Control of STING Agonistic/Antagonistic Activity Using Amine-Skeleton-Based c-di-GMP Analogues

Stimulator of Interferon Genes (STING) is a type of endoplasmic reticulum (ER)-membrane receptor. STING is activated by a ligand binding, which leads to an enhancement of the immune-system response. Therefore, a STING ligand can be used to regulate the immune system in therapeutic strategies. However, the natural (or native) STING ligand, cyclic-di-nucleotide (CDN), is unsuitable for pharmaceutical use because of its susceptibility to degradation by enzymes and its low cell-membrane permeability. In this study, we designed and synthesized CDN derivatives by replacing the sugar-phosphodiester moiety, which is responsible for various problems of natural CDNs, with an amine skeleton. As a result, we identified novel STING ligands that activate or inhibit STING. The cyclic ligand 7, with a cyclic amine structure containing two guanines, was found to have agonistic activity, whereas the linear ligand 12 showed antagonistic activity. In addition, these synthetic ligands were more chemically stable than the natural ligands

Vaginal Lymphoma with Immune Thrombocytopenic Purpura: An Unusual Case Report

The female genital tract is rarely the initial site of presentation in lymphoma or leukemia. We report a case of non-Hodgkin's lymphoma (NHL) presenting initially in the vagina. The patient, a 75-year-old woman, had a history of immune thrombocytopenic purpura (ITP). She presented with a chief complaint of genital bleeding and introital pain. On transvaginal ultrasonography, a vaginal tumor with an irregular wall was detected, and the internal echo showed a hypoechoic and echogenic pattern. Ultrasonography and magnetic resonance imaging (MRI) suggested that the vaginal tumor was likely to be a hematoma or a hemorrhagic tumor arising from ITP. Incision and resection for a hematoma or a hemorrhagic tumor were carried out in response to genital bleeding, introital pain, and pathological diagnosis. Postoperative microscopic examination confirmed that the tumor was a vaginal NHL. The final diagnosis using the Ann Arbor staging system was high-stage (stage IV) NHL. The patient received chemotherapy, and she remains in remission for 42 months after treatment

Extent of Helical Induction Caused by Introducing α‑Aminoisobutyric Acid into an Oligovaline Sequence

The preferred conformations of a dodecapeptide composed of l-valine (l-Val) and α-aminoisobutyric acid (Aib) residues, Boc-(l-Val-l-Val-Aib)₄-OMe (<b>3</b>), were analyzed in solution and in the crystalline state. Peptide <b>3</b> predominantly folded into a mixture of α- and 3₁₀-(<i>P</i>) helical structures in solution and a (<i>P</i>) α helix in the crystalline state

Extent of Helical Induction Caused by Introducing α‑Aminoisobutyric Acid into an Oligovaline Sequence

The preferred conformations of a dodecapeptide composed of l-valine (l-Val) and α-aminoisobutyric acid (Aib) residues, Boc-(l-Val-l-Val-Aib)₄-OMe (<b>3</b>), were analyzed in solution and in the crystalline state. Peptide <b>3</b> predominantly folded into a mixture of α- and 3₁₀-(<i>P</i>) helical structures in solution and a (<i>P</i>) α helix in the crystalline state

RNA nearest-neighbor parameters for inosine-cytosine pairs derived from a combined experiment-simulation approach

Recent advances in the RNA sequencing technology revealed that not only tRNAs but many mRNAs are chemically modified, e.g. deaminated, methylated or hydroxymethylated, in living cells. Furthermore, several evidences indicate that the RNA secondary structure change induced by the modification is deeply connected to the gene function. However, the structure prediction of the modified RNAs is difficult because the fundamental parameters to predict the structure are undetermined. Current RNA structure prediction model is built upon the nearest-neighbor model, which represents the score (energy) of the secondary structure as the sum of energies ("nearest-neighbor parameters") per two neighboring base pairs. These nearest-neighbor parameters are derived from the free-energy differences upon RNA duplex formation, which are typically determined from the UV adsorption measurements. Determining nearest neighbor parameters containing one modified RNA requires ca. 20 UV adsorption measurements. The cost for the synthesis of modified RNA sequences makes this approach difficult to scale with various RNA modifications.We developed a method that estimates the nearest neighbor parameters by combining the molecular dynamics (MD) simulation with the UV adsorption experiments. The free-energy differences were estimated in MD through free-energy perturbation method. The results were combined with the UV adsorption measurements to compensate the biases between the simulation and the experiment. With the new method, the required number of experiments to determine the parameters can be greatly reduced. We applied the method to estimate the nearest neighbor parameter containing inosine-cytosine pairs. The derived free-energy parameters were consistent to the parameters of canonical RNAs. Comparison to the recently reported inosine-containing nearest neighbor parameters from experiments (Wright et al., 2018) will also be discussed.Annual Meeting of the Biophysical Societ

Free-energy calculation of ribonucleic inosines and its application to nearest-neighbor parameters

Can current simulations quantitatively predict the stability of ribonucleic acids (RNAs)? In this research, we apply a free-energy perturbation simulation of RNAs containing inosine, a modified ribonucleic base, to the derivation of RNA nearest-neighbor parameters. A parameter set derived solely from 30 simulations was used to predict the free-energy difference of the RNA duplex with a mean unbiased error of 0.70 kcal/mol, which is a level of accuracy comparable to that obtained with parameters derived from 25 experiments. We further show that the error can be lowered to 0.60 kcal/mol by combining the simulation-derived free-energy differences with experimentally measured differences. This protocol can be used as a versatile method for deriving nearest-neighbor parameters of RNAs with various modified bases

Development of chimeric molecules that degrade the estrogen recep-tor using decoy oligonucleotide ligands

Targeted protein degradation using chimeric small molecules, such as proteolysis-targeting chimeras (PROTACs) and specif-ic and nongenetic inhibitors of apoptosis protein [IAP]-dependent protein erasers (SNIPERs), has attracted attention as a method to degrade intracellular target proteins via the ubiquitin-proteasome system (UPS). These chimeric molecules target a variety of proteins using small molecules that can bind to the proteins. However, it is difficult to develop such degraders in the absence of suitable small molecule ligands for the target proteins, such as for transcription factors (TFs). Therefore, we constructed the chimeric molecule LCL-ER(dec), which consists of a decoy oligonucleotide that can bind to the estrogen receptor alpha (ERalpha) and an IAP ligand, LCL161 (LCL), in a click reaction. LCL-ER(dec) was found to selectively degrade ERalpha via the UPS. These findings will be applicable to the development of other oligonucleotide-type degraders that target different TFs

Structural Optimization of Decoy Oligonucleotide-Based PROTAC That Degrades the Estrogen Receptor

Proteolysis-targeting chimeras (PROTACs) have attracted attention as a chemical method of protein knockdown via the ubiquitin–proteasome system. Some oligonucleotide-based PROTACs have recently been developed for disease-related proteins that do not have optimal small-molecule ligands such as transcription factors. We have previously developed the PROTAC LCL-ER­(dec), which uses a decoy oligonucleotide as a target ligand for estrogen receptor α (ERα) as a model transcription factor. However, LCL-ER­(dec) has a low intracellular stability because it comprises natural double-stranded DNA sequences. In the present study, we developed PROTACs containing chemically modified decoys to address this issue. Specifically, we introduced phosphorothioate modifications and hairpin structures into LCL-ER­(dec). Among the newly designed PROTACs, LCL-ER­(dec)-H46, with a T4 loop structure at the end of the decoy, showed long-term ERα degradation activity while acquiring enzyme tolerance. These findings suggest that the introduction of hairpin structures is a useful modification of oligonucleotides in decoy oligonucleotide-based PROTACs