Structural and Functional Analyses of Inhibition of Human Dihydroorotate Dehydrogenase by Antiviral Furocoumavirin.

Natural products are important sources of seed compounds for drug discovery. However, it has become difficult in recent years to discover new compounds with valuable pharmacological activities. On the other hand, among the vast number of natural products that have been isolated so far, a considerable number of compounds with specific biological activities are thought to be overlooked in screening that uses biological activity as an index. Therefore, it is conceivable that such overlooked useful compounds may be found by screening compound libraries that have been amassed previously through specific assays. Previously, NPD723, a member of the Natural Products Depository library comprised of a mixture of natural and non-natural products developed at RIKEN, and its metabolite H-006 were found to inhibit growth of various cancer cells at low nanomolar half-maximal inhibitory concentration. Subsequent analysis revealed that H-006 strongly inhibited human dihydroorotate dehydrogenase (DHODH), the rate-limiting enzyme in the de novo pyrimidine biosynthetic pathway. Here, we elucidated the crystal structure of the DHODH-flavin mononucleotide-orotic acid-H-006 complex at 1.7 Å resolution to determine that furocoumavirin, the S-enantiomer of H-006, was the actual inhibitor. The overall mode of interaction of furocoumavirin with the inhibitor binding pocket was similar to that described for previously reported tight-binding inhibitors. However, the structural information together with kinetic characterizations of site-specific mutants identified key unique features that are considered to contribute to the sub-nanomolar inhibition of DHODH by furocoumavirin. Our finding identified new chemical features that could improve the design of human DHODH inhibitors.

The structure of the rat vitamin B12 transporter TC and its complex with glutathionylcobalamin.

Vitamin B12 (cobalamin or Cbl) functions as a cofactor in two important enzymatic processes in human cells, and life is not sustainable without it. B12 is obtained from food and travels from the stomach, through the intestine, and into the bloodstream by three B12-transporting proteins: salivary haptocorrin (HC), gastric intrinsic factor, and transcobalamin (TC), which all bind B12 with high affinity and require proteolytic degradation to liberate Cbl. After intracellular delivery of dietary B12, Cbl in the aquo/hydroxocobalamin form can coordinate various nucleophiles, for example, GSH, giving rise to glutathionylcobalamin (GSCbl), a naturally occurring form of vitamin B12. Currently, there is no data showing whether GSCbl is recognized and transported in the human body. Our crystallographic data shows for the first time the complex between a vitamin B12 transporter and GSCbl, which compared to aquo/hydroxocobalamin, binds TC equally well. Furthermore, sequence analysis and structural comparisons show that TC recognizes and transports GSCbl and that the residues involved are conserved among TCs from different organisms. Interestingly, haptocorrin and intrinsic factor are not structurally tailored to bind GSCbl. This study provides new insights into the interactions between TC and Cbl.

Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.

Ever since the historic discovery of the cooperative oxygenation of its multiple subunits, hemoglobin (Hb) has been among the most exhaustively studied allosteric proteins. However, the lack of structural information on the intermediates between oxygenated and deoxygenated forms prevents our detailed understanding of the molecular mechanism of its allostery. It has been difficult to prepare crystals of intact oxy-deoxy intermediates and to individually identify the oxygen saturation for each subunit. However, our recent crystallographic studies have demonstrated that giant Hbs from annelids are suitable for overcoming these problems and can provide abundant information on oxy-deoxy intermediate structures. Here, we report the crystal structures of oxy-deoxy intermediates of a 400 kDa Hb (V2Hb) from the annelid Lamellibrachia satsuma, following up on a series of previous studies of similar giant Hbs. Four intermediate structures had average oxygen saturations of 78%, 69%, 55%, and 26%, as determined by the occupancy refinement of the bound oxygen based on ambient temperature factors. The structures demonstrate that the cooperative oxygen dissociation is weaker, large ternary and quaternary changes are induced at a later stage of the oxygen dissociation process, and the ternary and quaternary changes are smaller with local perturbations. Nonetheless, the overall structural transition seemed to proceed in the manner of the MWC two-state model. Our crystallographic snapshots of the allosteric transition of V2Hb provide important experimental evidence for a more detailed understanding of the allostery of Hbs by extension of the Monod-Wyman-Changeux (MWC) model.

Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.

Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a Rhizobia species (Br2DNiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site (∼20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.

In situ crystal data-collection and ligand-screening system at SPring-8.

In situ diffraction data collection using crystallization plates has been utilized for macromolecules to evaluate crystal quality without requiring additional sample treatment such as cryocooling. Although it is difficult to collect complete data sets using this technique due to the mechanical limitation of crystal rotation, recent advances in methods for data collection from multiple crystals have overcome this issue. At SPring-8, an in situ diffraction measurement system was constructed consisting of a goniometer for a plate, an articulated robot and plate storage. Using this system, complete data sets were obtained utilizing the small-wedge measurement method. Combining this system with an acoustic liquid handler to prepare protein-ligand complex crystals by applying fragment compounds to trypsin crystals for in situ soaking, binding was confirmed for seven out of eight compounds. These results show that the system functioned properly to collect complete data for structural analysis and to expand the capability for ligand screening in combination with a liquid dispenser.

Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.

Cooperative oxygen binding of hemoglobin (Hb) has been studied for over half a century as a representative example of the allostericity of proteins. The most important problem remaining to be solved is the lack of structural information on the intermediates between the oxygenated and deoxygenated forms. In order to characterize the intermediate structures, it is necessary to obtain intermediate-state crystals, determine their oxygen saturations and then determine the oxygen saturations of each of their constituent subunits, all of which are challenging issues even now. Here, intermediate forms of the 400 kDa giant Hb from the tubeworm Oligobrachia mashikoi are reported. To overcome the above problems without any artificial modifications to the protein or prosthetic groups, intermediate crystals of the giant Hb were prepared from fully oxygenated crystals by a soaking method. The oxygen saturation of the crystals was measured by in situ observation with a microspectrophotometer using thin plate crystals processed by an ultraviolet laser to avoid saturation of absorption. The oxygen saturation of each subunit was determined by occupancy refinement of the bound oxygen based on ambient temperature factors. The obtained structures reveal the detailed relationship between the structural transition and oxygen dissociation. The dimer subassembly of the giant Hb shows strong correlation with the local structural changes at the heme pockets. Although some local ternary-structural changes occur in the early stages of the structural transition, the associated global ternary-structural and quaternary-structural changes might arise at about 50% oxygen saturation. The models based on coarse snapshots of the allosteric transition support the conventional two-state model of Hbs and provide the missing pieces of the intermediate structures that are required for full understanding of the allosteric nature of Hbs in detail.

X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii.

Plant-type ferredoxin (Fd) is an electron transfer protein in chloroplast. Redox-dependent structural change of Fd controls its association with and dissociation from Fd-dependent enzymes. Among many X-ray structures of oxidized Fd have been reported so far, very likely a given number of them was partially reduced by strong X-ray. To understand the precise structural change between reduced and oxidized Fd, it is important to know whether the crystals of oxidized Fd may or may not be reduced during the X-ray experiment. We prepared the thin plate-shaped Fd crystals from Chlamydomonas reinhardtii and monitored its absorption spectra during experiment. Absorption spectra of oxidized Fd crystals were clearly changed to that of reduced form in an X-ray dose-dependent manner. In another independent experiment, the X-ray diffraction images obtained from different parts of one single crystal were sorted and merged to form two datasets with low and high X-ray doses. An Fo-Fo map calculated from the two datasets showed that X-ray reduction causes a small displacement of the iron atoms in the [2Fe-2S] cluster. Both our spectroscopic and crystallographic studies confirm X-ray dose-dependent reduction of Fd, and suggest a structural basis for its initial reduction step especially in the core of the cluster.

Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters.

The Escherichia coli uracil:proton symporter UraA is a prototypical member of the nucleobase/ascorbate transporter (NAT) or nucleobase/cation symporter 2 (NCS2) family, which corresponds to the human solute carrier family SLC23. UraA consists of 14 transmembrane segments (TMs) that are organized into two distinct domains, the core domain and the gate domain, a structural fold that is also shared by the SLC4 and SLC26 transporters. Here we present the crystal structure of UraA bound to uracil in an occluded state at 2.5 Å resolution. Structural comparison with the previously reported inward-open UraA reveals pronounced relative motions between the core domain and the gate domain as well as intra-domain rearrangement of the gate domain. The occluded UraA forms a dimer in the structure wherein the gate domains are sandwiched by two core domains. In vitro and in vivo biochemical characterizations show that UraA is at equilibrium between dimer and monomer in all tested detergent micelles, while dimer formation is necessary for the transport activity. Structural comparison between the dimeric UraA and the recently reported inward-facing dimeric UapA provides important insight into the transport mechanism of SLC23 transporters.

Early tissue formation on whole-area osteochondral defect of rabbit patella by covering with fibroin sponge.

Large osteochondral defects have been difficult to repair via tissue engineering treatments due to the lack of a sufficient number of source cells for repairing the defect and to the severe mechanical stresses affecting the replacement tissue. In the present study, whole-area osteochondral defects of rabbit patella were covered and wrapped with a fibroin sponge containing chondrocytes, with or without Green Fluorescent Protein (GFP) transgenic marking, on the surface facing the osteochondral defect. Five of eight osteochondral defects that were covered with the chondrocyte-seeded fibroin sponges showed hyaline cartilage-like repair containing no fibroin fragments at 6 weeks after surgery. The repaired tissue showed a layer formation, which showed intensive safranin-O and toluidine blue staining, and which showed positive type II collagen immunostaining. The average surface coverage of the repaired cartilage was 53%. On average, 48% of the cells in the repaired tissue were derived from GFP transgenic chondrocytes, which had been seeded in the fibroin sponge. The fibroin-sponge covering had the potential to allow the early repair of large osteochondral defects. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 104B: 1474-1482, 2016.

Fluctuation in Plasma 5-Fluorouracil Concentration During Continuous 5-Fluorouracil Infusion for Colorectal Cancer.

BACKGROUND/AIM: It is generally believed that the plasma concentration of 5-fluorouracil (5-FU) is constant when 5-FU is continually administered for chemotherapy. The aim of the present study was to verify whether this is true. PATIENTS AND METHODS: Nine patients with colorectal cancer were enrolled in this study. All patients received chemotherapy; four patients received FOLFIRI (leucovorin, 5-fluorouracil, irinotecan) and five received FOLFOX (leucovorin, 5-fluorouracil, oxaliplatin). 5-FU was administered continuously (2400 mg/m(2)) for 46 h. Serum was collected at 12 points after the start of administration. The concentration of 5-FU was evaluated using a new immunoassay method and gas chromatography-mass spectrometric (GC/MS) method. RESULTS: The concentrations of 5-FU fluctuated dramatically over time, with greater than 3-fold changes in each individual, and the pattern was not constant. CONCLUSION: Because the serum concentration of 5-FU fluctuates and displays various patterns, the dosage should not be based on body surface area. A new individualized method for determining the 5-FU dosage should be developed.

Factors associated with restricted hip extension during gait in women after total hip arthroplasty.

PURPOSE: A decreased peak hip extension angle in the late stance phase is a major gait abnormality in patients with THA. The purpose of this study was to determine the relationship between peak hip extension angle during gait and functional impairments such as muscle weakness and the limitation in joint range of motion and to identify the clinical factors influencing peak hip extension angle during gait. METHODS: 67 female volunteers with THA were examined. Biomechanical gait analysis was performed to measure peak hip extension angle during gait. Maximal isometric strength of the hip and knee, passive hip extension range of motion, leg length discrepancy, and hip pain were assessed. RESULTS: Peak hip extension angle during gait significantly correlated with passive hip extension range of motion (r = 0.259), hip pain (r = -0.264), isometric strengths of the hip musculature (r = 0.278-0.491), and knee extensor (r = 0.386). Stepwise multiple regression analysis revealed that hip abductor torque (ß = 0.355, P = 0.001), hip pain (ß = -0.353, P = 0.001), and passive hip extension range of motion (ß = 0.258, P = 0.011) were significant contributors to peak hip extension angle during gait (R2 = 0.408). CONCLUSIONS: Our findings suggest that THA rehabilitation aimed at improving gait ability should focus on strengthening the hip abductors, controlling hip pain and increasing range of motion of hip extension.

Long term results with the interlocking uncemented long stem in revision hip arthroplasty: a mean 15-year follow-up.

Stem fixation is difficult to achieve in severe proximal bone loss in revision hip surgery. In this study, we sought to present the results of distally-locked stem with screws (HUCKESTEP HIP stem) in 21 revision hips with mean follow-up period of 15 years. The preoperative mean Japanese Orthopaedic Association hip score had improved from 54 to 75 points. Further revisions were required for 2 stems, in one because of infection and the other because of screws fracture and subsidence. With removal of the stem for any reason as an end-point, the cumulative survival at 15 years was 90.4%. While this study had small number, the use of this interlocking stem for revision hips with extensive proximal bone defects provided satisfactory 15-year clinical and radiographic results.

Laparoscopic right hemicolectomy for ascending colon cancer with persistent mesocolon.

Persistent ascending or descending mesocolon is an embryological anomaly that occurs during the final process of intestinal development in organogenesis. Specifically, the primitive dorsal mesocolon fails to fuse with the parietal peritoneum in the fifth month of gestation. Herein, we describe a case of ascending colon cancer with persistent ascending and descending mesocolon treated by laparoscopic right hemicolectomy. Preoperative computed tomography imaging of the abdomen demonstrated that the descending colon shifted at the midline of the abdomen and the sigmoid colon was located under the ascending colon. The detailed preoperative imaging examination revealed malpositioning of the large intestine and aided in the procedural planning. Because persistent mesocolon may result in the formation of abnormal adhesions, an accurate preoperative diagnosis is essential. We propose that it is important to consider this anomaly when making the preoperative imaging diagnosis to ensure a safe operation.

SPring-8 BL41XU, a high-flux macromolecular crystallography beamline.

SPring-8 BL41XU is a high-flux macromolecular crystallography beamline using an in-vacuum undulator as a light source. The X-rays are monochromated by a liquid-nitrogen-cooling Si double-crystal monochromator, and focused by Kirkpatrick-Baez mirror optics. The focused beam size at the sample is 80 µm (H) × 22 µm (V) with a photon flux of 1.1 × 10(13) photons s(-1). A pinhole aperture is used to collimate the beam in the range 10-50 µm. This high-flux beam with variable size provides opportunities not only for micro-crystallography but also for data collection effectively making use of crystal volume. The beamline also provides high-energy X-rays covering 20.6-35.4 keV which allows ultra-high-resolution data to be obtained and anomalous diffraction using the K-edge of Xe and I. Upgrade of BL41XU for more rapid and accurate data collection is proceeding. Here, details of BL41XU are given and an outline of the upgrade project is documented.

Eicosapentaenoic acid modifies cytokine activity and inhibits cell proliferation in an oesophageal cancer cell line.

BACKGROUND/AIM: The present study investigated the effect of eicosapentaenoic acid (EPA) on nuclear factor-kappa B (NF-κB) activation, inflammatory interleukin-6 (IL-6) production, and cell proliferation in a human oesophageal carcinoma cell line (TE-1). MATERIALS AND METHODS: Lipopolysaccharide (LPS)-induced IL-6 production in TE-1 cells in the presence or absence of EPA was determined using enzyme-linked immunosorbent assay (ELISA). The proliferation of TE-1 cells was determined by the WST-1 assay. TE-1 cells were stained with Hoechst 33342 and propidium iodide to observe apoptosis. Immunohistochemical staining of NF-κB in TE-1 cells was performed. RESULTS: LPS increased IL-6 production in TE-1 cells, and EPA treatment prevented this effect. EPA treatment inhibited NF-κB activation and induced apoptosis of TE-1 cells. CONCLUSION: EPA inhibits NF-κB activation and IL-6 production in oesophageal cancer cells, their inducing apoptosis. These effects of EPA may be of benefit in improving the outcome of cancer surgery.

A point mutation in ftmD blocks the fumitremorgin biosynthetic pathway in Aspergillus fumigatus strain Af293.

Fumitremorgins (FTMs), tremorgenic mycotoxins produced by the human pathogen Aspergillus fumigatus, are prenylated indole alkaloids that have been extensively studied in view of their diverse chemical structures and biological activities. Their biosynthetic gene (ftm) cluster was identified on the basis of the genome sequence of A. fumigatus. However, it has been reported that the ftm cluster in genome reference strain Af293 is inactive, which makes complete understanding of the FTM pathway difficult. Hence, we used an FTM-producing strain of A. fumigatus, BM939, to dissect the FTM pathway. Here, we delineate the genetic determinant for the observed defect in the FTM pathway in A. fumigatus Af293. Metabolite profiling and sequence comparison of the two strains revealed a point mutation in ftmD as a possible cause of altered metabolite production in strain Af293. FTM production in Af293 was restored when a DNA fragment containing ftmD from BM939 was introduced. Biochemical analysis indicated that FtmD is a methyltransferase that catalyzes the conversion of 6-hydroxytryprostatin B into tryprostatin A. The mutated FtmD retained enzymatic activity but did not function under physiological conditions, resulting in blockage of the FTM pathway in A. fumigatus Af293.

Minimally invasive surgery using intraoperative real-time capsule endoscopy for small bowel lesions.

BACKGROUND: The small bowel has been considered the "black box" of gastroenterology. Identifying the exact site of small bowel hemorrhage is often difficult, thus complicating surgical treatment. We report two cases of small bowel bleeding lesions that were successfully managed by intraoperative real-time capsule endoscopy and minimally invasive surgery. METHODS: We developed a double-lumen tube similar to, but thinner and longer than, the Miller-Abbott tube. We insert the tube nasally, 3 or 4 days preoperatively, such that its balloon tip reaches the anus by the operative day. During surgery, the endoscopic capsule is connected to the balloon tip of the tube that protrudes from the anus. An assistant pulls on the nasal end of the tube, bringing the balloon tip and capsule back into the bowel. Capsule endoscopic images are displayed in a real-time video format. RESULTS: We employed this procedure in two patients with repeated melena. Various examinations including gastroendoscopy and total colonoscopy showed bleeding confined to the small bowel, but the exact lesion site was unknown. Minimally invasive surgery was successfully performed in both patients: open minilaparotomy in one and laparoscopy in the other. The small bowel and capsule endoscope were easily controlled during minilaparotomy, and real-time capsule endoscopic images clearly identified the bleeding lesion. Control of the small bowel was more difficult in the laparoscopic case; however, real-time capsule endoscopic images identified a small tumor that was successfully resected. CONCLUSIONS: Intraoperative capsule endoscopy combined with the tube provides surgeons real-time images indicating the exact site of lesions. The tube also helps surgeons control the position of the capsule endoscope and enables suction of intraluminal fluid or inflation of the lumen to allow clearer views during the operation. We conclude that combined use of capsule endoscopy and the tube facilitates management of bleeding lesions in the small bowel.

Current status of multichannel electrogastrography and examples of its use.

Electrogastrography (EGG) is a non-invasive diagnostic motility for recording gastric myoelectrical activity. Gastric myoelectrical activity was first recorded in 1922. Advances in recording equipment enabled widespread use of cutaneous EGG after 1985. Later, introduction of multichannel EGG (M-EGG) enabled measurement of electrical activity transmission. At present, M-EGG findings are used as objective indicators of gastric motility disorders caused by various diseases. EGG measures two categories of gastric electrical activity: electrical response activity, or spike potentials; and electrical control activity, or slow waves. The appearance of abnormal rhythmic electrical activity is indicative of abnormalities in gastric motility. The normal frequency range of gastric electrical activity (normogastria) is around 3 cycles per?min. Multiple EGG parameters assist in the assessment of gastric myoelectrical activity, and significant correlations between EGG and other gastric motility tests have been demonstrated in many studies. In Japan, however, EGG remains in the exploratory stage, and its clinical use is limited. There are large variations in procedures and systems used in previous studies, thus there is a need for standardization of EGG procedures and technical terminology. Here, we outline the current status of EGG and report the M-EGG procedures used in our department in addition to our M-EGG findings.

Evaluation of 5-FU plasma concentration by 13C breath test in patients treated with oral 5-FU analogs.

BACKGROUND/AIM: The objective of this study was to investigate the influence of digestive gastrointestinal absorption function on the pharmacokinetics of the orally-administered anticancer drug, Tegafur-gimestat-otastat potassium (TS-1), by measuring the plasma 5-fluorouracil (5-FU) concentration using stable isotope breath tests. PATIENTS AND METHODS: Twenty-nine patients with progressive/recurrent digestive organ cancer were enrolled for this pharmacokinetic study, and blood samples were obtained from each patient. The area under-the-time-concentration curve between 0 and 480 min (AUC0-480 min), time-of-drug concentration peak (T(max)), maximum drug concentration (C(max)) and the half-life period (t(1/2)) of 5-FU were investigated. Simultaneously, a continuous (13)C-acetate breath test was performed for each patient. The parameters measured with the breath test were the area under the (13)CO(2) excretion rate curve between 0-4 h (AUC(0-4h)), peak (13)CO(2) value and elimination rate constant (K(el)) value. RESULTS: The AUC(0-8h) and C(max) of 5-FU were significantly correlated with K(el) (p=0.012 and p=0.024, respectively), and the 5-FU C(max) value was significantly correlated with the peak value of (13)CO(2) (p=0.037). Multivariate regression analysis also found the C(max) of 5-FU to be associated with K(el) (p=0.0118). The C(max) and AUC(0-8h) of 5-FU were also significantly correlated (p<0.0001). CONCLUSION: The results of this study suggest that gastrointestinal absorption is closely-related to plasma 5-FU concentration after oral administration of TS-1.

An immunoassay method for the pharmacokinetics of 5-fluorouracil in patients with gastric cancer administered adjuvant chemotherapy.

Conventional gas chromatography-mass spectrometry (GC-MS) was compared with a new immunoassay method for measuring plasma (5-FU) concentrations in adjuvant chemotherapy with TS-1 for patients with gastric cancer. TS-1 was administered orally to patients after gastrectomy. Blood samples for pharmacokinetic analysis were collected on the seventh day of treatment. The mean area under the time concentration curve (AUC)(0-8), half-life (t(1/2)), and maximum drug concentration (C(max)) obtained by the two methods were as follows: GC-MS, 847.9 µg/ml/hr, 2.76 h, and 186.6 ng/ml; and immunoassay, 1311.2 µg/ml/hr, 3.5 h, and 259.8 ng/ml. Significant correlations were observed for AUC(0-8) (p=0.0001), C(max) (p=0.0007), and changes in the 5-FU concentration in blood over time (p=0.018) for the two methods. Compared with the conventional GC-MS method, the new immunoassay method provides similar results, but is simpler and results can be obtained earlier. This method will be useful for monitoring the 5-FU concentration in serum from patients with gastric cancer receiving TS-1.