a means to control the biological function of the peptide in question. Herein, we report the synthesis of O-acyl isopeptides and some of their applications.

[Development of stimulus-responsive amino acids and their application to chemical biology use]

An understanding of the physiological significance of peptides and proteins is indispensable in the fields of life sciences and drug development. Recently, methods for controlling peptide and protein activities using stimuli such as UV irradiation have been attracting much attention because of their potential for clarifying the physiological roles of the peptides/proteins. In this context, we have developed a stimulus-responsive amino acid that induces peptide-bond cleavage after exposure to a stimulus. Although it has previously been reported that stimulus-responsive units can respond to a specific stimulus, our stimulus-responsive amino acid is potentially applicable to any stimulus simply by changing the protective group. In this review, the design and synthesis of stimulus-responsive amino acids are described. Their applications in chemical biology, including their use for spatiotemporal control of the activity of peptides in living cells, are also reported.

Trimethyl lock: A trigger for molecular release in chemistry, biology, and pharmacology

The trimethyl lock is an o-hydroxydihydrocinnamic acid derivative in which unfavorable steric interactions between three pendant methyl groups encourage lactonization to form a hydrocoumarin. This reaction is extremely rapid, even when the electrophile is an amide and the leaving group is an amino group of a small-molecule drug, fluorophore, peptide, or nucleic acid. O-Acylation of the phenolic hydroxyl group prevents reaction, providing a trigger for the reaction. Thus, the release of an amino group from an amide can be coupled to the hydrolysis of a designated ester (or to another chemical reaction that regenerates the hydroxyl group). Trimethyl lock conjugates are easy to synthesize, making the trimethyl lock a highly versatile module for chemical biology and related fields.

Self-assembly pathways of E22Δ-type amyloid β peptide mutants generated from non-aggregative O-acyl isopeptide precursors

The recently identified E22Δ-type amyloid β peptide (Aβ) mutants are reported to favor oligomerization over fibrillization and to exhibit more-potent synaptotoxicity than does wild-type (WT) Aβ. Aβ(E22Δ) mutants can thus be expected to serve as tools for clarifying the impact of Aβ oligomers in Alzheimer's disease (or Alzheimer's-type dementia). However, the biochemical and biophysical properties of Aβ(E22Δ) have not been conclusively determined. Here, we evaluated the self-assembly pathways of Aβ(E22Δ) mutants generated from water-soluble, non-aggregative O-acyl isopeptide precursors. Circular dichroism spectroscopy, Western blot analysis, and thioflavin-T fluorescence intensity and cellular toxicity assays suggest that the self-assembly pathways of Aβ(E22Δ) differed from those of Aβ(WT). Aβ1-40(E22Δ) underwent a rapid random coil→β-sheet conformational change in its monomeric or low-molecular-weight oligomeric states, whereas Aβ1-40(WT) self-assembled gradually without losing its propensity to form random coil structures. The Aβ1-42(E22Δ) monomer formed β-sheet-rich oligomers more rapidly than did Aβ1-42(WT). Additionally, the Aβ1-42(E22Δ) oligomers appear to differ from Aβ1-42(WT) oligomers in size, shape, or both. These results should provide new insights into the functions of Aβ(E22Δ) mutants.

Epimerization-free synthesis of cyclic peptide by use of the O-acyl isopeptide method

A head-to-tail cyclization of a protected linear hexapeptide with a C-terminal O-acyl isopeptide proceeded to give a cyclic O-acyl isopeptide without epimerization. The cyclic O-acyl isopeptide possessed different secondary structures compared with the native cyclic peptide. The isopeptide was then efficiently converted to the desired cyclic peptide via an O-to-N acyl migration reaction using a silica gel-anchored base.

A selenide-based approach to photochemical cleavage of peptide and protein backbones at engineered backbone esters

A strategy for photochemical cleavage of peptide and protein backbones is described, which is based on a selenide-mediated cleavage of a backbone ester moiety. Studies in model systems establish the viability of the chemistry and suggest the method could be a valuable tool for chemical biology studies of proteins.

"Click peptide": pH-triggered in situ production and aggregation of monomer Abeta1-42

The intense and uncontrollable self-assembling nature of amyloid beta peptide (Abeta) 1-42 is known to cause difficulties in preparing monomeric Abeta1-42; this results in irreproducible or discrepant study outcomes. Herein, we report novel features of a pH click peptide of Abeta1-42 that was designed to overcome these problems. The click peptide is a water-soluble precursor peptide of Abeta1-42 with an O-acyl isopeptide structure between the Gly25-Ser26 sequence. The click peptide adopts and retains a monomeric, random coil state under acidic conditions. Upon change to neutral pH (pH click), the click peptide converts to Abeta1-42 promptly (t(1/2) approximately 10 s) and quantitatively through an O-to-N intramolecular acyl migration. As a result of this quick and irreversible conversion, monomer Abeta1-42 with a random coil structure is produced in situ. Moreover, the oligomerization, amyloid fibril formation and conformational changes of the produced Abeta1-42 can be observed over time. This click peptide strategy should provide a reliable experimental system to investigate the pathological role of Abeta1-42 in Alzheimer's disease.

O-acyl isopeptide method: efficient synthesis of isopeptide segment and application to racemization-free segment condensation

We report the establishment of the O-acyl isopeptide method-based racemization-free segment condensation reaction toward future chemical protein synthesis. Peptide segments containing C-terminal O-acyl Ser/Thr residues were successfully synthesized by use of a lower nucleophilic base cocktail for Fmoc removal, and then coupled to an amino group of a peptide-resin without side reactions or epimerization. We also succeeded in performing the segment condensation in a sequential manner and in solution phase conditions as well.

Isopeptide method: development of S-acyl isopeptide method for the synthesis of difficult sequence-containing peptides

A novel strategy for a more efficient synthesis of difficult sequence-containing peptides, the S-acyl isopeptide method, was developed and successfully applied. A model pentapeptide Ac-Val-Val-Cys-Val-Val-NH2 was synthesized via its water-soluble S-acyl isopeptide using an S-acyl isodipeptide unit, Boc-Cys(Fmoc-Val)-OH. An S-acyl isopeptide possessing excellent water solubility could be readily and quantitatively converted to the native peptide via an S--N intramolecular acyl migration reaction at pH 7.4. Thus, the S-acyl isopeptide method provides a useful tool in peptide chemistry.

A bromocoumarin-based linker for synthesis of photocleavable peptidoconjugates with high photosensitivity

A new bromocoumarin-based bi-functional linker was developed for preparing photocleavable peptides and proteins with high photolytic efficiency, which have many potential applications in the study and engineering of biological systems.