tRNA engineering strategies for genetic code expansion.

The advancement of genetic code expansion (GCE) technology is attributed to the establishment of specific aminoacyl-tRNA synthetase/tRNA pairs. While earlier improvements mainly focused on aminoacyl-tRNA synthetases, recent studies have highlighted the importance of optimizing tRNA sequences to enhance both unnatural amino acid incorporation efficiency and orthogonality. Given the crucial role of tRNAs in the translation process and their substantial impact on overall GCE efficiency, ongoing efforts are dedicated to the development of tRNA engineering techniques. This review explores diverse tRNA engineering approaches and provides illustrative examples in the context of GCE, offering insights into the user-friendly implementation of GCE technology.

Bioorthogonal CRISPR/Cas9-Drug Conjugate: A Combinatorial Nanomedicine Platform.

Bioconjugation of proteins can substantially expand the opportunities in biopharmaceutical development, however, applications are limited for the gene editing machinery despite its tremendous therapeutic potential. Here, a self-delivered nanomedicine platform based on bioorthogonal CRISPR/Cas9 conjugates, which can be armed with a chemotherapeutic drug for combinatorial therapy is introduced. It is demonstrated that multi-functionalized Cas9 with a drug and polymer can form self-condensed nanocomplexes, and induce significant gene editing upon delivery while avoiding the use of a conventional carrier formulation. It is shown that the nanomedicine platform can be applied for combinatorial therapy by incorporating the anti-cancer drug olaparib and targeting the RAD52 gene, leading to significant anti-tumor effects in BRCA-mutant cancer. The current development provides a versatile nanomedicine platform for combination treatment of human diseases such as cancer.

"Lighting up" fluoride: cellular imaging and zebrafish model interrogations using a simple ESIPT-based mycophenolic acid precursor-based probe.

The discovery and implementation of media that derive from bioinspired designs and bear optical readouts featuring large Stokes shifts are of continued interest to a wide variety of researchers and clinicians. Myco-F, a novel mycophenolic acid precursor-based probe features a cleavable tert-butyldimethylsiloxy group to allow for fluoride detection. Myco-F exhibits high selectivity and specificity towards F- (Stokes shift = 120 nm). All measurements were performed in complete aqueous media (LOD=0.38 µM). Myco-F enables detection of fluoride ions in living HEK293 cells and localizes in the eye region (among other regions) of the zebrafish. DFT calculations support the proposed ESIPT working photomechanism.

A Versatile Strategy for Screening Custom-Designed Warhead-Armed Cyclic Peptide Inhibitors.

Demand for peptide-based pharmaceuticals has been steadily increasing, but only limited success has been achieved to date. To expedite peptide-based drug discovery, we developed a general scheme for cell-based screening of cyclic peptide inhibitors armed with a user-designed warhead. We combined unnatural amino acid incorporation and split intein-mediated peptide cyclization techniques and integrated a yeast-based colorimetric screening assay to generate a new scheme that we call the custom-designed warhead-armed cyclic peptide screening platform (CWCPS). This strategy successfully discovered a potent inhibitor, CY5-6Q, that targets human histone deacetylase 8 (HDAC8) with a KD value of 15 nM. This approach can be a versatile and general platform for discovering cyclic peptide inhibitors.

Computational design of an apoptogenic protein that binds BCL-xL and MCL-1 simultaneously and potently.

One of the hallmarks of cancer cells is their ability to evade apoptosis, which confers survival advantages and resistance to anti-cancer drugs. Cancers often exhibit overexpression of anti-apoptotic BCL-2 proteins, the loss of which triggers apoptosis. In particular, the inhibition of both BCL-xL and MCL-1, but neither one individually, synergistically enhances apoptotic cell death. Here, we report computational design to produce a protein that inhibits both BCL-xL and MCL-1 simultaneously. To a reported artificial three-helix bundle whose second helix was designed to bind MCL-1, we added a fourth helix and designed it to bind BCL-xL. After structural validation of the design and further structure-based sequence design, we produced a dual-binding protein that interacts with both BCL-xL and MCL-1 with apparent dissociation constants of 820 pM and 196 pM, respectively. Expression of this dual binder in a subset of cancer cells induced apoptotic cell death at levels significantly higher than those induced by the pro-apoptotic BIM protein. With a genetic fusion of a mitochondria-targeting sequence or the BH3 sequence of BIM, the activity of the dual binder was enhanced even further. These data suggest that targeted delivery of this dual binder alone or as a part of a modular protein to cancers in the form of protein, mRNA, or DNA may be an effective way to induce cancer cell apoptosis.

Effects of Ti-doping amount and annealing temperature on electrochromic performance of sol-gel derived WO3.

Fine control of structural and morphological features in electrochromic materials is of paramount importance for realizing practical electrochromic devices (ECDs), which can dynamically adjust indoor light and temperature of buildings. To this end, herein we investigate impacts of two variants such as Ti-doping amount and the annealing temperature on physical and chemical properties of sol-gel derived electrochromic WO3 films. We use a wide range of titanium coupling agents (TCAs) as Ti-dopants ranging from 0 wt% to 20 wt% and vary the annealing temperature between 200 °C and 400 °C with 50 °C interval. Both variants greatly influence the physical properties of the resulting WO3 films, resulting in different crystallinities and morphologies. Through complementary analytical techniques, we find that the WO3 film featuring an amorphous phase with nano-porous morphology enhances the electrochemical and electrochromic performances. The specific TCA used in this study helps stabilize the amorphous WO3 structure and generate the nano-pores during the following thermal treatment via its thermal decomposition. As a result, the WO3 film having an optimal 8 wt% TCA annealed at 300 °C shows a high optical density of 73.78% in visible light (400-780 nm), rapid switching speed (t c = 5.12 s and t b = 4.74 s), and high coloration efficiency of 52.58 cm2 C-1 along with a superior cyclic stability. Thus, understanding a structure-property relationship is of paramount importance in engineering the advanced electrochromic WO3 for use in practical ECDs and other optoelectronic applications.

Phosphinate-benzoindocyanin fluorescent probe for endogenous mitochondrial peroxynitrite detection in living cells and gallbladder access in inflammatory zebrafish animal models.

Potent oxidants such as peroxynitrite (ONOO-) play important roles in the regulation of different physiopathological processes; their overproduction is thought to potentially cause several diseases in living organisms. Hence, the precise and selective monitoring of ONOO- is imperative for elucidating its interplay and roles in pathological and physiological processes. Herein, we present a novel diphenyl phosphinate-masked benzoindocyanin "turn-on" fluorogenic probe to help detect mitochondrial ONOO- in living cells and zebrafish models. A pale yellow color solution of BICBzDP turns rose-red upon the addition of ONOO-, selectively, contrary to that of other competitive bioactive molecules. BICBzDP displays an ultra-sensitivity detection limit (47.8 nM) with outstanding selectivity and sensitivity towards mitochondrial ONOO- and possesses a notable 68-fold fluorescence enhancement involving a large redshift of 91 nm. Importantly, further biological experimental investigations with BICBzDP indicate specific sensitivity and reliability of the probe to track the ONOO- level, not only in live cells, but also demonstrates dynamic fluctuations in the inflammatory zebrafish animal models. Thus, BICBzDP could be employed as a future potential biological tool for exploiting the role of ONOO- in a variety of different physiological systems.

Predicting the Cochlear Dead Regions Using a Machine Learning-Based Approach with Oversampling Techniques.

Background and Objectives: Determining the presence or absence of cochlear dead regions (DRs) is essential in clinical practice. This study proposes a machine learning (ML)-based model that applies oversampling techniques for predicting DRs in patients. Materials and Methods: We used recursive partitioning and regression for classification tree (CT) and logistic regression (LR) as prediction models. To overcome the imbalanced nature of the dataset, oversampling techniques to duplicate examples in the minority class or to synthesize new examples from existing examples in the minority class were adopted, namely the synthetic minority oversampling technique (SMOTE). Results: The accuracy results of the 10-fold cross-validation of the LR and CT with the original data were 0.82 (±0.02) and 0.93 (±0.01), respectively. The accuracy results of the 10-fold cross-validation of the LR and CT with the oversampled data were 0.66 (±0.02) and 0.86 (±0.01), respectively. Conclusions: This study is the first to adopt the SMOTE method to assess the role of oversampling methods on audiological datasets and to develop an ML-based model. Considering that the SMOTE method did not improve the model's performance, a more flexible model or more clinical features may be needed.

The effect of autocrine motility factor alone and in combination with methyl jasmonate on liver cancer cell growth.

Neoplastic cells secrete autocrine motility factor (AMF) to stimulate the motility of cancer cells. In this study, AMF secreted from HT-29 colorectal cancer cells selectively suppressed liver cancer cells by downregulating pAKT and ß-catenin. In addition, HT-29 AMF significantly augmented the activity of methyl jasmonate against liver cancer cells and is a promising alternative for liver cancer therapy.

Synergistic effects of autocrine motility factor and methyl jasmonate on human breast cancer cells.

Autocrine motility factor (AMF) stimulates the motility of cancer cells via an autocrine route and has been implicated in tumor progression and metastasis. Overexpression of AMF is correlated with the aggressive nature of breast cancer and is negatively associated with clinical outcomes. In contrast, AMF also has the ability to suppress cancer cells. In this study, AMFs from different cancer cells were demonstrated to have suppressive activity against MCF-7 and MDA-MB-231 breast cancer cells. In a growth and colony formation assay, AMF from AsPC-1 pancreatic cancer cells (ASPC-1:AMF) was determined to be more suppressive compared to other AMFs. It was also demonstrated that AsPC-1:AMF could arrest breast cancer cells at the G0/G1 cell cycle phase. Quantified by Western blot analysis, AsPC-1:AMF lowered levels of the AMF receptor (AMFR) and G-protein-coupled estrogen receptor (GPER), concomitantly regulating the activation of the AKT and ERK signaling pathways. JAK/STAT activation was also decreased. These results were found in estrogen receptor (ER)-positive MCF-7 cells but not in triple-negative MDA-MB-231 cells, suggesting that AsPC-1:AMF could work through multiple pathways led to apoptosis. More importantly, AsPC-1:AMF and methyl jasmonate (MJ) cooperatively and synergistically acted against breast cancer cells. Thus, AMF alone or along with MJ may be a promising breast cancer treatment option.

Noncanonical Amino Acids in Synthetic Biosafety and Post-translational Modification Studies.

The incorporation of noncanonical amino acids (ncAAs) has been extensively studied because of its broad applicability. In the past decades, various in vitro and in vivo ncAA incorporation approaches have been developed to generate synthetic recombinant proteins. Herein, we discuss the methodologies for ncAA incorporation, and their use in diverse research areas, such as in synthetic biosafety and for studies of post-translational modifications.

The interaction between ubiquitin and yeast polymerase η C terminus does not require the UBZ domain.

Polymerase η (Polη) is one of the Y-family polymerases that is recruited by monoubiquitinated proliferating cell nuclear antigen (Ub-PCNA) to DNA damage sites during translesion synthesis (TLS). This interaction is mediated by an ubiquitin-binding zinc-finger (UBZ) domain and a PCNA-interacting protein (PIP) box in Polη, which binds to ubiquitin and PCNA, respectively. Here, we show that without the UBZ domain, the PIP box of yeast Polη has a novel binding function with ubiquitin. Furthermore, the UBZ domain and the PIP box share the same binding surfaces for ubiquitin. The interaction with ubiquitin via the PIP box stabilizes the Ub-PCNA/Polη complex. Moreover, the PIP residues I624 and L625 contribute to Polη function in TLS in vivo.

Autocrine motility factor secreted by HeLa cells inhibits the growth of many cancer cells by regulating AKT/ERK signaling.

In cell competition, a secreted death signal can determine cell fate. However, the nature of such a signal remains unclear. In this study, conditioned medium from HeLa cells (HeLa CM) inhibited growth of A549 and MCF-7 cells. Through HeLa CM fractionation, glucose 6-phosphate isomerase/autocrine motility factor (GPI/AMF) was identified as the main growth inhibitor. Previously, AMF was known for its mitogenic, motogenic, and differentiation functions and was implicated in tumor progression and metastasis. HeLa CM lost its growth inhibitory property after treatment with erythrose-4-phosphate (E4P) or anti-GPI antibody. Purified HeLa recombinant AMF (rAMF) proteins inhibited the growth of A549, MDA-MB-232, MCF-7, AsPC-1, DU145, Hep-2, Hep G2, and HT-29 cells. However, growth of HL-60, SKOV3, U-87 MG, SNU-484, U-87 MG, and 3T3-L1 cells was little affected. In a Transwell assay, HeLa rAMF effectively reduced A549 cell migration and invasion. HeLa rAMF effectively induced apoptosis in A549 cells, apparently by reducing the levels of Bcl-2, GPI, and poly(ADP-ribose) polymerase (PARP)14 and activating caspase-3 and p53. HeLa rAMF antagonized HER2 and the AMF receptor (AMFR or GP78) in relation to the AKT/EKT signaling pathway. These results suggest that HeLa AMF could act as a diffusible death signal that could induce cancer cell-selective growth inhibition and apoptosis.

Glucose-dependent control of leucine metabolism by leucyl-tRNA synthetase 1.

Despite the importance of glucose and amino acids for energy metabolism, interactions between the two nutrients are not well understood. We provide evidence for a role of leucyl-tRNA synthetase 1 (LARS1) in glucose-dependent control of leucine usage. Upon glucose starvation, LARS1 was phosphorylated by Unc-51 like autophagy activating kinase 1 (ULK1) at the residues crucial for leucine binding. The phosphorylated LARS1 showed decreased leucine binding, which may inhibit protein synthesis and help save energy. Leucine that is not used for anabolic processes may be available for catabolic pathway energy generation. The LARS1-mediated changes in leucine utilization might help support cell survival under glucose deprivation. Thus, depending on glucose availability, LARS1 may help regulate whether leucine is used for protein synthesis or energy production.

Clinical characteristics and associated factors of canal switch in benign paroxysmal positional vertigo.

BACKGROUND: Canal switch benign paroxysmal positional vertigo (CS-BPPV) is a transition of BPPV involving one canal to another canal during or after canalith repositioning procedures (CRP). OBJECTIVE: To investigate the clinical characteristics of CS-BPPV and its associated factors. METHODS: The data of 2,303 patients with BPPV involving the lateral canal (LC) or posterior canal (PC) were retrospectively analyzed. Demographics, etiologies, and various clinical parameters related to CRP were compared between patients with and without CS-BPPV. RESULTS: Sixty-eight (2.95%) patients exhibited CS-BPPV. For patients with CS-BPPV from the PC to the LC, as well as those with CS-BPPV from the LC to the PC, the CRP number for the original canal in CS-BPPV was significantly greater than in non-CS-BPPV (P = 0.002). More CRP cycles were required to treat CS-BPPV than non-CS-BPPV involving the same canal. Multivariate analysis showed that CS-BPPV from the LC to the PC was significantly associated with multiple CRP cycles and use of the Gufoni maneuver (P = 0.038 and P < 0.001, respectively). CONCLUSIONS: The use of multiple cycles of CRP and the Gufoni maneuver were significantly associated with the onset of CS-BPPV. Furthermore, more CRP cycles were needed for the treatment of CS-BPPV than for non-CS-BPPV involving the same canal.

Site-Specific Labeling of Proteins Using Unnatural Amino Acids.

Labeling of a protein with a specific dye or tag at defined positions is a critical step in tracing the subtle behavior of the protein and assessing its cellular function. Over the last decade, many strategies have been developed to achieve selective labeling of proteins in living cells. In particular, the site-specific unnatural amino acid (UAA) incorporation technique has gained increasing attention since it enables attachment of various organic probes to a specific position of a protein in a more precise way. In this review, we describe how the UAA incorporation technique has expanded our ability to achieve site-specific labeling and visualization of target proteins for functional analyses in live cells.

Efficacy of three proton-pump inhibitor therapeutic strategies on laryngopharyngeal reflux disease; a prospective randomized double-blind study.

OBJECTIVES: Proton-pump inhibitor (PPI) prescribing practices in laryngopharyngeal reflux disease (LPR) differ among physicians. We assessed the improvement in reflux symptom index (RSI) and reflux finding score (RFS) after treating LPR with three different regimens. DESIGN: A prospective, double-blind, randomized clinical trial. SETTING: Chungnam national university hospital in Korea. PARTICIPANTS: From July 2015 to July 2017, 100 patients with LPR included in the study. The patients were prescribed one of the following regimens for 3 months: group A, ilaprazole 10 mg, once a day (QD), n = 29; group B, ilaprazole 10 mg, twice a day (BID), n = 27; and group C, ilaprazole 10 mg BID plus mosapride citrate 5 mg three times a day (TID), n = 44. MAIN OUTCOME MEASURES: The total RSI and RFS scores and each subitems in RSI and FRS of the patients were evaluated. RESULTS: Total RFS and RSI scores improved significantly at the 3-month follow-up in all groups, and the improvements were of similar magnitudes. Regarding the RFS, the degrees of improvement in vocal cord oedema (P = 0.002) and diffuse laryngeal oedema (P = 0.003) scores differed significantly among the three groups. Moreover, overweight or obese patients in group C showed the greatest improvement in RFS. However, age had no effect on treatment efficacy. CONCLUSION: Three PPI therapeutic strategies showed similar efficacies against LPR according to total RFS and RSI scores. The addition of a prokinetic resulted in improvements in specific endoscopic findings, such as vocal cord oedema and diffuse laryngeal oedema. Furthermore, the addition of a prokinetic to PPI therapy was particularly beneficial for overweight or obese patients.

Overriding Phthalate Decomposition When Exploring Mycophenolic Acid Intermediates as Selenium-Based ROS Biological Probes.

Hypochlorous (OCl-) acid is the most well-known bacterial oxidant to be produced by neutrophils. Excess amounts of OCl- can cause various disorders in living systems. Herein, we have designed, synthesized, and characterized two novel organoselenium-based target molecules (Probe-1 and Probe-OCl) based on a synthetic intermediate of mycophenolic acid for the aqueous detection of OCl-. Probe 1 has been recently reported (Org. Lett. 2018, 20, 3557-3561); both probes show immediate "turn-on" fluorescence (<1 s) upon the addition of OCl-, display an increase in the fluorescence quantum yield (3.7-fold in Probe-1 and 11.6-fold in Probe-OCl), and are completely soluble in aqueous media without the help of any cosolvent. However, a decrease in the "turn-on" intensity with the oxidized version of Probe-1 in cell assays due to the anhydride/phthalate functionality suggests that probe degradation occurs based on hydrolytic action (a probe degradation half-life of ∼1500 s at 15 µM Probe-1 and 150 µM OCl). Thus, the change of "anhydride" to "methylamide" begets Probe-OCl, which possesses more stability without sacrificing its water solubility properties and responses at short times. Further studies suggest that Probe-OCl is highly stable within physiological pH (pH = 7.4). Surprisingly, in live cell experiments involving U-2 OS cells and HeLa cells, Probe-OCl accumulated and aggregated in lipid droplets and gives a "turn-on" fluorescence response. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assays confirmed that Probe-OCl is not toxic. Cuvette aggregation studies were also performed (tetrahydrofuran/H2O) to demonstrate aggregation-induced fluorescence at longer times. Our current hypothesis is that the "turn-on" fluorescence effect is caused by the aggregation-induced emission mechanism available for Probe-OCl. In this case, in tandem, we reanalyzed the Mes-BOD-SePh derivative to compare and contrast cell localization as imaged by confocal microscopy; fluorescence emission occurs in the absence of, or prior to, Se oxidation.

Cyclic Peptides: Promising Scaffolds for Biopharmaceuticals.

To date, small molecules and macromolecules, including antibodies, have been the most pursued substances in drug screening and development efforts. Despite numerous favorable features as a drug, these molecules still have limitations and are not complementary in many regards. Recently, peptide-based chemical structures that lie between these two categories in terms of both structural and functional properties have gained increasing attention as potential alternatives. In particular, peptides in a circular form provide a promising scaffold for the development of a novel drug class owing to their adjustable and expandable ability to bind a wide range of target molecules. In this review, we discuss recent progress in methodologies for peptide cyclization and screening and use of bioactive cyclic peptides in various applications.

MSK1 functions as a transcriptional coactivator of p53 in the regulation of p21 gene expression.

Mitogen- and stress-activated kinase 1 (MSK1) is a chromatin kinase that facilitates activator-dependent transcription by altering chromatin structure through histone H3 phosphorylation. The kinase activity of MSK1 is activated by intramolecular autophosphorylation, which is initially triggered by the activation of upstream mitogen-activated protein kinases (MAPKs), such as p38 and ERK1/2. MSK1 has been implicated in the expression of p21, a p53 target gene; however, the precise connection between MSK1 and p53 has not been clearly elucidated. Here, using in vitro and cell-based transcription assays, we show that MSK1 functions as a transcriptional coactivator of p53 in p21 expression, an action associated with MAPK-dependent phosphorylation of MSK1 and elevated kinase activity. Of special significance, we show that MSK1 directly interacts with p53 and is recruited to the p21 promoter, where it phosphorylates histone H3 in a p53-dependent manner. In addition, phosphomimetic mutant analysis demonstrated that negative charges in the hydrophobic motif are critical for serine 212 phosphorylation in the N-terminal kinase domain, which renders MSK1 competent for histone kinase activity. These studies suggest that MSK1 acts through a direct interaction with p53 to function as a transcriptional coactivator and that MSK1 activation by upstream MAPK signaling is important for efficient p21 gene expression.