Molecular BioSystems

doi: 10.1039/c3mb90009fpmid: N/A

doi: 10.1039/c3mb90010jpmid: N/A

doi: 10.1039/c3mb90012fpmid: N/A

Yoshida, Minoru; Park, Seung Bum; Boone, Charles

doi: 10.1039/c3mb90008hpmid: 23546016

Wong, Clarence T. T.; Tung, Chun Ling; Li, Xuechen

doi: 10.1039/c2mb25437apmid: 23302767

Native chemical ligation (NCL) has become the method of choice in synthesizing large or cyclic peptides/proteins. To overcome the limitation of NCL requiring N-terminal cysteine to mediate ligation, a strategy involving thiol-mediated ligation followed by desulfurization has been developed and advanced to realize peptide ligation at other amino acid sites, including Phe, Val, Leu, Thr, Lys, Pro and Gln. The syntheses of these mercapto-containing unnatural amino acids used as cysteine surrogates will be discussed in this review article.

Toshima, Kazunobu

doi: 10.1039/c2mb25416fpmid: 23247895

Proteins and carbohydrates play crucial roles in a wide range of biological processes, including serious diseases. The development of novel and innovative methods for selective control of specific proteins and carbohydrates functions has attracted much attention in the field of chemical biology. In this account article, the development of novel chemical tools, which can degrade target proteins and carbohydrates by irradiation with a specific wavelength of light under mild conditions without any additives, is introduced. This novel class of photochemical agents promise bright prospects for finding not only molecular-targeted bioprobes for understanding of the structure–activity relationships of proteins and carbohydrates but also novel therapeutic drugs targeting proteins and carbohydrates.

Nakase, Ikuhiko; Tanaka, Gen; Futaki, Shiroh

doi: 10.1039/c2mb25467kpmid: 23306408

“Cell-penetrating peptides (CPPs)” is an inclusive term describing relatively small peptides (6−30 amino acid residues) having membrane translocation activity. Due to their efficacy in cellular internalisation and the accompanying low cytotoxicity, CPPs are regarded as promising vectors for intracellular delivery of various membrane-impermeable bioactive molecules. This review provides an overview of the current approaches and describes the potential of CPP-based siRNA delivery systems, specifically those using arginine-rich CPPs.

Jung, Deokho; Min, Kyoungmi; Jung, Juyeon; Jang, Wonhee; Kwon, Youngeun

doi: 10.1039/c2mb25422kpmid: 23318293

Recently, significant advances have been made in live cell imaging owing to the rapid development of selective labeling of proteins in vivo. Green fluorescent protein (GFP) was the first example of fluorescent reporters genetically introduced to protein of interest (POI). While GFP and various types of engineered fluorescent proteins (FPs) have been actively used for live cell imaging for many years, the size and the limited windows of fluorescent spectra of GFP and its variants set limits on possible applications. In order to complement FP-based labeling methods, alternative approaches that allow incorporation of synthetic fluorescent probes to target POIs were developed. Synthetic fluorescent probes are smaller than fluorescent proteins, often have improved photochemical properties, and offer a larger variety of colors. These synthetic probes can be introduced to POIs selectively by numerous approaches that can be largely categorized into chemical recognition-based labeling, which utilizes metal-chelating peptide tags and fluorophore-carrying metal complexes, and biological recognition-based labeling, such as (1) specific non-covalent binding between an enzyme tag and its fluorophore-carrying substrate, (2) self-modification of protein tags using substrate variants conjugated to fluorophores, (3) enzymatic reaction to generate a covalent binding between a small molecule substrate and a peptide tag, and (4) split-intein-based C-terminal labeling of target proteins. The chemical recognition-based labeling reaction often suffers from compromised selectivity of metal–ligand interaction in the cytosolic environment, consequently producing high background signals. Use of protein–substrate interactions or enzyme-mediated reactions generally shows improved specificity but each method has its limitations. Some examples are the presence of large linker protein, restriction on the choice of introducible probes due to the substrate specificity of enzymes, and competitive reaction mediated by an endogenous analogue of the introduced protein tag. These limitations have been addressed, in part, by the split-intein-based labeling approach, which introduces fluorescent probes with a minimal size (∼4 amino acids) peptide tag. In this review, the advantages and the limitations of each labeling method are discussed.

Itoh, Yukihiro; Suzuki, Takayoshi; Miyata, Naoki

doi: 10.1039/c3mb25410kpmid: 23511667

DNA methylation and posttranslational histone modifications regulate expression of various genes independently of changes in the DNA sequence. Such epigenetic mechanisms play important roles in controlling cellular functions, including the cell cycle, immunoresponses and signal transduction. On the other hand, epigenetic aberrations are associated with oncogenesis and proliferation of cancer cells, and epigenetic alterations have been identified in many human cancer cells. Furthermore, chemical–biological approaches have uncovered relationships between epigenetic dysregulation and cancer, and several small molecules that modulate epigenetic mechanisms have already been approved for cancer therapy. In this review, we deal with chemical epigenetics relevant to cancer therapy, focusing especially on small molecules that regulate epigenetic mechanisms related to DNA methylation and histone modification.

Futamura, Yushi; Muroi, Makoto; Osada, Hiroyuki

doi: 10.1039/c2mb25468apmid: 23354001

Recently, a phenotypic approach—screens that assess the effects of compounds on cells, tissues, or whole organisms—has been reconsidered and reintroduced as a complementary strategy of a target-based approach for drug discovery. Although the finding of novel bioactive compounds from large chemical libraries has become routine, the identification of their molecular targets is still a time-consuming and difficult process, making this step rate-limiting in drug development. In the last decade, we and other researchers have amassed a large amount of phenotypic data through progress in omics research and advances in instrumentation. Accordingly, the profiling methodologies using these datasets expertly have emerged to identify and validate specific molecular targets of drug candidates, attaining some progress in current drug discovery (e.g., eribulin). In the case of a compound that shows an unprecedented phenotype likely by inhibiting a first-in-class target, however, such phenotypic profiling is invalid. Under the circumstances, a photo-crosslinking affinity approach should be beneficial. In this review, we describe and summarize recent progress in both affinity-based (direct) and phenotypic profiling (indirect) approaches for chemical biology target identification.