Chromatographic Determination of Permeability-Relevant Lipophilicity Facilitates Rapid Analysis of Macrocyclic Peptide Scaffolds.

Hydrocarbon-determined shake-flask measurements have demonstrated great utility for optimizing lipophilicity during early drug discovery. Alternatively, chromatographic methods confer reduced experimental error and improved handling of complex mixtures. In this study, we developed a chromatographic approach for estimating hydrocarbon-water shake-flask partition coefficients for a variety of macrocyclic peptides and other bRo5 molecules including PROTACs. The model accurately predicts experimental shake-flask measurements with high reproducibility across a wide range of lipophilicities. The chromatographic retention times revealed subtle conformational effects and correlated with the ability to sequester hydrogen bond donors in low dielectric media. Estimations of shake-flask lipophilicity from our model also accurately predicted trends in MDCK passive cell permeability for a variety of thioether-cyclized decapeptides. This method provides a convenient, high-throughput approach for measuring lipophilic permeability efficiency and predicting passive cell permeability in bRo5 compounds that is suitable for multiplexing pure compounds or investigating the properties of complex library mixtures.

Optimization of α-amido boronic acids via cryo-electron microscopy analysis: Discovery of a novel highly selective immunoproteasome subunit LMP7 (ß5i)/LMP2 (ß1i) dual inhibitor.

The immunoproteasome subunit LMP7 (ß5i)/LMP2 (ß1i) dual blockade has been reported to suppress B cell differentiation and activation, suggesting that the dual inhibition of LMP7/LMP2 is a promising approach for treating autoimmune diseases. In contrast, the inhibition of the constitutive proteasome subunit ß5c correlates with cytotoxicity against non-immune cells. Therefore, LMP7/LMP2 dual inhibitors with high selectivity over ß5c may be desirable for treating autoimmune diseases. In this study, we present the optimization and discovery of α-amido boronic acids using cryo-electron microscopy (cryo-EM). The exploitation of structural differences between the proteasome subunits led to the identification of a highly selective LMP7/LMP2 dual inhibitor 19. Molecular dynamics simulation based on cryo-EM structures of the proteasome subunits complexed with 19 explained the inhibitory activity profile. In mice immunized with 4-hydroxy-3-nitrophenylacetyl conjugated to ovalbumin, results indicate that 19 is orally bioavailable and shows promise as potential treatment for autoimmune diseases.

Red dichromatic imaging and linked color imaging as reliable image-enhanced endoscopic procedures for detecting the distal end of the palisade vessels in the columnar metaplastic mucosa of the gastroesophageal junction zone.

BACKGROUND: There is a consensus that identifying the distal end of the palisade vessels (DEPV) is important for diagnosing gastroesophageal junction (GEJ). However, optimum observation methods have not been established. This study investigated the use of effective image-enhanced endoscopy (IEE) for DEPV detection. METHODS: One hundred endoscopic images in 20 cases of columnar metaplastic mucosa of the GEJ recorded with white-light imaging (Olympus-WLI and Fujifilm-WLI) and IEEs (narrow-band imaging; RDI1/2/3, red dichromatic imaging; texture and color enhancement imaging 1/2; blue-laser imaging; and LCI, linked color imaging) from two manufacturers were extracted and evaluated by 10 evaluators. Up to 24 radial straight lines from the center of the lumen were placed on the image, and the evaluators placed markings according to confidence level (high, low, and not detectable) at the DEPV locations. The detectability and reproducibility at the rate of the confidence level and coefficient of variance of markings among the evaluator were analyzed. RESULTS: In total, 15,180 markings were obtained. In terms of detectability, RDI1 (49.4%), RDI2 (53.0%), RDI3 (54.1%), TXI2 (49.7%), and LCI (34.6%) had a significantly higher rate of high confidence among the IEEs in each manufacturer. By contrast, Olympus-WLI (40.6%), Fujifilm-WLI (17.6%), narrow-band imaging (15.9%), and blue laser imaging (9.8%) presented with a significantly lower rates of high confidence. Regarding reproducibility, RDI3 and LCI had the lowest coefficient of variance for each manufacturer. CONCLUSIONS: RDI and LCI could be reliable modalities for detecting DEPVs in the columnar metaplastic mucosa of the GEJ zone.

Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation.

The effort to modulate challenging protein targets has stimulated interest in ligands that are larger and more complex than typical small-molecule drugs. While combinatorial techniques such as mRNA display routinely produce high-affinity macrocyclic peptides against classically undruggable targets, poor membrane permeability has limited their use toward primarily extracellular targets. Understanding the passive membrane permeability of macrocyclic peptides would, in principle, improve our ability to design libraries whose leads can be more readily optimized against intracellular targets. Here, we investigate the permeabilities of over 200 macrocyclic 10-mers using the thioether cyclization motif commonly found in mRNA display macrocycle libraries. We identified the optimal lipophilicity range for achieving permeability in thioether-cyclized 10-mer cyclic peptide-peptoid hybrid scaffolds and showed that permeability could be maintained upon extensive permutation in the backbone. In one case, changing a single amino acid from d-Pro to d-NMe-Ala, representing the loss of a single methylene group in the side chain, resulted in a highly permeable scaffold in which the low-dielectric conformation shifted from the canonical cross-beta geometry of the parent compounds into a novel saddle-shaped fold in which all four backbone NH groups were sequestered from the solvent. This work provides an example by which pre-existing physicochemical knowledge of a scaffold can benefit the design of macrocyclic peptide mRNA display libraries, pointing toward an approach for biasing libraries toward permeability by design. Moreover, the compounds described herein are a further demonstration that geometrically diverse, highly permeable scaffolds exist well beyond conventional drug-like chemical space.

Squamous Neoplastic Precursor Lesions of the Esophagus.

Clinicopathological and molecular studies have demonstrated that dysplasia is a precancerous and/or neoplastic lesion with malignant potential. Further, it is subclassified into two grades: high-grade and low-grade dysplasia. High-grade dysplasia is a clinically significant lesion requiring resection or ablation. Low-grade dysplasia has a much lower risk of carcinoma; thus, it should be followed by endoscopic surveillance. Because squamous dysplasia may progress to squamous cell carcinoma, periodic endoscopy is useful to detect the lesion in patients with risk factors. Squamous dysplasia is diagnosed histopathologically by evaluating both cytologic and structural changes.

An incidentally discovered paraganglioma that caused sinus arrest after resection.

Paragangliomas are neural-crest-derived nonepithelial neuroendocrine tumors distributed along the parasympathetic and sympathetic nerves. To our knowledge, no studies were reported regarding sinus arrest on day 4 after paraganglioma resection. A 66-year-old female patient with a history of pulmonary vein isolation visited our department for sigmoid colon cancer treatment. Enhanced computed tomography revealed an enhanced small nodule-like lymph node near the root of the inferior mesenteric artery. The patient underwent laparoscopic colectomy with regional lymph node dissection. Postoperatively, paroxysmal atrial fibrillation attacks developed, and the patient resumed oral medication. Additionally, sinus arrest after tachycardia developed. Changing the oral medication could maintain her circulatory dynamics. Pathological examination revealed that differentiated tubular adenocarcinoma infiltrated the submucosa. Immunohistochemically, the excised nodule as a lymph node was considered a functional paraganglioma. Our case indicates that paraganglioma resection and oral medication resumption may contribute to sinus arrest. When arrhythmias affecting the circulation occur perioperatively, the presence of a catecholamine-producing tumor should be considered in addition to cardiac disease. J. Med. Invest. 70 : 503-507, August, 2023.

A case report of contrast-enhanced harmonic ultrasonography for the diagnosis of an esophageal duplication cyst.

A 54-year-old man was referred to our hospital because of a suspected esophageal submucosal tumor on upper gastrointestinal radiography. Contrast-enhanced computed tomography showed a 52 mm homogeneous mass attached to the lower thoracic esophagus. Esophagogastroduodenoscopy revealed a 50 mm submucosal tumor in the lower esophagus, and endoscopic ultrasonography (EUS) showed a continuous hypoechoic lesion in the esophageal muscularis propria. Contrast-enhanced harmonic EUS revealed a non-echogenic area. T1 and T2 magnetic resonance imaging revealed a high-signal lesion. Based on imaging studies, an esophageal duplication cyst was diagnosed. Although asymptomatic, the patient underwent video-assisted thoracic surgery because of the possibility of rupture and the appearance of symptoms due to a future infection or enlargement, although this was not noted before. In our case, the esophageal duplication cyst appeared as a hypoechoic mass, requiring differentiation from submucosal tumor other than the cyst. Histologically, the cyst was covered by two layers of muscle covered by the chorioepithelial columnar epithelium. EUS fine-needle aspiration is effective in diagnosing submucosal tumor but also carries the risk of infection. Contrast-enhanced ultrasonography was used in this case to observe the interior and reach a preoperative diagnosis. Contrast-enhanced harmonic EUS appears to be effective in examining the interior of submucosal tumor lesions noninvasively.

Electrosurgical knife with the water-jet function of tip-type during endoscopic treatment injection.

Objectives: This study aimed to objectively evaluate the water-jet-functioned electrosurgical knife injection performances in a desktop experiment. Methods: Five types of water-jet-functioned electrosurgical knives, including two injection styles of sheath-type (A: DualKnife J, KD-655L; B: FlushKnife, DK2620-J-B20S; C: Splash M-Knife, DN-D2718B; D: ISSEN, SN1650-20) and tip-type (E: ORISE ProKnife, M00519361) were evaluated. These knives were compared with an injection needle (Control: SuperGrip 25G) as a control. The injection speed under constant pressure and the injection efficiency for each knife against prepared porcine stomach mucosa were evaluated. The additional clear gel injections using an injection needle were observed using an indigo blue-colored gel to evaluate the difference between the locations of water-jet holes. Results: Four types of knives, except for A, showed significantly higher water-jet speeds (A: 0.79 ± 0.03 g/20 s, B: 2.56 ± 0.05 g/20 s, C: 3.09 ± 0.06 g/20 s, D: 2.86 ± 0.05 g/20 s, and E: 1.79 ± 0.03 g/20 s) compared to that of the control (1.21 ± 0.03 g/20 s). Meanwhile, significantly higher efficacy of injection was found in the tip-type water-jet function knife, second to the injection needle (Control: 37.2% ± 35.5%, A: 20.9% ± 20.2%, B: 1.1% ± 2.2%, C: 6.2% ± 12.6%, D: 12.5% ± 15.6%, and E: 33.3% ± 32.2%). An additional injection experiment revealed that the injection with a piercing tip into the gel could achieve sufficient additional injection inside the stacked clear gel. Conclusions: The tip-type water-jet function electrosurgical knife is preferable for effective submucosal injection during endoscopic treatments.

Mouth-Opener Technique for Ultrasound-Guided Inferior Alveolar Nerve Block: A Case Series of Extraction of Impacted Mandibular Third Molars.

Extraction of the impacted mandibular third molar (IMTM) is common in oral surgery, but its postoperative pain is severe. Ultrasound-guided inferior alveolar nerve block (UGIANB) is an analgesic technique in the mandibular nerve region. We describe UGIANB using a mouth opener and report the cases with a good postoperative course. Six patients underwent the extraction of bilateral IMTMs under general anesthesia. After surgery, we performed UGIANB and administered 5 mL of 0.375% levobupivacaine on each side. The postoperative numerical rating scale pain scores were 1 (0-2) and 2.5 (0-5) (mean (range)), postoperative day one and seven, respectively. The postoperative quality of recovery-40 scores were 188.5 (8.1) and 191.7 (7.6) (mean (SD)), postoperative day one and seven, respectively. No procedural complications were encountered. We performed UGIANB with a mouth opener on a patient with IMTM extraction and were able to provide safe and good analgesia.

Evaluation of a quantitative PCR-based method for chimerism analysis of Japanese donor/recipient pairs.

Chimerism analysis is a surrogate indicator of graft rejection or relapse after allogeneic hematopoietic stem cell transplantation (HSCT). Although short tandem repeat PCR (STR-PCR) is the usual method, limited sensitivity and technical variability are matters of concern. Quantitative PCR-based methods to detect single nucleotide polymorphisms (SNP-qPCR) are more sensitive, but their informativity and quantitative accuracy are highly variable. For accurate and sensitive chimerism analysis, a set of KMR kits (GenDx, Utrecht, Netherlands), based on detection of insertions/deletions (indels) by qPCR, have been developed. Here, we investigated informativity and validated the accuracy of KMR kits in Japanese donor/recipient pairs and virtual samples of DNA mixtures representative of Japanese genetic diversity. We found that at least one recipient-specific marker among 39 KMR-kit markers was informative in all of 65 Japanese donor/recipient pairs. Moreover, the percentage of recipient chimerism estimated by KMRtrack correlated well with ratios of mixed DNA in virtual samples and with the percentage of chimerism in HSCT recipients estimated by STR-PCR/in-house SNP-qPCR. Moreover, KMRtrack showed better sensitivity with high specificity when compared to STR-PCR to detect recipient chimerism. Chimerism analysis with KMR kits can be a standardized, sensitive, and highly informative method to evaluate the graft status of HSCT recipients.

A case of pancreatic duct stones treated with electrohydraulic lithotripsy through a duodenal ulcer.

Video 1Crush the large-sized stones directly using an electrohydraulic lithotripsy device.

Gauze extension method for specimens resected by endoscopic submucosal dissection.

Video 1The gauze extension method for resected specimens.

Falciform ligament abscess with disseminated intrahepatic foci: a case report.

BACKGROUND: Falciform ligament abscess (FLA) is a rare disease, and its diagnosis can be challenging without typical image findings of an abscess. We report a patient with FLA that presented as a mass, with an indistinct border between it and the liver, in addition to disseminated foci within the liver. This made it difficult to determine whether it was FLA or a malignancy. CASE PRESENTATION: A 69-year-old man presented with epigastric pain. Contrast-enhanced computed tomography revealed a 25-mm mass below the middle of the diaphragm. Based on an initial diagnosis of infection of the falciform ligament, we administered conservative antibiotic treatment and there was initial improvement in the patient's clinical condition and laboratory data. However, he continued to experience mild epigastric pain. A month later, imaging studies revealed enlargement of the falciform ligament mass and the emergence of a new nodule in the liver, whereas laboratory findings showed re-elevated C-reactive protein levels. Since conservative treatment had failed, we decided to perform surgery. Considering the imaging study findings, malignant disease could not be ruled out. Based on the operative findings, we performed combined resection of the falciform ligament, left liver, and gallbladder. Histopathological examination of the resected specimens revealed extensive neutrophil infiltration and the presence of giant cells and foam cells within the lesions. These findings were indicative of abscess. Pseudomonas aeruginosa was cultured from the pus in the falciform ligament mass and bile in the gallbladder. Although multiple abscesses postoperatively developed in the residual portion of the liver, they could be treated through antibiotic therapy. CONCLUSIONS: FLA can spread to both adjacent and distant organs via its rich vascular and lymphatic networks. When FLA displays atypical image findings and/or an atypical clinical course, it can be difficult to distinguish it from malignant disease. In such cases, surgical treatment, with intraoperative pathological diagnosis, should be attempted.

Small-Intestinal Metastasis from Lung Carcinoma.

A 62-year-old man was referred to our hospital because of abdominal pain. Computed tomography revealed an approximately 7-cm-diameter tumor in the left abdomen with metastatic lymph nodes, an approximately 1-cm-diameter round tumor in contact with the subclavian artery in the apical lobe of the right lung, and mediastinal lymph node enlargement in contact with the superior vena cava. Esophagogastroduodenoscopy and colonoscopy revealed no abnormalities. Double-balloon endoscopy revealed a whole circumferential ulcer in the jejunum approximately 20 cm from the ligament of Treitz. Biopsy analysis of an ulcer specimen revealed a poorly differentiated carcinoma. Immunohistochemical staining of the specimen showed that it was positive for thyroid transcription factor 1 and cytokeratin 7 and negative for cytokeratin 20, GATA-binding protein 3, caudal-type homeobox protein 2, and paired box 8. Positron emission tomography revealed positive findings in the small-intestinal tumor, nearby mesenteric lymph nodes, lymph nodes around the abdominal aorta, lung tumor, and mediastinal lymph node in the apical lobe of the right lung. Accordingly, the patient was diagnosed as having a lung carcinoma with small-intestinal metastasis (T1b, N3, M1c; cStage IVB). Pathological examination helped distinguish the primary small-intestinal tumor from the metastatic small-intestinal tumor and detect the tumor origin.

Snare devices with thinner loop wire may provide higher performance for cold snare polypectomy in an experimental model.

Background and study aims Snare devices play an important role in treatment of intestinal polyps. However, there are no objective measurements for the characteristics of the various types of snare devices. Materials and methods Seven types of snare devices from four manufacturers were evaluated based on original measurements. The evaluated factors were stiffness, cutting quality, and change in force required for cutting depending on sheath shape. The latter two factors were evaluated by measuring the force required to cut 20 % gelatin cylinders, which simulated intestinal polyps. The cutting sharpness was evaluated by observing the sectional surface of cut gelatin cylinders using a stereomicroscope. The correlations between these measurements and characteristics of the snare devices were investigated. Results A strong positive correlation, with an R 2 value of 0.863, was shown between the force required to cut gelatin cylinders and loop wire diameter. Loop wire diameter also had a strong correlation, with an R 2 value of 0.7997, with the change in force required for cutting gelatin cylinders depending on sheath shape. No correlations were detected between loop stiffness and characteristics of snare devices. The edge-enhanced image revealed that the rougher surfaces of the gelatin cylinders were cut by snares with a thicker diameter. Conclusions Thinner loop wire may provide higher performance in cold snare polypectomy in an experimental model.

Magnifying endoscopy with narrow-band imaging is useful in differentiating gastric cancer from matched adenoma in white light imaging.

This study assessed the effect of magnifying endoscopy with narrow-band imaging (M-NBI) on the endoscopic differential diagnosis between intramucosal gastric carcinomas and adenomas with matched characteristics. Associations between magnified endoscopic findings and pathological high-grade cellular and architectural atypia were also investigated. In total, the records of 50 adenomas and 50 intramucosal well-differentiated adenocarcinomas matched by tumor size (≥ 20 mm or < 20 mm), shape (depression or non-depression), and color (red or non-red) were extracted. Fourteen endoscopists diagnosed adenoma or cancer in the 100 cases with conventional white light imaging (C-WLI), then did the same with C-WLI + M-NBI.The cancer diagnostic sensitivity, specificity, and accuracy were assessed. The sensitivity of C-WLI + M-NBI for cancer diagnosis was 79.9% compared to 71.6% with C-WLI (p < 0.001). There were no significant differences in specificity (40.1% vs. 36.3%, p = 0.296) and accuracy (55.9% vs. 58.1%, p = 0.163). High-grade cytological or architectural atypia was diagnosed more often with irregular microvascular pattern (IMVP) or microsurface pattern (IMSP), respectively, than the low-grade forms. In conclusion, IMVP and IMSP correlate with high-grade cytological and architectural atypia. M-NBI is useful in differentiating intramucosal carcinoma from adenoma and can reduce underdiagnosis of cancer.

A local QSAR model based on the stability of nitrenium ions to support the ICH M7 expert review on the mutagenicity of primary aromatic amines.

BACKGROUND: Aromatic amines, often used as intermediates for pharmaceutical synthesis, may be mutagenic and therefore pose a challenge as metabolites or impurities in drug development. However, predicting the mutagenicity of aromatic amines using commercially available, quantitative structure-activity relationship (QSAR) tools is difficult and often requires expert review. In this study, we developed a shareable QSAR tool based on nitrenium ion stability. RESULTS: The evaluation using in-house aromatic amine intermediates revealed that our model has prediction accuracy of aromatic amine mutagenicity comparable to that of commercial QSAR tools. The effect of changing the number and position of substituents on the mutagenicity of aromatic amines was successfully explained by the change in the nitrenium ion stability. Furthermore, case studies showed that our QSAR tool can support the expert review with quantitative indicators. CONCLUSIONS: This local QSAR tool will be useful as a quantitative support tool to explain the substituent effects on the mutagenicity of primary aromatic amines. By further refinement through method sharing and standardization, our tool can support the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) M7 expert review with quantitative indicators.

A New Amino Acid for Improving Permeability and Solubility in Macrocyclic Peptides through Side Chain-to-Backbone Hydrogen Bonding.

Despite the notoriously poor membrane permeability of peptides, many cyclic peptide natural products show high passive membrane permeability and potently inhibit a variety of "undruggable" intracellular targets. A major impediment to the design of cyclic peptides with good permeability is the high desolvation energy associated with the peptide backbone amide NH groups. While several strategies have been proposed to mitigate this deleterious effect, only few studies have used polar side chains to sequester backbone NH groups. We investigated the ability of N,N-pyrrolidinylglutamine (Pye), whose side chain contains a powerful hydrogen-bond-accepting C═O amide group but no hydrogen-bond donors, to sequester exposed backbone NH groups in a series of cyclic hexapeptide diastereomers. Analyses revealed that specific Leu-to-Pye substitutions conferred dramatic improvements in aqueous solubility and permeability in a scaffold- and position-dependent manner. Therefore, this approach offers a complementary tool for improving membrane permeability and solubility in cyclic peptides.