De novo design of a nanopore for single-molecule detection that incorporates a ß-hairpin peptide.

The amino-acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide, named SV28, that has a ß-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device for practical applications. The peptide forms multidispersely sized nanopore structures ranging from 1.7 to 6.3 nm in diameter and can detect DNAs. To form a monodispersely sized nanopore, we redesigned the SV28 by introducing a glycine-kink mutation. The resulting redesigned peptide forms a monodisperse pore with a diameter of 1.7 nm leading to detection of a single polypeptide chain. Such de novo design of a ß-hairpin peptide has the potential to create artificial nanopores, which can be size adjusted to a target molecule.

Mass Spectrometry-Based Solid Phase Peptide Reaction Assay for Detecting Allergenicity Using an Immobilized Peptide-Conjugating Photo-Cleavable Linker.

The biological process of skin sensitization depends on the ability of a sensitizer to modify endogenous proteins. A direct peptide reactivity assay (DPRA), based on the biological process of skin sensitization, was developed as an alternative to controversial animal experiments. Although DPRA has been endorsed by industries and is internationally accepted as promising, it has several drawbacks, such as incompatibility with hydrophobic chemicals, inability to perform detailed reaction analysis, and ability to evaluate only single components. Here, we demonstrated that sensitizers and peptide adducts can be easily identified using a mass spectrometry-based solid-phase peptide reaction assay (M-SPRA). We synthesized peptides with a photo-cleavable linker immobilized on resins. We showed the potential of M-SPRA in predicting skin sensitization by measuring the peptide adducts that were selectively eluted from the resin after cleaving the linker post-reaction. M-SPRA provides more detailed information regarding chemical reactivity and accurate assessment of test samples, including mixtures. M-SPRA may be helpful for understanding the binding mechanism of sensitizers (toxicology), which may assist in further refining reactivity assays and aiding in the interpretation of reactivity data.

Development of a chromophore-solid phase peptide reaction assay (C-SPRA) for assessing skin sensitization in vitro.

We developed an in vitro chromophore-solid phase peptide reaction assay (C-SPRA) using microbead-immobilized peptides and chromophores. Peptide-resins (microbeads) reacted with 14 representative chemicals to demonstrate the test's capacity to predict skin sensitization. C-SPRA enables accurate and high-throughput assessments of various chemicals, including poorly water-soluble sensitizers that are regarded as weakly potent by other methods.

Peptidomimetic Synthesis: Drug Discovery for Alzheimer's Disease.

The biomolecular system mainly consists of nucleic acids, proteins, peptides, and sugar chains, and they play a critical role in cell growth, differentiation induction, apoptosis, and immunity. Among these components, peptides are the most commonly studied due to their relatively low molecular weight and high biocompatibility as well as in vitro and in vivo lability and often applied as drugs, agricultural chemicals, food, and tools in diagnostic and biological research. Peptidomimetics have been reported to function as protein-protein interaction inhibitors and thus could serve in many biomolecular systems. This chapter describes the synthesis of peptidomimetics used for discovery of drugs that target ß-secretase inhibitors and amyloid-ß aggregation inhibitors in Alzheimer's disease. For this purpose, natural amino acids and other synthetic acids or amines were used in a solid-phase peptide synthesis (SPPS).

Peptides for Silica Precipitation: Amino Acid Sequences for Directing Mineralization.

BACKGROUND: Peptides are promising compounds for use in inorganic or organic-inorganic hybrid syntheses (mineralization) and offer several advantages over proteins. Meanwhile, silica-based nanomaterials have been extensively investigated for many years because of their potential application in a diverse range of technologies, including catalysis, sensing, separation, enzyme immobilization, and gene and drug delivery. Considerable progress has been made over the past decade in understanding the molecular mechanisms underpinning biosilicification and the biomimetic synthesis of patterned nanosilica using peptides. OBJECTIVES: This mini-review focuses on various peptide sequences, especially short peptide sequences (30 residues or less), for silica mineralization. METHODS: We first briefly review early studies on silica mineralization using proteins to provide background information. This is followed by a discussion of promising peptide sequences and attempts to discern the relationship between amino acid sequence, their potential for mineralization, and the properties of the mineral product. RESULTS: The synthetic control of silica mineralization using engineered proteins, such as recombinant silicateins and silaffins, was inspired by silica biomineralization by natural proteins from organisms (sponges, diatoms, and plants). Concurrently, several papers described the utility of well-structured protein assemblies as templates for silica mineralization. These template-directed syntheses of well-structured silica deposits were first conducted using natural proteins or protein assemblies such as collagen fibers and virus hollow protein tubes. Then we reviewed a selection of short peptides (30 residues or less) that had been successfully used for silica mineralization. Almost all peptides developed to date can be sorted by classification like proteins (synthetic control of silica mineralization or utility of templates for silica mineralization): the first class of peptides is used for peptide-directed synthesis, and the second is used for template-directed synthesis after the peptides have assembled and formed nanostructure such as fibers and tubes. The presented peptides were classified and arranged according to the classification. Additionally, we briefly introduced silica mineralization triggered by the combination of short silica-precipitating peptides and template molecules. CONCLUSION: In this mini-review we focused on various peptide sequences, especially short peptide sequences of 30 residues or less, designed for silica mineralization. The peptides have been used both for peptide-directed silica mineralization and for template-directed silica mineralization. The recent advances in peptide-driven mineralization reviewed here suggest that it will soon be possible to completely control the silica mineralization process using peptides. Mineralization systems using peptides will provide researchers with new tools for controlling various inorganic syntheses and the production of organic-inorganic materials for nanobiochemistry and materials chemistry research.

DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity.

The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA-PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Micro-scale analyses via TEM and AFM showed that G-rich DNA alone forms G-wires in the presence of Ca2+, and that the peptide disrupted this formation, resulting in the formation of particles. The addition of the protease and digestion of the peptide regenerated the G-wires. Macro-scale analyses by DLS, zeta potential, CD, and gel filtration were in agreement with the microscopic observations. These results imply that the secondary structure change (DNA G-quadruplex <--> DNA/PNA hybrid structure) induces a change in the well-formed nanostructure (G-wire <--> particles). Our findings demonstrate a control system for forming DNA G-wire structures dependent on protease activity using designed peptides. Such systems hold promise for regulating the formation of nanowire for various applications, including electronic circuits for use in nanobiotechnologies.

Recent progress in prodrug design strategies based on generally applicable modifications.

The development of prodrugs has progressed with the aim of improving drug bioavailability by overcoming various barriers that reduce drug benefits in clinical use, such as stability, duration, water solubility, side effect profile, and taste. Many conventional drugs act as the precursors of an active agent in vivo; for example, the anti-HIV agent azidothymidine (AZT) is converted into its corresponding active triphosphate ester in the body, meaning that AZT is a prodrug in the broadest sense. However prodrug design is generally difficult owing to the lack of general versatility. Thus, these prodrugs, broadly defined, are often discovered by chance or trial-and-error. Recently, many prodrugs that could release the corresponding parent drugs with or without enzymatic action under physiological conditions have been reported. These prodrugs can be easily designed and synthesized because of their generally applicable modifications. This digest paper provides an overview of recent development in prodrug strategies for drugs with a carboxylic acid or hydroxyl/amino group on the basis of a generally applicable modification strategy, such as esterification, amidation, or benzylation.

Site-specific control of multiple mineralizations using a designed peptide and DNA.

We have developed a site-specific method for precipitating multiple inorganic compounds using target DNA and a designed peptide consisting of a peptide nucleic acid (PNA) sequence and an inorganic compound-precipitating sequence. This system for controlled site-specific precipitation represents a powerful tool for use in nanobiotechnology and materials science.

Novel prodrugs with a spontaneous cleavable guanidine moiety.

Water-soluble prodrug strategy is a practical alternative for improving the drug bioavailability of sparingly-soluble drugs with reduced drug efficacy. Many water-soluble prodrugs of sparingly-soluble drugs, such as the phosphate ester of a drug, have been reported. Recently, we described a novel water-soluble prodrug based on O-N intramolecular acyl migration. However, these prodrug approaches require a hydroxy group in the structure of their drugs, and other prodrug approaches are often restricted by the structure of the parent drugs. To develop prodrugs with no restriction in the structure, we focused on a decomposition reaction of arginine methyl ester. This reaction proceeds at room temperature under neutral conditions, and we applied this reaction to the prodrug strategy for drugs with an amino group. We designed and synthesized novel prodrugs of representative sparingly soluble drugs phenytoin and sulfathiazole. Phenytoin and sulfathiazole were obtained as stable salt that were converted to parent drugs under physiological conditions. Phenytoin prodrug 3 showed a short half-life (t1/2) of 13min, whereas sulfathiazole prodrug 7 had a moderate t1/2 of 40min. Prodrugs 3 and 7 appear to be suitable for use as an injectable formulation and orally administered drug, respectively.

A novel N-terminal degradation reaction of peptides via N-amidination.

The cleavage of amide bonds requires considerable energy. It is difficult to cleave the amide bonds in peptides at room temperature, whereas ester bonds are cleaved easily. If peptide bonds can be selectively cleaved at room temperature, it will become a powerful tool for life science research, peptide prodrug, and tissue-targeting drug delivery systems. To cleave a specific amide bond at room temperature, the decomposition reaction of arginine methyl ester was investigated. Arginine methyl ester forms a dimer; the dimer releases a heterocyclic compound and ornithine methyl ester at room temperature. We designed and synthesized N-amidinopeptides based on the decomposition reaction of arginine methyl ester. Alanyl-alanine anilide was used as the model peptide and could be converted into N-degraded peptide, alanine anilide, via an N-amidination reaction at close to room temperature. Although the cleavage rate in pH 7.4 phosphate buffered saline (PBS) at 37°C was slow (t1/2=35.7h), a rapid cleavage rate was observed in 2% NaOH aq (t1/2=1.5min). To evaluate the versatility of this reaction, a series of peptides with Lys, Glu, Ser, Cys, Tyr, Val, and Pro residue at the N-terminal were synthesized; they showed rapid cleavage rates of t1/2 values from 1min to 10min.

New directions for protease inhibitors directed drug discovery.

Proteases play crucial roles in various biological processes, and their activities are essential for all living organisms-from viruses to humans. Since their functions are closely associated with many pathogenic mechanisms, their inhibitors or activators are important molecular targets for developing treatments for various diseases. Here, we describe drugs/drug candidates that target proteases, such as malarial plasmepsins, ß-secretase, virus proteases, and dipeptidyl peptidase-4. Previously, we reported inhibitors of aspartic proteases, such as renin, human immunodeficiency virus type 1 protease, human T-lymphotropic virus type I protease, plasmepsins, and ß-secretase, as drug candidates for hypertension, adult T-cell leukaemia, human T-lymphotropic virus type I-associated myelopathy, malaria, and Alzheimer's disease. Our inhibitors are also described in this review article as examples of drugs that target proteases. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 563-579, 2016.

Novel ß-amyloid aggregation inhibitors possessing a turn mimic.

Amyloid ß peptide, the main component of senile plaques found in the brain of Alzheimer disease (AD) patients, is a molecular target for AD therapeutic intervention. A number of potential AD therapeutics have been reported, including inhibitors of ß-secretase, γ-secretase, and Aß aggregation, and anti-amyloid agents, such as neprilysin, insulin degrading enzyme (IDE), and Aß antibodies. Recently, we reported potent small-sized ß-secretase (BACE1) inhibitors, which could serve as anti-AD drugs. However AD is a progressive disorder, where dementia symptoms gradually worsen over several decades, and therefore may require many years to get cured. One possible way to achieve a greater therapeutic effect is through simultaneous administration of multiple drugs, similar to those used in Highly Active Anti-Retroviral Therapy (HAART) used to treat AIDS. In order to overcome AD, we took a drug discovery approach to evaluate, novel ß-amyloid aggregation inhibitors. Previously, we reported that a tong-type compound possessing a turn mimic as the inhibitor of HIV-1 protease dimerization. Oligomerized amyloid ß peptides contain a turn structure within the molecule. Here, we designed and synthesized novel ß-amyloid aggregation inhibitors with a turn-mimic template, based on the turn conformer of the oligomerized amyloid ß peptides.

Structure-activity relationship study of BACE1 inhibitors possessing a chelidonic or 2,6-pyridinedicarboxylic scaffold at the P(2) position.

We have previously reported potent substrate-based pentapeptidic BACE1 inhibitors possessing a hydroxymethylcarbonyl isostere as a substrate transition-state mimic. While these inhibitors exhibited potent activities in enzymatic and cellular assays (KMI-429 in particular inhibited Aß production in vivo), these inhibitors contained some natural amino acids that seemed to be required to improve enzymatic stability in vivo and permeability across the blood-brain barrier, so as to be practical drug. Recently, we synthesized non-peptidic and small-sized BACE1 inhibitors possessing a heterocyclic scaffold at the P2 position. Herein we report the SAR study of BACE1 inhibitors possessing this heterocyclic scaffold, a chelidonic or 2,6-pyridinedicarboxylic moiety.

Novel BACE1 inhibitors with a non-acidic heterocycle at the P1' position.

We have reported potent peptidic and non-peptidic BACE1 inhibitors with a hydroxymethylcarbonyl (HMC) isostere as a substrate transition-state mimic. However, our potent inhibitors possess a tetrazole ring at the P1' position. It is desirable that central nervous system (CNS) drugs do not possess an acidic moiety. In this study, we synthesized non-acidic BACE1 inhibitors with heterocyclic derivatives at the P1' position. KMI-1764 (27) exhibited potent inhibitory activity (IC50=27nM). Interestingly, these non-acidic inhibitors tended to follow the quantitative structure-activity relationship (QSAR) equation and interacted with BACE1-Arg235 in the binding model.

The transcriptional co-repressor TLE3 regulates development of trophoblast giant cells lining maternal blood spaces in the mouse placenta.

TLE3 is a transcriptional co-repressor that interacts with several DNA-binding repressors, including downstream effectors of the Notch signaling pathway. We generated Tle3-deficient mice and found that they die in utero and their death is associated with abnormal development of the placenta with major defects in the maternal vasculature. In the normal placenta, maternal blood spaces are lined, not as usual in the mammalian circulation by endothelial cells, but rather by specialized embryo-derived cells of the trophoblast cell lineage named trophoblast giant cells (TGC). Tle3 mRNA is expressed in those specialized TGC and Tle3 mutants show severe defects in differentiation of TGC-lined channels and lacunar spaces that take blood out of the labyrinth zone of the placenta and into the uterine veins. The mutants also show somewhat milder defects on the arterial-side of the maternal vascular circuit in spiral arteries and canals that take blood into the labyrinth. Notch2 and Tle3 expression patterns overlap in several TGC subtypes and we found that Tle3 and Notch2 mutants have some overlapping features. However, they also show differences implying that TLE3 may mediate some but not all of the effects of Notch2 signaling during placenta development. Therefore, formation of the different types of maternal blood spaces by different TGC subtypes is regulated by distinct molecular mechanisms.

[Significance of quantum chemical interactions for medicinal science and design of ß-secretase inhibitors].

This review discusses the importance of quantum chemical interactions in biomolecules for medicinal science and their relevance to the author's ß-secretase (BACE1) inhibitor drug discovery research. Although molecular mechanics/dynamics (MM/MD) methods are available in many in silico design tools used for drug discovery, they cannot accurately evaluate quantum effects between biomolecules and drugs. The key roles of biomolecular quantum chemical interactions in drug discovery are discussed using the arginine side chain as an example. Arginine is recognized as a charged amino acid in commonly used drug design software, unlike other amino acids with π-electron orbitals, such as phenylalanine, tyrosine, and tryptophan. Quantum chemical interactions via the arginine side chain are crucial for molecular recognition, and are found in many X-ray crystal structures, such as protein-protein, protein homodimer, RNA aptamer-protein, and enzyme-inhibitor complexes. This review describes the essential role of quantum chemical interactions via the arginine side chain in the mechanism of BACE1 inhibition, and proposes an "electron donor/acceptor bioisostere" concept for medicinal science based on quantum chemical interactions. Several potent BACE1 inhibitors, as well as the first peptides with BACE1 inhibiting activity were designed and synthesized based on studies of quantum chemical interactions via arginine side chain and the "electron donor bioisostere" concept.

Advances in the identification of ß-secretase inhibitors.

INTRODUCTION: Alzheimer's disease (AD), which is characterized by progressive intellectual deterioration, is the most common cause of dementia. ß-Secretase (or BACE1) expression is a trigger for amyloid ß peptide formation, a cause of AD, and thus is a molecular target for the development of drugs against AD. Many BACE1 inhibitors have been identified by academic and pharmaceutical research groups and a number of advanced technologies in drug discovery have been applied to the drug discovery. AREAS COVERED: The purpose of this review is to present and discuss the methodologies used for BACE1 inhibitor drug discovery via substrate- and structure-based design, high-throughput screening and fragment-based drug design. The authors also review the advantages and disadvantages of these methodologies. EXPERT OPINION: Many BACE1 inhibitors have been designed using X-ray crystal structure-based drug design as well as through in silico screening. Nevertheless, there are serious problems with regards to deciding the best X-ray crystal structure for designing BACE1 inhibitors through computational approaches. There are two prominent configurations of BACE1 but there is still room for improvement. Future developments may make it possible to identify BACE1 inhibitors as potential drug candidates.

The application of bioisosteres in drug design for novel drug discovery: focusing on acid protease inhibitors.

INTRODUCTION: A bioisostere is a powerful concept for medicinal chemistry. It allows the improvement of the stability; oral absorption; membrane permeability; and absorption, distribution, metabolism and excretion (ADME) of drug candidate, while retaining their biological properties. The term 'bioisostere' is derived from 'isostere', whose physical and chemical properties, such as steric size, hydrophobicity, and electronegativity, are similar to those of a functional or atomic group, and is considered to possess biological properties. Here, the authors highlight the recent applications of bioisosteres in drug design, mainly based on our drug discovery studies. AREAS COVERED: This review discusses the application of bioisosteres for novel drug discovery with focus on the authors' drug discovery studies such as renin, HIV-protease, and ß-secretase inhibitors. The authors highlight that some bioisosteres can form the scaffolding for drug candidates, namely substrate transition state, amide/ester, and carboxylic acid bioisosteres. Moreover, the authors propose the new terms 'electron-donor bioisostere' and 'conformational bioisostere' for drug discovery. EXPERT OPINION: The authors discuss the importance of bioisostere's design concept based on specific interaction with the corresponding biomolecule. In addition, some strategies for drug discovery based on the bioisostere concept are introduced. Many bioisosteres, which are recognized by corresponding target biomolecules as exhibiting similar biological properties, have been reported to date; most of the recently developed bioisosteres were designed by cheminformatics approaches. Some molecular design softwares and databases are introduced.

Novel BACE1 inhibitors possessing a 5-nitroisophthalic scaffold at the P2 position.

Recently, we reported substrate-based pentapeptidic BACE1 inhibitors possessing a hydroxymethylcarbonyl isostere as a substrate transition-state mimic. These inhibitors showed potent inhibitory activities in enzymatic and cell assays. We also designed and synthesized non-peptidic and small-sized inhibitors possessing a heterocyclic scaffold at the P(2) position. By studying the structure-activity relationship of these inhibitors, we found that the σ-π interaction of an inhibitor with the BACE1-Arg235 side chain played a key role in the inhibition mechanism. Hence, we optimized the inhibitors with a focus on their P(2) regions. In this Letter, a series of novel BACE1 inhibitors possessing a 5-nitroisophthalic scaffold at the P(2) position are described along with the results of the related structure-activity relationship study. These small-sized inhibitors are expected improved membrane permeability and bioavailability.