High-throughput de novo screening of receptor agonists with an automated single-cell analysis and isolation system

Therapeutic peptides: current applications and future directions

Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.

High-Throughput Analysis of Mammalian Receptor Tyrosine Kinase Activation in Yeast Cells

Tyrosine phosphorylation is an essential posttranslational modification in intracellular signaling molecules. Since tyrosine phosphorylation occurs in less than 0.1 % of all phosphorylated amino acids in mammalian cells, it is difficult to detect the nascent phosphotyrosine at a high signal-to-noise ratio due to high intracellular backgrounds (i.e., unexpected crosstalks among endogenous signaling molecules). In order to address this issue, we reconstituted the mammalian signaling pathway involving an extracellular ligand and a receptor tyrosine kinase (RTK) in Saccharomyces cerevisiae, a lower eukaryote that lacks endogenous tyrosine kinases. In this chapter, we describe a method for high-throughput analysis of ligand-receptor interaction by combining the yeast cell-surface display technique with an automated single-cell analysis and isolation system. Yeast cells coexpressing the cell-wall-anchored form of the human epidermal growth factor (EGF) and the human EGF receptor (EGFR) fused with a signal peptide at the N terminus facilitated the interaction of EGF with EGFR in an autocrine manner, followed by EGFR oligomerization and subsequent autophosphorylation. Furthermore, yeast cells expressing cell-wall-anchored forms of a conformationally constrained random peptide library instead of EGF are treated with a fluorophore-labeled anti-phosphorylated EGFR antibody and then subjected to the automated single-cell analysis and isolation system. The yeast cells with the highest level of fluorescence were shown to display novel and efficient EGFR agonistic peptides. Thus, our yeast display technique serves as a quantitative measurement for RTK activation, which is applicable to high-throughput de novo screening of RTK agonistic peptides.

Hierarchical design of artificial proteins and complexes toward synthetic structural biology

In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.

The Current State of Peptide Drug Discovery: Back to the Future?

Over the past decade, peptide drug discovery has experienced a revival of interest and scientific momentum, as the pharmaceutical industry has come to appreciate the role that peptide therapeutics can play in addressing unmet medical needs and how this class of compounds can be an excellent complement or even preferable alternative to small molecule and biological therapeutics. In this Perspective, we give a concise description of the recent progress in peptide drug discovery in a holistic manner, highlighting enabling technological advances affecting nearly every aspect of this field: from lead discovery, to synthesis and optimization, to peptide drug delivery. An emphasis is placed on describing research efforts to overcome the inherent weaknesses of peptide drugs, in particular their poor pharmacokinetic properties, and how these efforts have been critical to the discovery, design, and subsequent development of novel therapeutics.

One-step micromolding of complex 3D microchambers for single-cell analysis

Herein we examined the extent of replicability of the PDMS microchamber device transferred from the master mold with complex 3D structures fabricated via micro stereolithography. Due to the elastomeric properties of PDMS, the reversely tapered micromold, with the diameter ratio of ∼5 from the largest to the narrowest part, was precisely transferred without breaking. We obtained the mathematical model to estimate the stress exerted on the mold during the demolding process. Finally, we tested the applicability of this unusual microchamber for single-cell trapping and an enzyme assay.

Cytokine-dependent activation of JAK-STAT pathway in Saccharomyces cerevisiae

Protein phosphorylation is an important post-translational modification for intracellular signaling molecules, mostly found in serine and threonine residues. Tyrosine phosphorylations are very few events (less than 0.1% to phosphorylated serine/threonine residues), but capable of governing cell fate decisions involved in proliferation, differentiation, apoptosis, and oncogenic transformation. Hence, it is important for drug discovery and system biology to measure the intracellular level of phosphotyrosine. Although mammalian cells have been conventionally utilized for this purpose, accurate determination of phosphotyrosine level often suffers from high background due to the unexpected crosstalk among endogenous signaling molecules. This situation led us firstly to establish the ligand-induced activation of homomeric receptor tyrosine kinase (i.e., epidermal growth factor receptor) in Saccharomyces cerevisiae, a lower eukaryote possessing organelles similar to higher eukaryote but not showing substantial level of tyrosine kinase activity. In this study, we expressed heteromeric receptor tyrosine kinase (i.e., a complex of interleukin-5 receptor (IL5R) α chain, common β chain, and JAK2 tyrosine kinase) in yeast. When coexpressed with a cell wall-anchored form of IL5, the yeast exerted the autophosphorylation of JAK2, followed by the phosphorylation of transcription factor STAT5a and subsequent nuclear accumulation of phosphorylated STAT5a. Taken together, yeast could be an ideal host for sensitive detection of phosphotyrosine generated by a wide variety of tyrosine kinases. Biotechnol. Bioeng. 2016;113: 1796-1804. © 2016 Wiley Periodicals, Inc.