SpyTag Peptide with Alkoxyl Aspartic Acids for pH-Dependent Activation of the SpyCatcher/Tag System.

The SpyCatcher/SpyTag system is a protein pair that forms a covalent isopeptide bond without an additional energy supply. The ability to connect fused proteins makes this system an attractive tool for several protein engineering applications. Conditional activation of the SpyCatcher/SpyTag complex formation further expands the use of this system. Here, we evaluated the pH activation of SpyTag using alkoxyaspartic acids in the isopeptide-forming residue. We found that a peptide with an ethoxy group can be activated by hydrolysis under high pH conditions. However, the hydrolysis induces isoaspartate (isoAsp) formation, which is confirmed by an isoAsp-inserted short peptide. We overcame this problem by changing the C-terminal side of the aspartic acid position to Pro, which does not form isoAsp under high pH conditions. The findings of this study provide fundamental knowledge of the synthetic construction of the modified SpyTag peptide.

Synthesis and evaluation of catecholamine derivatives as amyloid-beta aggregation inhibitors.

Effectively inhibition of amyloid ß (Aß) aggregation is considered an important method for treatment of the Alzheimer's disease. Herein, inspired by the ability of trans-clovamide to effectively inhibit Aß aggregation, we synthesized a series of structurally related catecholamine derivatives and tested them as Aß aggregation inhibitors using the Thioflavin T assay. The results show that they demonstrated a higher inhibitory rate against Aß aggregation. Furthermore, these compounds exhibited high water solubilities and low cytotoxicities. Additionally, transmission electron microscopy images and dynamic light scattering of their Aß aggregations were observed. Docking simulations revealed that the catechol moiety of the synthesized compounds can form hydrogen bonds with the key regions of Aß and thereby inhibit Aß aggregation.

Development of 1,5-diarylpyrazoles as EGFR/JNK-2 dual inhibitors: design, synthesis, moleecular docking, and bioactivity evaluation.

The eradication of multifactorial diseases, such as cancer, requires the design of drug candidates that attack multiple targets that contribute to the progression and proliferation of such diseases. Here, 1,5-diarylpyrazole derivatives bearing vanillin or sulfanilamide are developed as potential dual inhibitors of epidermal growth factor receptor (EGFR)/c-Jun N-terminal kinase 2 (JNK-2) for possible anticancer activity. These derivatives inhibited the growths of DLD-1, HeLa, K-562, SUIT-2 and HepG2 cancer cell lines, with minimum concentration required to inhibit half of the cellular growth (IC50) values of 2.7-63 µM. The tests confirmed that 5b and 5d were potent JNK-2 inhibitors, with IC50 of 2.0 and 0.9 µM, respectively, whereas 6 h selectively inhibited EGFR protein kinase (EGFR-PK) (IC50 = 1.7 µM). Notably, 6c inhibited both kinases, with IC50 values of 2.7 and 3.0 µM against EGFR-PK and JNK-2, respectively, offering a reference for designing mutual inhibitors of EGFR/JNK-2. The docking studies revealed the ability of the pyrazole ring to bind to the hinge region of the ATP binding site, thereby supporting the experimental inhibitory results. Furthermore, the developed compounds could induce apoptosis and induce cell cycle arrest at different cell phases.

Structure-Activity Relationship Study of N-Hydroxyphtalimide Derivatives for the Detection of Amines during Fmoc-Solid-Phase Peptide Synthesis.

Previously, we developed a method for the detection of unprotected amino groups based on their reversible reaction with N-hydroxyphthalimide (NHPI) to form intensely colored products, which can be useful when conducting solid-phase peptide synthesis. Here, we describe a structure-activity relationship study of NHPI derivatives to identify the derivative best suited for this method using a spectrophotometer toward the estimation of chemical yields. We found that the products resulting from the reaction of the derivative with an unprotected amino group were only intensely colored if the structure of the derivative incorporated an NHPI framework. We also prepared five peptides, including those containing N-methyl and D-amino acid, and Pro residues, using our reversible detection method to detect unprotected amino groups. The mechanism of the detection reaction was also studied by the structural analysis of the NHPI (1) and diisopropylamine complex and concluded to entail salt formation between the N-hydroxy group and amine.

Heterologous expression of α-1,3-glucanase Agn1p from Schizosaccharomyces pombe, and efficient production of nigero-oligosaccharides by enzymatic hydrolysis from solubilized α-1,3;1,6-glucan.

The glycoside hydrolase family 71 α-1,3-glucanase (Agn1p) of Schizosaccharomyces pombe was expressed in Escherichia coli Rosetta-gami B (DE3). Agn1p (0.5 nmol/mL) hydrolyzed insoluble α-1,3-glucan (1%), and about 3.3 mm reducing sugars were released after 1440 min of reaction. The analysis of reaction products by high-performance liquid chromatography revealed that pentasaccharides accumulated in the reaction mixture as the main products, along with a small amount of mono-, di-, tri-, tetra-, and hexasaccharides. Soluble glucan was prepared from insoluble α-1,3;1,6-glucan by alkaline and sonication treatment to improve the hydrolytic efficiency. As a result, this solubilized α-1,3;1,6-glucan maintained a solubilized state for at least 6 h. Agn1p (0.5 nmol/mL) hydrolyzed the solubilized α-1,3;1,6-glucan (1%), and about 8.2 mm reducing sugars were released after 240 min of reaction. Moreover, Agn1p released about 12.3 mm reducing sugars from 2% of the solubilized α-1,3;1,6-glucan.

Development and Assessment of 1,5-Diarylpyrazole/Oxime Hybrids Targeting EGFR and JNK-2 as Antiproliferative Agents: A Comprehensive Study through Synthesis, Molecular Docking, and Evaluation.

New 1,5-diarylpyrazole oxime hybrid derivatives (scaffolds A and B) were designed, synthesized, and then their purity was verified using a variety of spectroscopic methods. A panel of five cancer cell lines known to express EGFR and JNK-2, including human colorectal adenocarcinoma cell line DLD-1, human cervical cancer cell line Hela, human leukemia cell line K562, human pancreatic cell line SUIT-2, and human hepatocellular carcinoma cell line HepG2, were used to biologically evaluate for their in vitro cytotoxicity for all the synthesized compounds 7a-j, 8a-j, 9a-c, and 10a-c. The oxime containing compounds 8a-j and 10a-c were more active as antiproliferative agents than their non-oxime congeners 7a-j and 9a-c. Compounds 8d, 8g, 8i, and 10c inhibited EGFR with IC50 values ranging from 8 to 21 µM when compared with sorafenib. Compound 8i inhibited JNK-2 as effectively as sorafenib, with an IC50 of 1.0 µM. Furthermore, compound 8g showed cell cycle arrest at the G2/M phase in the cell cycle analysis of the Hela cell line, whereas compound 8i showed combined S phase and G2 phase arrest. According to docking studies, oxime hybrid compounds 8d, 8g, 8i, and 10c exhibited binding free energies ranging from -12.98 to 32.30 kcal/mol at the EGFR binding site whereas compounds 8d and 8i had binding free energies ranging from -9.16 to -12.00 kcal/mol at the JNK-2 binding site.

Geriatric Risk Prediction Models for Major Gastroenterological Surgery Using the National Clinical Database in Japan: A Multicenter Prospective Cohort Study.

OBJECTIVES: To investigate the effect of geriatric variables on 5 newly added outcomes and create risk models for predicting these outcomes. SUMMARY OF BACKGROUND DATA: Because there is a current lack of geriatric research focusing on geriatric outcomes using a national surgical database in Japan, there is a need to investigate outcomes associated with major gastro-enterological surgery using these data. METHODS: This multicenter prospective cohort study was conducted at 26 surgery departments across 21 institutions in Japan using the NCD surgical registry. in total, 22 new geriatric variables were imported from the ACS National Surgical Quality Improvement Program geriatric pilot study. The following 5 geriatric outcomes were defined: (1) postoperative delirium, (2) physical function on postoperative day 30, (3) fall risk on discharge, (4) discharge other than home with social service, and (5) functional decline on discharge, and geriatric risk prediction models for major gastroenterological surgery were created. RESULTS: Between January 2018 and December 2018, data on 3981 procedures from 7 major gastroenterological surgeries were collected and analyzed. Older age and preoperative geriatric variables (Origin status from home, History of dementia, Use of mobility aid, fall history, and not competent on admission) were strongly associated with postoperative outcomes. Geriatric risk prediction models for these outcomes were created, with C-statistic values ranging from 0.74 to 0.90, demonstrating model validity and sufficiency of fit. CONCLUSIONS: The risk models for the newly defined 5 geriatric outcomes that we created can be used in the decision-making process or provision of care in geriatric patients.

Design, synthesis, and evaluation of the self-assembled antimicrobial peptides based on the ovalbumin-derived peptide TK913.

The preparation, self-assembly, and antimicrobial activity of peptides based on TK913 is described. TK9Z4 incorporating a Pro-Pro motif exhibited self-assembly but no cytotoxicity. However, peptide TKZ3 (obtained by changing the amino acid sequence of TK9Z4) showed morphological changes at different concentrations, potent antimicrobial activity, low cytotoxicity, and trypsin resistance. Accordingly, TKZ3 is proposed as new AMP derived from ovalbumin-derived peptides.

Synthesis and Configuration Confirmation of the ATHOD Fatty Amino Acid Residue in the Burkholdines.

Eight possible diastereomers of the 3-amino-5,6,7-trihydroxy octadecanoic acid (ATHOD) moiety of the burkholdines (Bks) have been synthesized and their configurations assigned. Though the relative configuration of the triol in the ATHOD residue of the Bks was proposed to be anti-anti-anti in the literature, 1H NMR spectra of our synthesized anti-anti-anti ATHOD derivative was inconsistent with that of the isolated ATHOD residue, suggesting that the assignment of the relative configuration of that residue in the literature was incorrect. However, by comparison of the NMR data of our ATHOD derivatives with that of configurationally defined samples of 2-amino-4-pentanol using Kishi's NMR database method, we conclude that the absolute configuration of the ATHOD moiety is (3R,5S,6R,7S). In addition, we revealed that the ATHOD residue present in the occidiofungins A-D has the same configuration as that in all the Bks.

New pharmaceuticals approved by FDA in 2020: Small-molecule drugs derived from amino acids and related compounds.

Amino acids (AAs) play an important role in the modern health industry as key synthetic precursors for pharmaceuticals, biomaterials, biosensors, and drug delivery systems. Currently, over 30% of small-molecule drugs contain residues of tailor-made AAs or derived from them amino-alcohols and di-amines. In this review article, we profile 12 AA-derived new pharmaceuticals approved by the FDA in 2020. These newly introduced drugs include Tazverik (epithelioid sarcoma), Gemtesa (overactive bladder), Zeposia (multiple sclerosis), Byfavo (induction and maintenance of procedural sedation), Cu 64 dotatate, and Gallium 68 PSMA-11 (both PET imaging), Rimegepant (acute migraine), Zepzelca (lung cancer), Remdesivir (COVID-19), Amisulpride (nausea and vomiting), Setmelanotide (obesity), and Lonafarnib (progeria syndrome). For each compound, we describe the spectrum of biological activity, medicinal chemistry discovery, and synthetic preparation.

Comprehensive evaluation of three-dimensional anatomy of perigastric vessels using enhanced multidetector-row computed tomography.

BACKGROUND: To perform laparoscopic gastrectomy safely, we aimed to comprehensively re-evaluate perigastric vessel anatomies using a three-dimensional angiography reconstructed from enhanced multidetector-row computed tomography data. METHODS: Perigastric vessel anatomy was preoperatively analyzed using a multidetector-row computed tomography-based three-dimensional angiography reconstructed in 127 patients undergoing gastric surgery. RESULTS: Of the 67 left gastric veins that ran along the dorsal side of the arteries, 59 (88.1%) ran along the dorsal side of the common hepatic artery and flowed into the portal vein. In 18 cases, a common trunk of one to three left gastric arteries and the replaced left hepatic artery was observed. The left inferior phrenic artery ramified from the left gastric artery in 5.5% of the cases. The right gastric artery was classified into distal (73.2%), caudal (18.1%), and proximal (8.7%) types. The infra-pyloric artery was also classified into distal (64.6%), caudal (26.0%), and proximal (9.4%) types. The posterior gastric artery branched as a common trunk with the superior polar artery in the proximal (37.9%) and distal (18.4%) regions of the splenic artery. The left gastroepiploic artery ramified from the splenic (18.1%) and inferior terminal arteries (81.9%). No, one, and two gastric branches of the left gastroepiploic artery, which ramified between the roots of the left gastroepiploic artery and its omental branch, were found in 36.5%, 49.2%, and 14.3% of the cases, respectively. CONCLUSIONS: Preoperative 3D angiography is useful for the precise evaluation of perigastric vessel anatomies, and may help us to perform laparoscopic gastrectomy and robotic surgery safely.

Surface Engineering of Top7 to Facilitate Structure Determination.

Top7 is a de novo designed protein whose amino acid sequence has no evolutional trace. Such a property makes Top7 a suitable scaffold for studying the pure nature of protein and protein engineering applications. To use Top7 as an engineering scaffold, we initially attempted structure determination and found that crystals of our construct, which lacked the terminal hexahistidine tag, showed weak diffraction in X-ray structure determination. Thus, we decided to introduce surface residue mutations to facilitate crystal structure determination. The resulting surface mutants, Top7sm1 and Top7sm2, crystallized easily and diffracted to the resolution around 1.7 Å. Despite the improved data, we could not finalize the structures due to high R values. Although we could not identify the origin of the high R values of the surface mutants, we found that all the structures shared common packing architecture with consecutive intermolecular ß-sheet formation aligned in one direction. Thus, we mutated the intermolecular interface to disrupt the intermolecular ß-sheet formation, expecting to form a new crystal packing. The resulting mutant, Top7sm2-I68R, formed new crystal packing interactions as intended and diffracted to the resolution of 1.4 Å. The surface mutations contributed to crystal packing and high resolution. We finalized the structure model with the R/Rfree values of 0.20/0.24. Top7sm2-I68R can be a useful model protein due to its convenient structure determination.

The Hydrophobicity and Antifungal Potentiation of Burkholdine Analogues.

The burkholdines are a family of cyclic lipopeptides reported to exhibit antifungal activity. We synthesized a series of 18 burkholdine analogues in good yield by conventional Fmoc-SPPS followed by cyclization with DIPCI/HOBt in the solution phase. Although none of the synthesized peptides exhibited antifungal activity, several did potentiate the antibiotic effect of the antibiotic G418, including the Thr-bearing Bk analogue (4b) and the tartaramide-bearing Bk analogue (5b). This work exemplifies the potential of burkholdine analogues as potentiating agents.

Tailor-Made Amino Acids in Pharmaceutical Industry: Synthetic Approaches to Aza-Tryptophan Derivatives.

Over the recent years there has been a noticeable upsurge of interest in aza-analogs of tryptophan which are isosteric to the latter and found numerous applications in medicinal, bioorganic chemistry, and peptide research. In the present review article, five aza-tryptophan derivatives are profiled, including aza-substitution in the positions 2, on the five-membered ring, as well as in positions 4, 5, 6, and 7 on the six-membered ring. A detailed and comprehensive literature overview of the synthetic methods for the preparation of these aza-tryptophans is presented and general facets of the biological properties and most promising applications are discussed.

Nitric oxide protects against ferroptosis by aborting the lipid peroxidation chain reaction.

Ferroptosis is a type of iron-dependent necrotic cell death, which is typically triggered by the depletion of intracellular glutathione (GSH), which is associated with increased lipid peroxidation. Nitric oxide (NO) is a highly reactive gaseous radical mediator with anti-oxidation properties that terminates lipid peroxidation reactions. In the current study, we report the anti-ferroptotic action of NOC18, an NO donor that spontaneously releases NO, in cells under various ferroptotic conditions in vitro. Our results indicate that, when mouse hepatoma Hepa 1-6 cells are incubated with NOC18, cell death induced by various ferroptotic stimuli such as cysteine (Cys) starvation, the inhibition of glutathione peroxidase 4 (GPX4) and treatment with tertiary-butyl hydroperoxide (TBHP) is significantly reduced. Treatment with NOC18 failed to improve the decrease in the levels of Cys or GSH and the accumulation of ferrous iron upon ferroptotic stimuli. The fluorescent intensity of C11-BODIPY581/591, a probe that is used to detect lipid peroxidation products, was increased somewhat by treatment with NOC18 under conditions of Cys starvation, and the accumulation of lipid peroxidation end-products, as evidenced by the levels of 4-hydroxynonenal, were effectively suppressed. The pre-incubation of TBHP with NOC7, a short-lived NO donor completely eliminated its ability to trigger ferroptosis. These collective results indicate that NO exerts a cytoprotective action against various ferroptotic stimuli by aborting the lipid peroxidation chain reaction.

Association of surgeon and hospital volume with postoperative mortality after total gastrectomy for gastric cancer: data from 71,307 Japanese patients collected from a nationwide web-based data entry system.

BACKGROUND: Despite interest in surgeon and hospital volume effects on total gastrectomy (TG), clinical significance has not been confirmed in a large-scale population. This study aimed at clarifying the association of surgeon and hospital volume on postoperative mortality after TG for gastric cancer among Japanese patients in National Clinical Database (NCD). METHODS: Between 2011 and 2015, we retrospectively extracted data on TG for gastric cancer from the NCD. The primary outcome was operative mortality. We divided surgeon volume as the number of TGs performed by a patient's surgeon in the previous year: S1 (0-2 cases), S2 (3-9), S3 (10-25), S4 (26-79) and hospital volume by the number of TGs performed in the previous year: H1 (0-11 cases), H2 (12-26), H3 (27-146). We calculated the 95% confidence interval (CI) for the mortality rate based on odds ratios (OR) estimated from a hierarchical logistic regression model. RESULTS: We analyzed 71,307 patients at 2051 institutions. Low-volume surgeons and hospitals had significantly older and poorer-risk patients with various comorbidities. The operative mortality rate decreased with surgeon volume, 2.5% in S1 and 0.6% in S4. The operative mortality was 3.1% in H1, 1.7% in H2, and 1.2% in H3. After risk adjustment for surgeon, hospital volume and patient characteristics, hospital volume was significantly associated with operative morality (H3: OR = 0.53, 95% CI 0.43-0.63). CONCLUSIONS: We demonstrate hospital volume has an impact on postoperative mortality after TG in a nationwide population study. These findings suggest centralization may improve outcomes after TG.

Preoperative risk factors for postoperative intra-abdominal infectious complication after gastrectomy for gastric cancer using a Japanese web-based nationwide database.

BACKGROUND: Postoperative intra-abdominal infectious complication (PIIC) after gastrectomy for gastric cancer worsens in-hospital death or long-term survival. However, the methodology for PIIC preoperative risk assessment remains unestablished. We aimed to develop a preoperative risk model for postgastrectomy PIIC. METHODS: We collected 183,936 patients' data on distal or total gastrectomy performed in 2013-2016 for gastric cancer from the Japanese National Clinical Database and divided into development (2013-2015; n = 140,558) and validation (2016; n = 43,378) cohort. The primary outcome was the incidence of PIIC. The risk model for PIIC was developed using 18 preoperative factors: age, sex, body mass index, activities of daily living, 12 comorbidity types, gastric cancer stage, and surgical procedure in the development cohort. Secondarily, we developed another model based on the new scoring system for clinical use using selected factors. RESULTS: The overall incidence of PIIC was 4.7%, including 2.6%, 1.7%, and 1.3% in anastomotic leakage, pancreatic fistula, and intra-abdominal abscess, respectively. Among the 18 preoperative factors, male [odds ratio, (OR) 1.92], obesity (OR, 1.52-1.96), peripheral vascular disease (OR, 1.55), steroid use (OR, 1.83), and total gastrectomy (OR, 1.89) strongly correlated with PIIC incidence. The entire model using the 18 factors had good discrimination and calibration in the validation cohort. We selected eight relevant factors to create a simple scoring system, using which we categorized the patients into three risk groups, which showed good calibration. CONCLUSION: Using nationwide clinical practice data, we created a preoperative risk model for postgastrectomy PIIC for gastric cancer.

Design and synthesis of pyrimidine-5-carbonitrile hybrids as COX-2 inhibitors: Anti-inflammatory activity, ulcerogenic liability, histopathological and docking studies.

Two new series of 1,3,4-oxadiazole and coumarin derivatives based on pyrimidine-5-carbonitrile scaffold have been synthesized and evaluated for their COX-1/COX-2 inhibitory activity. Compounds 10c, 10e, 10h-j, 14e-f, 14i and 16 were found to be the most potent and selective inhibitors of COX-2 (IC50 0.041-0.081 µM, SI 139.74-321.95). Eight compounds were further investigated for their in vivo anti-inflammatory activity. The most active derivatives 10c, 10j and 14e displayed superior in vivo anti-inflammatory activity (% edema inhibition 39.3-48.3, 1 h; 58.4-60.5, 2 h; 70.8-83.2, 3 h; 78.9-89.5, 4 h) to the reference drug celecoxib (% edema inhibition 38.0, 1 h; 48.8, 2 h; 58.4, 3 h; 65.4, 4 h). These derivatives were also tested for their ulcerogenic liability, compound 10j showed better safety profile with reference to celecoxib while 10c and 14e exhibited mild lesions. Molecular docking studies of 10c, 10j, and 14e in the COX-2 active site revealed similar orientation and binding interactions as selective COX-2 inhibitors with a higher liability to access the selectivity side pocket.

Asymmetric synthesis of (S)-3-methyleneglutamic acid and its N-Fmoc derivative via Michael addition-elimination reaction of chiral glycine Ni (II) complex with enol tosylates.

The use of chiral Ni (II)-complexes of glycine Schiff bases has recently emerged as a leading methodology for asymmetric synthesis of structurally diverse Tailor-Made Amino Acids™, playing a key role in the design of modern pharmaceuticals. Here, we report first example of enantioselective preparation of (S)-3-methyleneglutamic acid and its N-Fmoc derivative via a new type of Michael addition-elimination reaction between chiral nucleophilic glycine equivalent and enol tosylates. This reaction was found to proceed with excellent yield (91%) and diastereoselectivity (>99/1 de) allowing straightforward asymmetric synthesis of (S)-3-methyleneglutamic acid derivatives and analogues. The observed results bode well for general application of this Ni (II) complex approach for preparation and biological studies of this previously unknown type of Tailor-Made Amino Acids™.

Comparative study of different chiral ligands for dynamic kinetic resolution of amino acids.

Dynamic kinetic resolution (DKR) of unprotected amino acids (AAs), via intermediate formation of Ni(II) complexes, is currently a leading methodology for preparation of natural and tailor-made AAs in enantiomerically pure form. In this work, we conduct a comparative case study of synthetic performance of four different ligands in DKR of six AAs representing aryl-, benzyl-, alkyl-, and long alkyl-type derivatives. The results of this study allow for rational selection of ligand/AA type to develop a practical procedure for preparation of target enantiomerically pure AAs.