Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides.

Naturally occurring peptides with high membrane permeability often have ester bonds on their backbones. However, the impact of amide-to-ester substitutions on the membrane permeability of peptides has not been directly evaluated. Here we report the effect of amide-to-ester substitutions on the membrane permeability and conformational ensemble of cyclic peptides related to membrane permeation. Amide-to-ester substitutions are shown to improve the membrane permeability of dipeptides and a model cyclic hexapeptide. NMR-based conformational analysis and enhanced sampling molecular dynamics simulations suggest that the conformational transition of the cyclic hexapeptide upon membrane permeation is differently influenced by an amide-to-ester substitution and an amide N-methylation. The effect of amide-to-ester substitution on membrane permeability of other cyclic hexapeptides, cyclic octapeptides, and a cyclic nonapeptide is also investigated to examine the scope of the substitution. Appropriate utilization of amide-to-ester substitution based on our results will facilitate the development of membrane-permeable peptides.

CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides.

Recently, cyclic peptides have been considered breakthrough drugs because they can interact with "undruggable" targets such as intracellular protein-protein interactions. Membrane permeability is an essential indicator of oral bioavailability and intracellular targeting, and the development of membrane-permeable peptides is a bottleneck in cyclic peptide drug discovery. Although many experimental data on membrane permeability of cyclic peptides have been reported, a comprehensive database is not yet available. A comprehensive membrane permeability database is essential for developing computational methods for cyclic peptide drug design. In this study, we constructed CycPeptMPDB, the first web-accessible database of cyclic peptide membrane permeability. We collected information on a total of 7334 cyclic peptides, including the structure and experimentally measured membrane permeability, from 45 published papers and 2 patents from pharmaceutical companies. To unambiguously represent cyclic peptides larger than small molecules, we used the hierarchical editing language for macromolecules notation to generate a uniform sequence representation of peptides. In addition to data storage, CycPeptMPDB provides several supporting functions such as online data visualization, data analysis, and downloading. CycPeptMPDB is expected to be a valuable platform to support membrane permeability research on cyclic peptides. CycPeptMPDB can be freely accessed at http://cycpeptmpdb.com.

Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations.

Cyclic peptides have attracted attention as a promising pharmaceutical modality due to their potential to selectively inhibit previously undruggable targets, such as intracellular protein-protein interactions. Poor membrane permeability is the biggest bottleneck hindering successful drug discovery based on cyclic peptides. Therefore, the development of computational methods that can predict membrane permeability and support elucidation of the membrane permeation mechanism of drug candidate peptides is much sought after. In this study, we developed a protocol to simulate the behavior in membrane permeation steps and estimate the membrane permeability of large cyclic peptides with more than or equal to 10 residues. This protocol requires the use of a more realistic membrane model than a single-lipid phospholipid bilayer. To select a membrane model, we first analyzed the effect of cholesterol concentration in the model membrane on the potential of mean force and hydrogen bonding networks along the direction perpendicular to the membrane surface as predicted by molecular dynamics simulations using cyclosporine A. These results suggest that a membrane model with 40 or 50 mol % cholesterol was suitable for predicting the permeation process. Subsequently, two types of membrane models containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 40 and 50 mol % cholesterol were used. To validate the efficiency of our protocol, the membrane permeability of 18 ten-residue peptides was predicted. Correlation coefficients of R > 0.8 between the experimental and calculated permeability values were obtained with both model membranes. The results of this study demonstrate that the lipid membrane is not just a medium but also among the main factors determining the membrane permeability of molecules. The computational protocol proposed in this study and the findings obtained on the effect of membrane model composition will contribute to building a schematic view of the membrane permeation process. Furthermore, the results of this study will eventually aid the elucidation of design rules for peptide drugs with high membrane permeability.

Clinical characteristics of adult T-cell leukemia/lymphoma infiltration in the gastrointestinal tract.

BACKGROUND: Adult T-cell leukemia/lymphoma (ATLL) is a peripheral T-cell malignancy caused by human T-cell leukemia virus type 1. The clinical course of ATLL is very heterogeneous, and many organs, including the gastrointestinal (GI) tract, can be involved. However, there are few detailed reports on ATLL infiltration in the GI tract. We investigated the clinical characteristics of ATLL infiltration in the GI tract. METHODS: This retrospective observational single-center study included 40 consecutive ATLL patients who underwent GI endoscopy. The patients' demographic and clinical characteristics and endoscopic findings were analyzed retrospectively. Patients with ATLL who were diagnosed by histological examination were divided into two groups based on GI tract infiltration. RESULTS: Multivariate analysis revealed that the absence of skin lesions was significantly associated with GI infiltration (P < 0.05). Furthermore, the infiltration group tended to have similar macroscopic lesions in the upper and lower GI tracts, such as diffuse type, tumor-forming type, and giant-fold type. CONCLUSIONS: GI endoscopy may be considered for ATLL patients without skin lesions.

[A Case of Neuroendcrine Carcinoma of the Prostate Diagnosed by Prostate Re-Biopsy during Hormonal Treatment and Effectively Treated by Multidisciplinary Therapy].

A 73-year-old Japanese man visited the urology clinic with the chief complaint of gross hematuria in June 2015. His prostate specific antigen (PSA) level was 146.7 ng/ml and he was diagnosed with prostate adenocarcinoma with a Gleason Score of 5+4. With bone metastasis in the right femur (cT3aN0M1), he was treated by orchiectomy and bicalutamide. He had gross hematuria in October 2017 and a prostate tumor was detected by computed tomography (CT) and magnetic resonance imaging without increasing PSA levels. Prostate re-biopsy showed prostate neuroendocrine carcinoma and local radiation therapy (74 Gy) was performed. Follow-up CT revealed a left adrenal tumor with a positive positron emission tomographic scan in October 2018. Under the diagnosis of metastatic neuroendocrine carcinoma, chemotherapy using cisplatinum and etoposide was performed. The tumor shrunk after five courses of treatment, followed by regrowth in April 2019. Radiation therapy (50 Gy) was added to the left adrenal tumor and it shrunk again. However, a left retroperitoneal tumor was detected in July 2019 and it was resected under laparoscopic surgery and diagnosed as metastatic neuroendocrine carcinoma. Since then, no recurrence has been observed.

A rare association between true thymic hyperplasia and thyroid follicular tumor: a case report.

BACKGROUND: True thymic hyperplasia is a rare condition characterized by enlargement of the thymus while its normal structure is retained. True thymic hyperplasia is known to accompany Graves' disease, but no association between true thymic hyperplasia and thyroid follicular tumor has been reported so far. We report a case of true thymic hyperplasia in a patient with a thyroid follicular tumor. CASE PRESENTATION: A 52-year-old Japanese man was referred to our hospital for evaluation of a thyroid mass and a mediastinal mass. His serum thyroglobulin level was high, and hemithyroidectomy was performed to remove the thyroid mass. The resected mass was diagnosed as a follicular tumor of uncertain malignant potential. After resection of the thyroid lesion, the patient's serum thyroglobulin levels were markedly decreased. Seven months later, the patient underwent resection of the mediastinal mass. On pathological examination, the mass was found to consist of lobules, which formed a corticomedullary structure with Hassall's bodies, indicating a normal thymic mass with hyperplastic thymic tissue, less organized cellular cords, and intermingled adipose tissue. Immunostaining for cytokeratin 19 and cytokeratin 7 indicated that the lesion was consistent with thymic tissue. The lesion was diagnosed as true thymic hyperplasia, and the histological findings suggested that secondary atrophy had occurred. No evidence of recurrence was observed at 24 months after surgery. CONCLUSIONS: We present a case of a combination of true thymic hyperplasia and thyroidal follicular tumors that, to our knowledge, has not been reported previously. High serum thyroglobulin levels might play a role in hyperplasia of the thymus. Although true thymic hyperplasia is a rare disorder, it should be included in the differential diagnosis of a mediastinal mass in patients with thyroid disease.

A case of carcinoma ex pleomorphic adenoma arising from multinodular pleomorphic adenoma of the buccal region.

In multinodular lesions or tumors with mixed benign and malignant components, malignant elements may be undetectable using fine-needle aspiration biopsy/cytology in preoperative pathological diagnosis of some cases, because of sampling error.

Malignant mesothelioma with squamous differentiation.

AIMS: We report the autopsy findings of a 58-year-old man with malignant mesothelioma in the left pleural cavity. METHODS AND RESULTS: The patient had a history of asbestos exposure, and the chest computed tomography scan on initial admission demonstrated an extrapleural sign, suggesting a nodular lesion in the chest wall. However, no nodular lesions were detectable in either of his lungs. In spite of chemotherapy, he died 4 months after the initial admission. An autopsy revealed markedly thickened pleura in a large section of the left pleural cavity without visible intrapulmonary primary tumour lesions. Histological examination of a biopsy specimen obtained prior to chemotherapy and that of an autopsy specimen showed that the pleural tumour was composed of a mixture of mesothelioma and tumour cells with squamous differentiation mimicking squamous cell carcinoma. CONCLUSIONS: To the best of our knowledge, this is the first case report of mesothelioma with extensive squamous differentiation in the English-language literature. The extensive squamous differentiation reminiscent of squamous cell carcinoma can be a pitfall in the pathological diagnosis of pleural cytology and that of biopsy specimens from patients with mesothelioma. Here, we report autopsy findings of a case of malignant mesothelioma with portions of extensive squamous differentiation, mimicking a squamous cell carcinoma.

Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques.

c-Yes kinase is considered as one of the attractive targets for anti-cancer drug design. The DFG (Asp-Phe-Gly) motif present in most of the kinases will adopt active and inactive conformations, known as DFG-in and DFG-out and their inhibitors are classified into type I and type II, respectively. In the present study, two screening protocols were followed for identification of c-Yes kinase inhibitors. (i) Structure-based virtual screening (SBVS) and (ii) Structure-based (SB) and Pharmacophore-based (PB) tandem screening. In SBVS, the c-Yes kinase structure was obtained from homology modeling and seven ensembles with different active site scaffolds through molecular dynamics (MD) simulations. For SB-PB tandem screening, we modeled ligand bound active and inactive conformations. Physicochemical properties of inhibitors of Src kinase family and c-Yes kinase were used to prepare target focused libraries for screenings. Our screening procedure along with docking showed 520 probable hits in SBVS and tandem screening (120 and 400, respectively). Out of 5000 compounds identified from different computational methods, 2410 were examined using kinase inhibition assays. It includes 266 compounds (5.32%) identified from our method. We observed that 14 compounds (12%) are identified by the present method out of 168 that showed > 30% inhibition. Among them, three compounds are novel, unique, and showed good inhibition. Further, we have studied the binding of these compounds at the DFG-in and DFG-out conformations and reported the probable class (type I or type II). Hence, we suggest that these compounds could be novel drug leads for regulation of colorectal cancer.

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes.

We propose a new iterative screening contest method to identify target protein inhibitors. After conducting a compound screening contest in 2014, we report results acquired from a contest held in 2015 in this study. Our aims were to identify target enzyme inhibitors and to benchmark a variety of computer-aided drug discovery methods under identical experimental conditions. In both contests, we employed the tyrosine-protein kinase Yes as an example target protein. Participating groups virtually screened possible inhibitors from a library containing 2.4 million compounds. Compounds were ranked based on functional scores obtained using their respective methods, and the top 181 compounds from each group were selected. Our results from the 2015 contest show an improved hit rate when compared to results from the 2014 contest. In addition, we have successfully identified a statistically-warranted method for identifying target inhibitors. Quantitative analysis of the most successful method gave additional insights into important characteristics of the method used.

Thoracoscopic enucleation in the left decubitus position for leiomyoma of the upper thoracic esophagus: Utility of preoperative diagnosis applying endoscopic ultrasound-guided fine needle aspiration.

INTRODUCTION: We report a relatively rare case of esophageal leiomyoma in the upper thoracic esophagus enucleated by thoracoscopic procedures. The usefulness of preoperative diagnosis and an adequate surgical approach are described along with a review of the relevant literature. PRESENTAION OF CASE: A submucosal tumor 45mm in diameter was detected in the upper thoracic esophagus of a 69-year-old man. The tumor was preoperatively diagnosed from histopathological biopsy under endoscopic ultrasound-guided fine needle aspiration. Thoracoscopic enucleation was therefore preoperatively scheduled under the left decubitus position in consideration of the low risk of malignant disease. Histopathological diagnosis of the resected specimen was benign leiomyoma and patient outcomes were good. DISCUSSION: The need for preoperative biopsy of esophageal submucosal tumor is a controversial issue. However, preoperative biopsy provided the benefits to decide the operative procedure or confirm adequate resection, and our experience suggested that preoperative biopsy did not adversely influence subsequent enucleation. CONCLUSION: Precise preoperative diagnosis is necessary to avoid excessive surgery when managing esophageal submucosal tumor.

Myopericytoma in urinary bladder: a case report.

BACKGROUND: Myopericytoma is reported to occur mainly in the skin and superficial soft tissue of the extremities. In contrast, occurrence in the urinary bladder is extremely rare. CASE PRESENTATION: We describe a 75-year-old Japanese man who developed a submucosal tumor at the right trigone of his bladder that led to interference with the discharge of right ureteral calculus. No invasive growth was observed by magnetic resonance imaging. Transurethral resection was successfully performed; histopathological analysis revealed perivascular proliferation of spindle-shaped to oval-shaped, cytologically bland tumor cells with eosinophilic cytoplasm. On immunohistochemical examination, the tumor cells were positive for alpha-smooth muscle actin, desmin, CD34 and h-caldesmon. CONCLUSION: Cystoscopic and pathological findings were compatible with a diagnosis of myopericytoma of the urinary bladder.

Development of a Support Vector Machine-Based System to Predict Whether a Compound Is a Substrate of a Given Drug Transporter Using Its Chemical Structure.

The aim of this study was to develop an in silico prediction system to assess which of 7 categories of drug transporters (organic anion transporting polypeptide [OATP] 1B1/1B3, multidrug resistance-associated protein [MRP] 2/3/4, organic anion transporter [OAT] 1, OAT3, organic cation transporter [OCT] 1/2/multidrug and toxin extrusion [MATE] 1/2-K, multidrug resistance protein 1 [MDR1], and breast cancer resistance protein [BCRP]) can recognize compounds as substrates using its chemical structure alone. We compiled an internal data set consisting of 260 compounds that are substrates for at least 1 of the 7 categories of drug transporters. Four physicochemical parameters (charge, molecular weight, lipophilicity, and plasma unbound fraction) of each compound were used as the basic descriptors. Furthermore, a greedy algorithm was used to select 3 additional physicochemical descriptors from 731 available descriptors. In addition, transporter nonsubstrates tend not to be in the public domain; we, thus, tried to compile an expert-curated data set of putative nonsubstrates for each transporter using personal opinions of 11 researchers in the field of drug transporters. The best prediction was finally achieved by a support vector machine based on 4 basic and 3 additional descriptors. The model correctly judged that 364 of 412 compounds (internal data set) and 111 of 136 compounds (external data set) were substrates, indicating that this model performs well enough to predict the specificity of transporter substrates.

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target.

A search of broader range of chemical space is important for drug discovery. Different methods of computer-aided drug discovery (CADD) are known to propose compounds in different chemical spaces as hit molecules for the same target protein. This study aimed at using multiple CADD methods through open innovation to achieve a level of hit molecule diversity that is not achievable with any particular single method. We held a compound proposal contest, in which multiple research groups participated and predicted inhibitors of tyrosine-protein kinase Yes. This showed whether collective knowledge based on individual approaches helped to obtain hit compounds from a broad range of chemical space and whether the contest-based approach was effective.

In silico prediction of major drug clearance pathways by support vector machines with feature-selected descriptors.

We have previously established an in silico classification method ("CPathPred") to predict the major clearance pathways of drugs based on an empirical decision with only four physicochemical descriptors-charge, molecular weight, octanol-water distribution coefficient, and protein unbound fraction in plasma-using a rectangular method. In this study, we attempted to improve the prediction performance of the method by introducing a support vector machine (SVM) and increasing the number of descriptors. The data set consisted of 141 approved drugs whose major clearance pathways were classified into metabolism by CYP3A4, CYP2C9, or CYP2D6; organic anion transporting polypeptide-mediated hepatic uptake; or renal excretion. With the same four default descriptors as used in CPathPred, the SVM-based predictor (named "default descriptor SVM") resulted in higher prediction performance compared with a rectangular-based predictor judged by 10-fold cross-validation. Two SVM-based predictors were also established by adding some descriptors as follows: 1) 881 descriptors predicted in silico from the chemical structures of drugs in addition to 4 default descriptors ("885 descriptor SVM"); and 2) selected descriptors extracted by a feature selection based on a greedy algorithm with default descriptors ("feature selection SVM"). The prediction accuracies of the rectangular-based predictor, default descriptor SVM, 885 descriptor SVM, and feature selection SVM were 0.49, 0.60, 0.72, and 0.91, respectively, and the overall precision values for these four methods were 0.72, 0.77, 0.86, and 0.98, respectively. In conclusion, we successfully constructed SVM-based predictors with limited numbers of descriptors to classify the major clearance pathways of drugs in humans with high prediction performance.

[A case report of gastrointestinal stromal tumor of the small intestine presenting with liver abscesses caused by Streptococcus constellatus].

A 49-year-old woman visited a local hospital in October 2007 with complaint of fever and melena. Abdominal ultrasonography and abdominal computed tomography revealed an irregular mass in the lower abdomen, together with multiple masses in the liver. She was admitted because of anemia, and the high fever was determined to be an inflammatory response. Blood tests revealed elevated biliary enzyme levels. Percutaneous biopsy of the liver mass was performed, which revealed liver abscesses caused by Streptococcus constellatus. On abdominal angiography, the mass was suspected to be a tumor of the small intestine. In late November 2007, laparoscopy-assisted partial small bowel resection was performed, and pathological examination of the surgical specimen confirmed gastrointestinal stromal tumor (GIST) of the small bowel. Because reports of small intestinal GIST with liver abscesses caused by Streptococcus constellatus are rare, this case description could provide valuable information.

Printed silver nanowire antennas with low signal loss at high-frequency radio.

Silver nanowires are printable and conductive, and are believed to be promising materials in the field of printed electronics. However, the resistivity of silver nanowire printed lines is higher than that of metallic particles or flakes even when sintered at high temperatures of 100-400 °C. Therefore, their applications have been limited to the replacement of transparent electrodes made from high-resistivity materials, such as doped metallic oxides, conductive polymers, carbon nanotubes, or graphenes. Here we report that using printed silver nanowire lines, signal losses obtained in the high-frequency radio were lower than those obtained using etched copper foil antennas, because their surfaces were much smoother than those of etched copper foil antennas. This was the case even though the resistivity of silver nanowire lines was 43-71 µΩ cm, which is much higher than that of etched copper foil (2 µΩ cm). When printed silver nanowire antennas were heated at 100 °C, they achieved signal losses that were much lower than those of silver paste antennas comprising microparticles, nanoparticles, and flakes. Furthermore, using a low temperature process, we succeeded in remotely controlling a commercialized radio-controlled car by transmitting a 2.45 GHz signal via a silver nanowire antenna printed on a polyethylene terephthalate film.

Late recurrence of malignant melanoma in the duodenum.

Melanoma is a malignancy originating from melanocytes. The primary melanoma usually occurs on the skin, retina, anal canal or occasionally at other organs such as the esophagus, penis or vagina. Although melanoma represents about one-third of all metastatic lesions in the gastrointestinal tract, metastasis of melanoma to the GI tract, detected radiologically or endoscopically, is relatively rare. In most cases of malignant melanoma, recurrence and death occur within 10 years after treatment of the primary lesion. We herein report a case showing a recurrence 17 years after extirpation of primary malignant melanoma in the foot. A 65-year-old man, with a history of extirpation of a malignant melanoma in the sole of his foot 17 years before, presented with anorexia and severe anemia, and multiple duodenal tumors were pointed out with upper gastrointestinal endoscopy. Histologic examination of the endoscopic biopsy specimen revealed proliferation of large polygonal cells with distinct nucleoli, and malignant melanoma was diagnosed immunohistochemically. Further examination, including computed tomography and positron emission tomography with fluorodeoxyglucose, revealed systemic metastasis.

Two-stage operation for hepatocellular carcinoma with synchronous bilateral adrenal gland metastasis.

Hepatocellular carcinoma (HCC) frequently metastasizes to the adrenal glands. The surgical strategy for HCC associated with bilateral adrenal gland metastasis is complicated because of the possibility of both postoperative hepatic failure and adrenal insufficiency. We herein report a patient with HCC with synchronous bilateral adrenal gland metastasis that was treated successfully with a two-stage operation. A 58-year-old man with HCC (12 cm in diameter) in the right lobe of the liver and bilateral adrenal gland tumors (right, 4 cm in diameter; left, 5 cm in diameter) was admitted to our hospital. Extended right hemihepatectomy and right adrenalectomy were performed simultaneously. The postoperative course was uneventful. Three months after this operation, left adrenalectomy was performed via a retroperitoneal approach. Hydrocortisone supplement was given, and the postoperative course was again uneventful. No recurrence was observed during the 10-month follow-up period. Two-stage surgery is a safe treatment option for giant HCC with synchronous bilateral adrenal gland metastasis.

Intrapancreatic accessory spleen mimicking endocrine tumor of the pancreas: case report and review of the literature.

Accessory spleen is an anomaly that is observed in about 10% of individuals by the autopsy study, and most accessory spleens are located close to the splenic hilum. Although accessory spleen is a frequently encountered entity, intrapancreatic accessory spleen (IPAS) is rarely recognized radiologically and is sometimes mistaken for another type of pancreatic neoplasm. Only 10 IPAS cases surgically resected as solid pancreatic mass have been reported in the English literature. We herein report a case of IPAS mimicking an endocrine tumor of the pancreas and review of the literature.