Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins

Vibrational spectroscopy combined with theoretical calculations is a powerful tool for analyzing the interaction and conformation of peptides at the atomistic level. Nonetheless, identifying the structure becomes increasingly difficult as the peptide size grows large. One example is acetyl-SIVSF-N-methylamide, a capped pentapeptide, whose atomistic structure has remained unknown since its first observation [T. Sekiguchi, M. Tamura, H. Oba, P. Çarçarbal, R. R. Lozada-Garcia, A. Zehnacker-Rentien, G. Grégoire, S. Ishiuchi and M. Fujii, Angew. Chem., Int. Ed., 2018, 57, 5626-5629]. Here, we propose a novel conformational search method, which exploits the structure-spectrum correlation using a similarity score that measures the agreement of theoretical and experimental spectra. Surprisingly, the two conformers have distinctly different energy and geometry. The second conformer is 25 kJ mol-1 higher in energy than the other, lowest-energy conformer. The result implies that there are multiple pathways in the early stage of the folding process: one to the global minimum and the other to a different basin. Once such a structure is established, the second conformer is unlikely to overcome the barrier to produce the most stable structure due to a vastly different hydrogen bond network of the backbone. Our proposed method can characterize the lowest-energy conformer and kinetically trapped, high-energy conformers of complex biomolecules.

Conformation-Dependent Influences of Hydrophobic Amino Acids in Two In-Register Parallel β-Sheet Amyloids, an α-Synuclein Amyloid and a Local Structural Model of PrPSc

Prions are unconventional pathogens that encode the pathogenic information in conformations of the constituent abnormal isoform of prion protein (PrP^Sc), independently of the nucleotide genome. Therefore, conformational diversity of PrP^Sc underlies the existence of many prion strains and species barriers of prions, although the conformational information is extremely limited. Interestingly, differences between polymorphic or species-specific residues responsible for the species/strain barriers are often caused by conservative replacements between hydrophobic amino acids. This implies that subtle differences among hydrophobic amino acids are significant for PrP^Sc structures. Here we analyzed the influence of different hydrophobic residues on the structures of an in-register parallel β-sheet amyloid of α-synuclein (αSyn) using molecular dynamics (MD) simulation and applied the knowledge from the αSyn amyloid to modeling a local structure of human PrP^Sc encompassing residues 107-143. We found that mutations equivalent to polymorphisms that cause transmission barriers substantially affect the stabilities of the local structures; for example, the G127V mutation, which makes the host resistant to various human prion diseases, greatly destabilized the local structure of the model amyloid. Our study indicates that subtle differences among hydrophobic side chains can considerably affect the interaction network, including hydrogen bonds, and demonstrates specifically how and in what structures hydrophobic residues can exert unique effects on in-register parallel β-sheet amyloids.

Lead Optimization of Influenza Virus RNA Polymerase Inhibitors Targeting PA-PB1 Interaction

Influenza viruses are responsible for contagious respiratory illnesses in humans and cause seasonal epidemics and occasional pandemics worldwide. Previously, we identified a quinolinone derivative PA-49, which inhibited the influenza virus RNA-dependent RNA polymerase (RdRp) by targeting PA-PB1 interaction. This paper reports the structure optimization of PA-49, which resulted in the identification of 3-((dibenzylamino)methyl)quinolinone derivatives with more potent anti-influenza virus activity. During the optimization, the hit compound 89, which was more active than PA-49, was identified. Further optimization and scaffold hopping of 89 led to the most potent compounds 100 and a 1,8-naphthyridinone derivative 118, respectively. We conclusively determined that compounds 100 and 118 suppressed the replication of influenza virus and exhibited anti-influenza virus activity against both influenza virus types A and B in the range of 50% effective concentration (EC₅₀) = 0.061-0.226 μM with low toxicity (50% cytotoxic concentration (CC₅₀) >10 μM).

Idiopathic multicentric Castleman disease with novel heterozygous Ile729Met mutation in exon 10 of familial Mediterranean fever gene

Objective

While the aetiology of idiopathic multicentric Castleman disease (iMCD) remains unclear, the involvement of autoinflammatory mechanisms has been suggested. Herein we report a Japanese patient with iMCD with a novel heterozygous Ile729Met mutation in exon 10 of the Mediterranean fever (MEFV) gene.

Methods

We performed genetic analysis via targeted next-generation sequencing analysis and Sanger sequencing and conducted molecular dynamics simulations to investigate the hydrophobic interactions around the 729th amino acid in human pyrin.

Results

In February 2011, a 59-year-old man was diagnosed with IgG4-related disease at our department based on the findings of cervical and hilar lymphadenopathies, typical lung lesions and cervical lymph node biopsy. The patient was followed up without treatment, as he was asymptomatic. However, he had been experiencing prolonged fatigue and fever with high levels of CRP since June 2017. Axillary lymph node biopsy findings led to the diagnosis of iMCD. He was successfully treated with an IL-6 inhibitor and has been in remission for 12 months. Genetic analyses for hereditary autoinflammatory disease–related genes were performed, revealing a novel heterozygous Ile729Met mutation in exon 10 of the MEFV gene. We identified that this novel mutation significantly altered the local interaction of the human pyrin B30.2 domain by molecular dynamics simulation analysis and experimentally had the potential for inflammasome activation with increased inflammatory cytokines.

Conclusion

The abnormal function of pyrin due to a mutation in the MEFV gene in this patient may have contributed to the development of MCD by inducing IL-6 production via inflammasome signalling.

A Quinolinone Compound Inhibiting the Oligomerization of Nucleoprotein of Influenza A Virus Prevents the Selection of Escape Mutants

The emergence of resistance to currently available anti-influenza drugs has heightened the need for antivirals with novel mechanisms of action. The influenza A virus (IAV) nucleoprotein (NP) is highly conserved and essential for the formation of viral ribonucleoprotein (vRNP), which serves as the template for replication and transcription. Recently, using in silico screening, we identified an antiviral compound designated NUD-1 (a 4-hydroxyquinolinone derivative) as a potential inhibitor of NP. In this study, we further analyzed the interaction between NUD-1 and NP and found that the compound interferes with the oligomerization of NP, which is required for vRNP formation, leading to the suppression of viral transcription, protein synthesis, and nuclear export of NP. We further assessed the selection of resistant variants by serially passaging a clinical isolate of the 2009 H1N1 pandemic influenza virus in the presence of NUD-1 or oseltamivir. NUD-1 did not select for resistant variants after nine passages, whereas oseltamivir selected for resistant variants after five passages. Our data demonstrate that NUD-1 interferes with the oligomerization of NP and less likely induces drug-resistant variants than oseltamivir; hence, it is a potential lead compound for the development of novel anti-influenza drugs.

Disulfide-crosslink scanning reveals prion-induced conformational changes and prion strain-specific structures of the pathological prion protein PrPSc

Prions are composed solely of the pathological isoform (PrP^Sc) of the normal cellular prion protein (PrP^C). Identification of different PrP^Sc structures is crucially important for understanding prion biology because the pathogenic properties of prions are hypothesized to be encoded in the structures of PrP^Sc However, these structures remain yet to be identified, because of the incompatibility of PrP^Sc with conventional high-resolution structural analysis methods. Previously, we reported that the region between the first and the second α-helix (H1∼H2) of PrP^C might cooperate with the more C-terminal side region for efficient interactions with PrP^Sc From this starting point, we created a series of PrP variants with two cysteine substitutions (C;C-PrP) forming a disulfide-crosslink between H1∼H2 and the distal region of the third helix (Ctrm). We then assessed the conversion capabilities of the C;C-PrP variants in N2a cells infected with mouse-adapted scrapie prions (22L-ScN2a). Specifically, Cys substitutions at residues 165, 166, or 168 in H1∼H2 were combined with cysteine scanning along Ctrm residues 220-229. We found that C;C-PrPs are expressed normally with glycosylation patterns and subcellular localization similar to WT PrP, albeit differing in expression levels. Interestingly, some C;C-PrPs converted to protease-resistant isoforms in the 22L-ScN2a cells, but not in Fukuoka1 prion-infected cells. Crosslink patterns of convertible C;C-PrPs indicated a positional change of H1∼H2 toward Ctrm in PrP^Sc-induced conformational conversion. Given the properties of the C;C-PrPs reported here, we propose that these PrP variants may be useful tools for investigating prion strain-specific structures and structure-phenotype relationships of PrP^Sc.

Structure-based drug discovery for combating influenza virus by targeting the PA-PB1 interaction

Influenza virus infections are serious public health concerns throughout the world. The development of compounds with novel mechanisms of action is urgently required due to the emergence of viruses with resistance to the currently-approved anti-influenza viral drugs. We performed in silico screening using a structure-based drug discovery algorithm called Nagasaki University Docking Engine (NUDE), which is optimised for a GPU-based supercomputer (DEstination for Gpu Intensive MAchine; DEGIMA), by targeting influenza viral PA protein. The compounds selected by NUDE were tested for anti-influenza virus activity using a cell-based assay. The most potent compound, designated as PA-49, is a medium-sized quinolinone derivative bearing a tetrazole moiety, and it inhibited the replication of influenza virus A/WSN/33 at a half maximal inhibitory concentration of 0.47 μM. PA-49 has the ability to bind PA and its anti-influenza activity was promising against various influenza strains, including a clinical isolate of A(H1N1)pdm09 and type B viruses. The docking simulation suggested that PA-49 interrupts the PA–PB1 interface where important amino acids are mostly conserved in the virus strains tested, suggesting the strain independent utility. Because our NUDE/DEGIMA system is rapid and efficient, it may help effective drug discovery against the influenza virus and other emerging viruses.

Phylogenetic inference of the porcine Rotavirus A origin of the human G1 VP7 gene

Rotavirus A (RVA) is an important cause of acute gastroenteritis in children worldwide. The most common VP7 genotype of human RVA is G1, but G1 is rarely detected in porcine strains. To understand the evolutionary relationships between human and porcine G1 VP7 genes, we sequenced the VP7 genes of three Japanese G1 porcine strains; the first two (PRV2, S80B) were isolated in 1980 and the third (Kyusyu-14) was isolated in 2001. Then, we performed phylogenetic and in-silico structural analyses. All three VP7 sequences clustered into lineage VI, and the mean nucleotide sequence identity between any pair of porcine G1 VP7 sequences belonging to lineage VI was 91.9%. In contrast, the mean nucleotide sequence identity between any pair of human G1 VP7 sequences belonging to lineages I-V was 95.5%. While the mean nucleotide sequence identity between any pair of porcine lineage VI strain and human lineage I-V strain was 85.4%, the VP7 genes of PRV2 and a rare porcine-like human G1P[6] strain (AU19) were 98% identical, strengthening the porcine RVA origin of AU19. The phylogenetic tree suggests that human G1 VP7 genes originated from porcine G1 VP7 genes. The time of their most recent common ancestor was estimated to be 1948, and human and porcine RVA strains evolved along independent pathways. In-silico structural analyses identified 7 amino acid residues within the known neutralisation epitopes that show differences in electric charges and shape between different porcine and human G1 strains. When compared with much divergent porcine G1 VP7 lineages, monophyletic, less divergent human G1 VP7 lineages support the hypothesis that all human G1 VP7 genes included in this study originated from a rare event of a porcine RVA transmitting to humans that was followed by successful adaptation to the human host. By contrast, AU19 represents interspecies transmission that terminated in dead-end infection.

3,3-Dibromo-2-trifluoromethyl acrylic acid ethyl ester: a versatile platform for the stereoselective preparation of functionalized-α-trifluoromethyl α,β-unsaturated lactones and trifluoromethyl pyrazolinones

Synthetic routes to multi-functionalized-α-trifluoromethyl α,β-unsaturated lactones and trifluoromethyl pyrazolinones.

Effects of gastric acidity on peristomal infection after percutaneous endoscopic gastrostomy placement

Peristomal infection is a common complication following percutaneous endoscopic gastrostomy (PEG) placement. This study investigated the effect of gastric acidity on peristomal infection, including type of bacteria and the relationship between bacteria cultured from the oropharynx and PEG tube site. Sixty-seven patients with dysphagia underwent PEG placement at Otaki Hospital between 1998 and 2001. Gastric acidity was evaluated by 24h pH monitoring. Patients were observed for peristomal infection for two weeks after PEG placement, with specimens collected from the oropharynx and PEG tube site. Twenty-one (31.3%) of the patients who had undergone PEG insertion developed peristomal infections. Of 52 patients who were not colonised with meticillin-resistant Staphylococcus aureus (MRSA) in the oropharynx, 11 cases (21.2%) developed peristomal infection. The median gastric pH of infected patients (11 cases) was 5.05+/-2.55 (mean+/-SD) and in patients without infection (41 cases) it was 3.06+/-1.83 (P=0.019). Peristomal infection developed in 66.7% (10/15) of patients carrying MRSA compared with only 21.2% (11/52) of patients who were not colonised by MRSA (P<0.001). The incidence of peristomal infection was affected by gastric acidity and the presence of MRSA in the oropharynx.

Internal tissue displacement measurement based on ultrasonic wave Doppler signal digital detection and its application to fetal movement monitoring

We have developed a fetal movement monitoring system based on small displacement measurement of internal tissues. When ultrasonic pulses are transmitted to the fetus, the reflected ultrasonic waves which have a Doppler frequency shift due to the fetal movements are detected by using an ultrasonic pulsed Doppler technique. In this paper, we propose a displacement measurement method for internal tissues which is based on the Doppler signal digital detection technique. In the method, the received ultrasonic RF signals are sampled with a sampling frequency of four times higher than the centre frequency of the ultrasonic waves; the Doppler frequency shift signals are derived using digital signal processing. From the detected signals, the internal displacements are estimated using the arc-tangent method. The basic algorithm of the detection method has already been used in the area of blood flow sensing, however, we apply the algorithm to the displacement measurement of internal tissues. The comparison between the proposed method and the conventional method is presented. The fetal movement quantitative monitoring system based on the method which has been constructed is shown.

[A cross-sectional analysis on relationships between maximum oxygen uptake and risk factors for cardiovascular diseases]

We examined the relationships between maximum oxygen uptake (Vo2max) and cardiovascular risk factors including age (year), systolic blood pressure (mmHg), diastolic blood pressure (mmHg), serum total cholesterol level (mg/dl), serum high-density lipoprotein level (mg/dl), serum triglyceride level (mg/dl), blood glucose level (mg/dl), serum uric acid level (mg/dl), body fat (%bw), Body Mass Index (BMI), alcohol (points/day), cigarettes (/day), and physical activity (METs.exercise time/30 days). The alcohol point was defined as follows: beer 633ml = a glass of whiskey and water - sake 180ml = 1 point, and totaled at 30 days. The subjects of our study were 162 males (aged 40.6 +/- 13.1) and 133 females (aged 41.3 +/- 11.1) who underwent medical and physical examinations at the Fukui Industrial Health Center from April, 1991 to June, 1992. As a result of simple correlation analysis in males, Vo2max had significantly negative correlations with age (r = -0.223, p < 0.01), systolic blood pressure (r = -0.228, p < 0.01), diastolic blood pressure (r = -0.239, p < 0.01), or serum triglyceride level (r = -0.258, p < 0.001), serum uric acid level (p < 0.05), body fat (r = -0.230, p < 0.01), and BMI (r = -0.312, p < 0.001), and was positively correlated with physical activity (r = -0.249, p < 0.01). On the other hand, in females, age (r = -0.224, p < 0.01), systolic blood pressure (r = -0.222, p < 0.01), diastolic blood pressure (r = -0.267, p < 0.01), serum triglyceride level (r = -0.261, p < 0.001), body fat (r = -0.280, p < 0.01), and BMI (r = -302, p < 0.001), had significantly negative correlations with VO2max. However, partial correlations were tested after controlling body fat, BMI, cigarette, alcohol, physical activity, and age, none of the factors correlated with VO2max significantly. These findings suggest that the risk factors for cardiovascular diseases are related to VO2max, and the life style has an influence on these correlations. Thus, VO2max may be a comprehensive indicator for health promotion among the working population. Furthermore a longitudinal study is required to determine whether the increase in VO2max is related to the improvement in the risk of cardiovascular diseases.

Evaluation of cerebral blood flow in patients with idiopathic orthostatic hypotension using Tc-99m HMPAO brain SPECT during postural testing

To determine whether regional cerebral blood flow (rCBF) would change on standing in patients with idiopathic orthostatic hypotension (IOH), Tc-99m HMPAO SPECT studies were performed during postural testing in five patients with IOH. After 10 minutes of quiet rest on a bed, the patients arose quickly and, at the same time, the radiotracer was injected intravenously. SPECT data were obtained with a ring-type SPECT scanner. Another dose of Tc-99m HMPAO was injected with the subjects in the supine position, and SPECT was performed again. Image subtraction was used to evaluate the change in rCBF caused by postural testing. In all patients, the authors observed a decrease of rCBF ni the frontal cortex and basal ganglia. This preliminary study suggests that changes in rCBF occur in patients with IOH on standing, and Tc-99m HMPAO SPECT performed during postural testing may have an important role in evaluating these changes.

[A study of crossed cerebellar diaschisis on 123I-IMP SPECT images and its redistribution phenomenon]

Crossed cerebellar diaschisis (CCD) is interpreted as a functional deactivation, presumably caused by a loss of excitatory or inhibitory afferent inputs on the corticopontocerebellar pathway and others. A redistribution phenomenon (RD) is usually observed in the contralateral cerebellum with CCD on delayed images of 123I-IMP SPECT. This phenomenon was analyzed in a view point of rCBF measurement in 24 patients with brain tumor, infarction and so forth. Regional CBF was measured by the microsphere method with 123I-IMP and a delayed-to-early counts ratio (D/E ratio) was used. As a result, there was no relation between rCBF and the D/E ratio in the cerebellum, which means that RD is occurred by other factors except for rCBF in the cerebellum. Regional CBF and the D/E ratio in the contralateral and ipsilateral cerebellum was 46.3 ml/100 g/min, 1.01 and 57.0 ml/100 g/min, 0.86, respectively. These results mean that the high activity of IMP gradually decreased in the ipsilateral cerebellum, while, the low activity in the contralateral cerebellum was almost stable, and the difference of both activity reduced after 5 hours and RD was observed on the delayed image. The data indicate that retention mechanism of IMP and vascular permeability are not affected in the cerebellum with CCD.

Chimeric HU-IHF proteins that alter DNA-binding ability

Chimeric proteins between Escherichia coli histone-like HU and IHF were constructed by genetic engineering, in which part of the arm region was replaced by the corresponding region of IHF alpha (designated as HupANhimA) or IHF beta (HupANhimD); alternatively, an alpha-helix 2-beta 1 region was replaced by the corresponding region of IHF alpha (HupAXhimA) or IHF beta (HupAXhimD) (symbols N and X indicate NotI and XhoI junctions). These proteins were synthesized in a hupA-hupB double-deletion mutant. HupANhimA exhibited marked reduction in nonspecific DNA binding in vitro, and a drastic loss of HU activity in replicative transposition of Mu phage in vivo. HupANhimD also showed a significant reduction in the ability for DNA binding, though this protein supported Mu phage development. In contrast, the other two chimeric HU proteins showed only slight changes in nonspecific DNA-binding ability: they retained activities for transposition of Mu phage in vivo. These observations confirm that the flexible arm of HU-2, a domain proposed for DNA binding [Tanaka et al., Nature 310 (1984) 376-381; Goshima et al., Gene 96 (1990) 141-145], plays an important role in the physiological function of this protein. The results indicate that a unique conformation of the arm structure of HU protein, particularly the N-terminal half of a two-strand antiparallel beta-ribbon of the structure, is important for the DNA-binding ability of this protein.