Lantern-type G-quadruplex fluorescent sensors for detecting divalent metal ions.

Three thioflavin T (ThT) derivatives, namely ThT/ethylenediaminetetraacetic acid conjugates (E1T, E2T, and E1T1P), were designed and synthesized as sensing components for divalent metal ion detection. Furthermore, these ThT derivatives were used to design lantern-type G-quadruplex (G4) fluorescent sensors. The fluorescence intensities of the ThT derivatives decreased by 1.2- to 5.6-folds in the presence of Ni2+ and Cu2+, respectively, regardless of the topology of the utilized G4. Conversely, when Mn2+ and Zn2+ coexisted in antiparallel G4, the fluorescence intensities of E2T increased to approximately 3.3- and 2.3-folds, respectively, depending on the concentration of the divalent metal ion, allowing for quantitative analyses. The Job plot analysis revealed that the binding ratio of G4 and E2T changed from 2:1 to 1:2 with the increasing concentration of the divalent metal ions. These results indicated that the basic principle of such a lantern-type G4 sensor can be applied to the detection of divalent metal ions and other types of targets, such as proteins, and small molecules via ThT derivatization.

Prophylactic Effect of Amiodarone Infusion on Reperfusion Ventricular Fibrillation After Release of Aortic Cross-Clamp in Patients with Left Ventricular Hypertrophy Undergoing Aortic Valve Replacement: ARandomized Controlled Trial.

OBJECTIVE: To investigate whether prophylactic amiodarone infusion prevents ventricular fibrillation after aortic cross-clamp release and attenuates cytokine production in patients with left ventricular hypertrophy undergoing cardiac surgery. DESIGN: Prospective, randomized controlled trial. SETTING: A public hospital. PARTICIPANTS: The study comprised 68 patients undergoing aortic valve replacement for severe aortic stenosis. INTERVENTIONS: Patients were randomly assigned to receive a 150mg bolus then 30mg/h continuous infusion of amiodarone (amiodarone group) or a 1 mg/kg bolus then 1 mg/kg/h continuous infusion of lidocaine (lidocaine group). The primary outcome was the ventricular fibrillation incidence rate after aortic cross-clamp release. Secondary outcomes included perioperative serum interleukin-6 and tumor necrosis factor-alpha levels. MEASUREMENTS AND MAIN RESULTS: The ventricular fibrillation incidence rate was significantly lower in the amiodarone than in the lidocaine group (20.6% v 50%, relative risk 0.41; 95% confidence interval [CI] 0.20-0.86; p = 0.021). Interleukin-6 levels 1hour after aortic cross-clamp release and at intensive care unit admission were significantly lower in the amiodarone than in the lidocaine group (geometric mean [95% CI] 117.4pg/mL [87.1-158.4] v 339.5pg/mL [210.6-547.2]; p < 0.01 and 211.1pg/mL [162.8-73.6] v 434.1pg/mL [293.7-641.5]; p < 0.01, respectively). Tumor necrosis factor-alpha levels 1hour after aortic cross-clamp release were significantly lower in the amiodarone than in the lidocaine group (geometric mean [95% CI] 1.624pg/mL [1.359-1.940] v 2.283pg/mL [1.910-2.731]; p = 0.02). CONCLUSIONS: Amiodarone prevented reperfusion ventricular fibrillation in patients with left ventricular hypertrophy undergoing aortic valve replacement to a greater extent than did lidocaine. Furthermore, amiodarone inhibited postoperative interleukin-6 and tumor necrosis factor-alpha production.

Discovery of evocalcet, a next-generation calcium-sensing receptor agonist for the treatment of hyperparathyroidism.

The calcium-sensing receptor (CaSR) plays an important role in sensing extracellular calcium ions and regulating parathyroid hormone secretion by parathyroid gland cells, and the receptor is a suitable target for the treatment of hyperparathyroidism. Cinacalcet hydrochloride is a representative CaSR agonist which widely used for the hyperparathyroidism. However, it has several issues to clinical use, such as nausea/vomiting and strong inhibition of CYP2D6. We tried to improve these issues of cinacalcet for a new pharmaceutical agent as a preferable CaSR agonist. Optimization from cinacalcet resulted in the identification of pyrrolidine compounds and successfully led to the discovery of evocalcet as an oral allosteric CaSR agonist. Evocalcet, which exhibited highly favorable profiles such as CaSR agonistic activity and good DMPK profiles, will provide a novel therapeutic option for secondary hyperparathyroidism.

Association of Preoperative Right and Left Ventricular Diastolic Dysfunction With Postoperative Atrial Fibrillation in Patients Undergoing Lung Surgery: A Prospective Observational Study.

OBJECTIVES: To clarify the relationship between right and left ventricular (RV and LV) diastolic function and postoperative atrial fibrillation (POAF). The early effects of major lung surgery on cardiac function in the intraoperative period during lung surgery were evaluated, using transesophageal echocardiography. DESIGN: Single-center prospective observational study. SETTING: A public hospital. PARTICIPANTS: Patients undergoing elective lobectomy with lymph node dissection for lung cancer (n = 116). INTERVENTIONS: Transesophageal echocardiography examination was performed under general anesthesia before skin incision (preoperative) and after chest closure (postoperative). According to measured echocardiographic variables, ventricular systolic and diastolic functions were classified at each time point. MEASUREMENTS AND MAIN RESULTS: Of the 116 patients, 24 (20.7%) experienced POAF. Preoperative RV and LV diastolic dysfunction were more common in patients with POAF than in those without POAF (58.3 v 28.3%, p = 0.008; 54.2 v 19.6%, p = 0.001, respectively). Among patients without preoperative diastolic dysfunction, a small number developed RV and LV diastolic dysfunction immediately after surgery (9.2% and 16.5%, respectively) and these distributions were comparable between patients with POAF and those without POAF. RV systolic dysfunction was observed in 6.5% of patients immediately after surgery and was not related to the occurrence of POAF. Multivariate analysis revealed older age, chronic obstructive pulmonary disease (COPD), and preoperative biventricular diastolic dysfunction as risk factors for POAF. CONCLUSIONS: Preoperative biventricular diastolic dysfunction, as well as older age and COPD, are associated with POAF in patients undergoing lobectomy. Major lung surgery has minimal early effects on postoperative systolic and diastolic functions.

Construction of a T m-value prediction model and molecular dynamics study of AmNA-containing gapmer antisense oligonucleotide.

RNase H-dependent antisense oligonucleotides (gapmer ASOs) represent a class of nucleic acid therapeutics that bind to target RNA to facilitate RNase H-mediated RNA cleavage, thereby regulating the expression of disease-associated proteins. Integrating artificial nucleic acids into gapmer ASOs enhances their therapeutic efficacy. Among these, amido-bridged nucleic acid (AmNA) stands out for its potential to confer high affinity and stability to ASOs. However, a significant challenge in the design of gapmer ASOs incorporating artificial nucleic acids, such as AmNA, is the accurate prediction of their melting temperature (T m ) values. The T m is a critical parameter for designing effective gapmer ASOs to ensure proper functioning. However, predicting accurate T m values for oligonucleotides containing artificial nucleic acids remains problematic. We developed a T m prediction model using a library of AmNA-containing ASOs to address this issue. We measured the T m values of 157 oligonucleotides through differential scanning calorimetry, enabling the construction of an accurate prediction model. Additionally, molecular dynamics simulations were used to elucidate the molecular mechanisms by which AmNA modifications elevate T m , thereby informing the design strategies of gapmer ASOs.

Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information.

Idiopathic pulmonary fibrosis (IPF) is a progressive disease characterized by severe lung fibrosis and a poor prognosis. Although the biomolecules related to IPF have been extensively studied, molecular mechanisms of the pathogenesis and their association with serum biomarkers and clinical findings have not been fully elucidated. We constructed a Bayesian network using multimodal data consisting of a proteome dataset from serum extracellular vesicles, laboratory examinations, and clinical findings from 206 patients with IPF and 36 controls. Differential protein expression analysis was also performed by edgeR and incorporated into the constructed network. We have successfully visualized the relationship between biomolecules and clinical findings with this approach. The IPF-specific network included modules associated with TGF-ß signaling (TGFB1 and LRC32), fibrosis-related (A2MG and PZP), myofibroblast and inflammation (LRP1 and ITIH4), complement-related (SAA1 and SAA2), as well as serum markers, and clinical symptoms (KL-6, SP-D and fine crackles). Notably, it identified SAA2 associated with lymphocyte counts and PSPB connected with the serum markers KL-6 and SP-D, along with fine crackles as clinical manifestations. These results contribute to the elucidation of the pathogenesis of IPF and potential therapeutic targets.

[Successful management of sigmoidectomy with sildenafil citrate in a patient with acute exacerbation of chronic thromboembolic pulmonary hypertension].

An 84-year-old woman with pulmonary hypertension (PH) secondary to chronic pulmonary thromboembolism suffered from continuous warfarin dependent bleeding from sigmoid colon cancer. Sigmoidectomy was scheduled to control continuous bleeding. Six hours after discontinuation of anticoagulant therapy for elective sigmoidectomy, the patient showed hypoxia, pulmonary thromboembolism and pulmonary hypertension with right ventricular systolic pressure (RVSP) of 81 mmHg. The operation was postponed and heparin was infused. Since two-day heparinization therapy did not improve PH, oral administration of sildenafil citrate 60 mg daily was initiated. Seven days after initiation of sildenafil administration, RVSP decreased to 49 mmHg without improvement of hypoxia. Sigmoidectomy was performed under general anesthesia. The patient showed severe hypotension managed with noradrenaline and dopamine infusion during and after surgery, resulting from interaction between sildenafil and vasodilators. The patient was discharged 36 days after the operation without complications.

DruMAP: A Novel Drug Metabolism and Pharmacokinetics Analysis Platform.

We developed a novel drug metabolism and pharmacokinetics (DMPK) analysis platform named DruMAP. This platform consists of a database for DMPK parameters and programs that can predict many DMPK parameters based on the chemical structure of a compound. The DruMAP database includes curated DMPK parameters from public sources and in-house experimental data obtained under standardized conditions; it also stores predicted DMPK parameters produced by our prediction programs. Users can predict several DMPK parameters simultaneously for novel compounds not found in the database. Furthermore, the highly flexible search system enables users to search for compounds as they desire. The current version of DruMAP comprises more than 30,000 chemical compounds, about 40,000 activity values (collected from public databases and in-house data), and about 600,000 predicted values. Our platform provides a simple tool for searching and predicting DMPK parameters and is expected to contribute to the acceleration of new drug development. DruMAP can be freely accessed at: https://drumap.nibiohn.go.jp/.

Latent inter-organ mechanism of idiopathic pulmonary fibrosis unveiled by a generative computational approach.

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive disease characterized by complex lung pathogenesis affecting approximately three million people worldwide. While the molecular and cellular details of the IPF mechanism is emerging, our current understanding is centered around the lung itself. On the other hand, many human diseases are the products of complex multi-organ interactions. Hence, we postulate that a dysfunctional crosstalk of the lung with other organs plays a causative role in the onset, progression and/or complications of IPF. In this study, we employed a generative computational approach to identify such inter-organ mechanism of IPF. This approach found unexpected molecular relatedness of IPF to neoplasm, diabetes, Alzheimer's disease, obesity, atherosclerosis, and arteriosclerosis. Furthermore, as a potential mechanism underlying this relatedness, we uncovered a putative molecular crosstalk system across the lung and the liver. In this inter-organ system, a secreted protein, kininogen 1, from hepatocytes in the liver interacts with its receptor, bradykinin receptor B1 in the lung. This ligand-receptor interaction across the liver and the lung leads to the activation of calmodulin pathways in the lung, leading to the activation of interleukin 6 and phosphoenolpyruvate carboxykinase 1 pathway across these organs. Importantly, we retrospectively identified several pre-clinical and clinical evidence supporting this inter-organ mechanism of IPF. In conclusion, such feedforward and feedback loop system across the lung and the liver provides a unique opportunity for the development of the treatment and/or diagnosis of IPF. Furthermore, the result illustrates a generative computational framework for machine-mediated synthesis of mechanisms that facilitates and complements the traditional experimental approaches in biomedical sciences.

Structural dynamics of the N-terminal SH2 domain of PI3K in its free and CD28-bound states.

Protein conformational changes with fluctuations are fundamental aspects of protein-protein interactions (PPIs); understanding these motions is required for the rational design of PPI-regulating compounds. Src homology 2 (SH2) domains are commonly found in adapter proteins involved in signal transduction and specifically bind to consensus motifs of proteins containing phosphorylated tyrosine (pY). Here, we analysed the interaction between the N-terminal SH2 domain (nSH2) of the regulatory subunit in phosphoinositide 3-kinase (PI3K) and the cytoplasmic region of the T-cell co-receptor, CD28, using NMR and molecular dynamics (MD) simulations. First, we assigned the backbone signals of nSH2 on 1 H-15 N heteronuclear single quantum coherence spectra in the absence or presence of the CD28 phosphopeptide, SDpYMNMTPRRPG. Chemical shift perturbation experiments revealed allosteric changes at the BC loop and the C-terminal region of nSH2 upon CD28 binding. NMR relaxation experiments showed a conformational exchange associated with CD28 binding in these regions. The conformational stabilisation of the C-terminal region correlated with the regulation of PI3K catalytic function. Further, using 19 F- and 31 P-labelled CD28 phosphopeptide, we analysed the structural dynamics of CD28 and demonstrated that the aromatic ring of the pY residue fluctuated between multiple conformations upon nSH2 binding. Our MD simulations largely explained the NMR results and the structural dynamics of nSH2 and CD28 in both bound and unbound states. Notably, in addition to its major conformation, we detected a minor conformation of nSH2 in the CD28 bound state that may explain the allosteric conformational change in the BC loop.

Phosphoenolpyruvic acid, an intermediary metabolite of glycolysis, as a potential cytoprotectant and anti-oxidant in HeLa cells.

This study examined the cytoprotective and anti-oxidative properties of phosphoenolpyruvic acid (PEP), a glycolysis metabolite with a high-energy phosphate group. PEP (0.1-10 mM) significantly attenuated the decrease in cell viability induced by hydrogen peroxide (H(2)O(2)) in HeLa cells in a dose-dependent manner. PEP also inhibited the decrease in calcein-acetomethoxy-stained cells and the increase in propidium iodide-stained cells that were induced by H(2)O(2). The H(2)O(2)-stimulated increase in intracellular reactive oxygen species was significantly reduced by PEP. PEP also demonstrated scavenging potential against hydroxyl radicals, as assessed by the electron paramagnetic resonance method. In addition, PEP demonstrated scavenging potential against the 1,1-diphenyl-2-picrylhydrazyl radical, a representative artificial radical, although the potential is very weak. PEP (10 mM) slightly inhibited the decrease in cellular ATP content induced by H(2)O(2), but did not show any effects at low doses (0.1, 1 mM). PEP (0.1-10 mM) also attenuated the cell injury but not the decrease in intracellular ATP content, induced by 2-deoxy-D-glucose, a glycolysis inhibitor. These results indicate that PEP exerts cytoprotective effects and has anti-oxidative potential, although the precise cytoprotective mechanisms are not fully elucidated. We suggest that PEP is a functional carbohydrate metabolite with cytoprotective and anti-oxidative activity, and is potentially useful as a therapeutic agent against diseases that involve the oxidative stress.

Structure-Activity Relationships of Anti-microRNA Oligonucleotides Containing Cationic Guanidine-Modified Nucleic Acids.

Anti-microRNA oligonucleotides (AMOs) are valuable tools for the treatment of diseases caused by the dysregulation of microRNA expression. However, the correlation between chemical modifications in AMO sequences and the microRNA-inhibitory activity has not been fully elucidated. In this study, we synthesized a series of AMOs containing cationic guanidine-bridged nucleic acids (GuNA) and evaluated their activities using a dual luciferase assay. We also optimized the site of GuNA substitution and found an effective design for the inhibition of microRNA-21, which was partially different from that of conventional nucleic acid derivatives. This study showed that GuNA-substituted AMOs are effective in inhibiting the function of microRNA.

Utilizing public and private sector data to build better machine learning models for the prediction of pharmacokinetic parameters.

One solution to compensate for the shortage of publicly available data is to collect more quality-controlled data from the private sector through public-private partnerships. However, several issues must be resolved before implementing such a system. Here, we review the technical aspects of public-private partnerships using our initiative in Japan as an example. In particular, we focus on the procedure for collecting data from multiple private sector companies and building prediction models and discuss how merging public and private sector datasets will help to improve the chemical space coverage and prediction performance. Teaser: Japan's first public-private consortium in pharmacokinetics has incorporated data from multiple pharmaceutical companies to create useful predictive models.

Association between cerebrovascular carbon dioxide reactivity and postoperative short-term and long-term cognitive dysfunction in patients with diabetes mellitus.

PURPOSE: Our intent was to identify whether cerebrovascular CO(2) reactivity in diabetic patients is a risk factor for postoperative cognitive dysfunction after coronary artery bypass graft (CABG) surgery. METHODS: One hundred twenty-four diabetic patients undergoing elective CABG were studied and analyzed. Diabetic patients were divided into three groups: normal CO(2) reactivity group (above 5%/mmHg), medium CO(2) reactivity group (between 5 and 3%/mmHg), or impaired CO(2) reactivity group (below 3%/mmHg). After the induction of anesthesia and before the start of surgery, cerebrovascular CO(2) reactivity was measured for all patients. Hemodynamic parameters (arterial and jugular venous blood gas values) were measured during cardiopulmonary bypass. All patients underwent a battery of neurological and neuropsychological tests the day before surgery, 7 days after surgery, and 6 months after surgery. RESULTS: At 7 days, the rate of cognitive dysfunction in the impaired CO(2) group was higher than in the other three groups (normal, 30%; medium, 25%; impaired, 57%; *P < 0.01 compared with the other groups). In contrast, at 6 months postoperatively, no significant difference in the rate of cognitive dysfunction was found among the three groups. Age, hypertension, CO(2) reactivity, the duration for which jugular venous oxygen saturation (SjvO(2)) was less than 50%, ascending aorta atherosclerosis, diabetic retinopathy, and insulin therapy were independent predictors of short-term cognitive dysfunction in diabetic patients, and HbA1c, diabetic retinopathy, and insulin therapy were independent predictors of long-term cognitive dysfunction in diabetic patients. CONCLUSIONS: We found that impaired cerebrovascular CO(2) reactivity was associated with postoperative short-term cognitive dysfunction in diabetic patients.

Preoperative depression is a risk factor for postoperative short-term and long-term cognitive dysfunction in patients with diabetes mellitus.

PURPOSE: To identify whether the presence of preoperative depression in patients with diabetes mellitus is a risk factor for postoperative cognitive dysfunction after coronary artery bypass graft (CABG) surgery. METHODS: Data from 90 patients with diabetes mellitus undergoing elective CABG were analyzed. Hemodynamic data (arterial and jugular venous blood gas values) were measured during cardiopulmonary bypass. Preoperatively, all patients were given the 21-item Beck depression inventory to identify the presence of depression. In addition, all patients underwent a battery of neurological and neuropsychological tests the day before surgery, 7 days after surgery, and 6 months after surgery. RESULTS: The rate of cognitive dysfunction was 50% at 7 days and 23% at 6 months after surgery. Age, hypertension, presence of depression, duration of SjvO(2) ≤ 50%, ascending aorta atherosclerosis, diabetic retinopathy, and insulin therapy were independent predictors of short-term cognitive dysfunction, whereas HbA1c, diabetic retinopathy, insulin therapy, and presence of depression were independent predictors of long-term cognitive dysfunction. CONCLUSIONS: We found that the presence of depression preoperatively is associated with short-term and long-term postoperative cognitive dysfunction in patients with diabetes mellitus.

[Coronary artery spasm immediately after insertion of a laryngeal mask airway during induction of general anesthesia].

We describe the case of a 73-year-old woman scheduled for tendon sheath release for carpal tunnel syndrome under general anesthesia. Preoperatively, she had hypertension and complete right bundle branch block with normal left ventricular function. During general anesthetic induction, immediately after insertion of the laryngeal mask airway, her electrocardiogram (ECG) showed remarkable ST segment elevation followed by complete atrio-ventricular block. Transcutaneous cardiac pacing was immediately started and nitroglycerin was administered. Nine minutes after starting cardiac pacing, the level of the ST segment and heart rate returned to baseline. The surgical procedure was postponed and the patient was admitted to the coronary care unit. Thereafter, her ECG remained normal. Coronary artery spasm was suspected due to the transient nature of the cardiac symptoms, although the cause of the spasm was not clear. Coronary artery spasm can occur even in patients with relatively low cardiovascular risks. Hence, it is essential to be vigilant about all kinds of circulatory changes, including ECG changes, and to be prepared with the drugs and devices required to deal with sudden untoward cardiac events.