Novel chemical scaffolds of the tumor marker AKR1B10 inhibitors discovered by 3D QSAR pharmacophore modeling.

AIM: Recent evidence suggests that aldo-keto reductase family 1 B10 (AKR1B10) may be a potential diagnostic or prognostic marker of human tumors, and that AKR1B10 inhibitors offer a promising choice for treatment of many types of human cancers. The aim of this study was to identify novel chemical scaffolds of AKR1B10 inhibitors using in silico approaches. METHODS: The 3D QSAR pharmacophore models were generated using HypoGen. A validated pharmacophore model was selected for virtual screening of 4 chemical databases. The best mapped compounds were assessed for their drug-like properties. The binding orientations of the resulting compounds were predicted by molecular docking. Density functional theory calculations were carried out using B3LYP. The stability of the protein-ligand complexes and the final binding modes of the hit compounds were analyzed using 10 ns molecular dynamics (MD) simulations. RESULTS: The best pharmacophore model (Hypo 1) showed the highest correlation coefficient (0.979), lowest total cost (102.89) and least RMSD value (0.59). Hypo 1 consisted of one hydrogen-bond acceptor, one hydrogen-bond donor, one ring aromatic and one hydrophobic feature. This model was validated by Fischer's randomization and 40 test set compounds. Virtual screening of chemical databases and the docking studies resulted in 30 representative compounds. Frontier orbital analysis confirmed that only 3 compounds had sufficiently low energy band gaps. MD simulations revealed the binding modes of the 3 hit compounds: all of them showed a large number of hydrogen bonds and hydrophobic interactions with the active site and specificity pocket residues of AKR1B10. CONCLUSION: Three compounds with new structural scaffolds have been identified, which have stronger binding affinities for AKR1B10 than known inhibitors.

Effects of L-glutamine supplementation on degradation rate and rumen fermentation characteristics in vitro.

OBJECTIVE: Two follow-up studies (exp. 1 and 2) were conducted to determine the effects of L-glutamine (L-Gln) supplementation on degradation and rumen fermentation characteristics in vitro. METHODS: First, rumen liquor from three cannulated cows was used to test L-Gln (50 mM) degradation rate and ammonia-N production at 6, 12, 24, 36, and 48 h after incubation (exp. 1). Second, rumen liquor from two cannulated steers was used to assess the effects of five levels of L-Gln including 0% (control), 0.5%, 1%, 2%, and 3% at 0, 3, 6, 12, 24, 36, and 48 h after incubation on fermentation characteristics, gas production, and degradability of nutrients (exp. 2). RESULTS: In exp. 1, L-Gln degradation rate and ammonia-N concentrations increased over time (p<0.001). In exp. 2, pH was reduced significantly as incubation time elapsed (p<0.001). Total gas production tended to increase in all groups as incubation time increased. Acetate and propionate tended to increase by increasing glutamine (Gln) levels, whereas levels of total volatile fatty acids (VFAs) were the highest in 0.5% and 3% Gln groups (p<0.001). The branched-chain VFA showed both linear and quadratic effects showing the lowest values in the 1% Gln group particularly after 6 h incubation (p<0.001). L-Gln increased crude protein degradability (p<0.001), showing the highest degradability in the 0.5% Gln group regardless of incubation time (p<0.05). Degradability of acid detergent fiber and neutral detergent fiber showed a similar pattern showing the highest values in 0.5% Gln group (p<0.10). CONCLUSION: Although L-Gln showed no toxicity when it was supplemented at high dosages (2% to 3% of DM), 0.5% L-Gln demonstrated the positive effects on main factors including VFAs production in-vitro. The results of this study need to be verified in further in-vivo study.

Traumatic cervical cord transection without facet dislocations--a proposal of combined hyperflexion-hyperextension mechanism: a case report.

A patient is presented with a cervical spinal cord transection which occurred after a motor vehicle accident in which the air bag deployed and the seat belt was not in use. The patient had complete quadriplegia below the C5 level and his imaging study showed cervical cord transection at the level of the C5/6 disc space with C5, C6 vertebral bodies and laminar fractures. He underwent a C5 laminectomy and a C4-7 posterior fusion with lateral mass screw fixation. Previous reports have described central cord syndromes occurring in hyperextension injuries, but in adults, acute spinal cord transections have only developed after fracture-dislocations of the spine. A case involving a post-traumatic spinal cord transection without any evidence of radiologic facet dislocations is reported. Also, we propose a combined hyperflexion-hyperextension mechanism to explain this type of injury.

The effect of single-nucleotide polymorphisms within heat shock protein beta 1 on beef quantity in Korean native steers.

Heat shock protein beta 1 (HSPB1), a member of the heat-shock family of protein, is a relatively small (27 kDa) molecular chaperone protein associated with cellular development. The relationship between HSPB1 expression and muscle growth in beef cattle has previously been reported, but there have been no reports of DNA markers related to meat quantity in Korean native steers. Therefore, the aim of this study was to evaluate the relationship of single-nucleotide polymorphisms (SNPs) within HSPB1 in terms of the carcass traits related to muscle growth in Korean native steers. Through direct sequencing, we discovered three SNPs: g.111 T > C SNP (rs208395876) and g.2548 C > G SNP (rs483014585) were respectively located in 5 '  UTR (untranslated region) and 3 '  UTR. Further, g.2352 T > C SNP (rs110832311) was located in the adjacent region of the RNA splicing site. The least square means of steers with a CC genotype of g.111 T > C SNP had a significantly higher meat ratio ( P   =  0.04), while the least square means of steers with a CC genotype of g.2352 T > C SNP had a significantly higher meat ratio ( P   =  0.002) and lower back-fat thickness ( P   =  0.004) than those of the other genotype. Moreover, although the least square means of steers with CC-CC, CT-CC, and TT-CC genotypes were significantly decreased for back-fat thickness, they were significantly increased for the meat ratio. Therefore, our results suggested that g.111 T > C SNP and g.2352 T > C SNP could be a causal mutation related to an adipose metabolism in Korean cattle steer.

Clinicopathological considerations in patients with lumbosacral extraforaminal stenosis.

Lumbosacral extraforaminal stenosis is not uncommon among patients being treated for radicular symptoms. Patients who had lumbosacral extraforaminal stenosis were reviewed, and cadaver dissection was used to determine the anatomy of extraforaminal lesions. A total of 167 patients with lumbosacral spinal stenosis who underwent surgery from March 2004 to February 2006 were reviewed retrospectively. Among these, extraforaminal stenosis was observed in 26 patients (mean age 61.4 y; range 46-79). Leg pain and neurogenic claudication were common in patients with extraforaminal stenosis. One level was involved for 15 patients and 2 levels were involved for 11 patients. Complete decompression of the dorsal root ganglion or a root compressed by the fibrocartilagenous ligamentum flavum or a hypertrophied superior facet was performed. The mean follow-up was 8.3 months (range 6-26 months). The causes of extraforaminal stenosis were superior facet hypertrophy, especially hypertrophy of the superior lateral portion, or thickening of the ligamentum flavum, intertransverse ligament, or transforaminal ligament. T1-weighted, coronal MRI showed root impingement in the far-lateral zone. Postoperative outcomes were assessed using the Prolo scale; 13 patients demonstrated excellent outcomes, while 11 patients had good outcomes. No major complications or recurrences were observed during follow-up. Therefore, lumbosacral extraforaminal stenosis should be included in the differential diagnosis of lumbar radicular pain. A precise diagnosis using MRI is important, and complete decompression with an understanding of the extraforaminal anatomy is required.

Thrombosed giant aneurysm of the pericallosal artery with inconclusive findings of multiple neuroimaging studies.

A 65-year-old woman presented with a thrombosed giant pericallosal artery aneurysm manifesting as headache and memory loss that developed over a 2-year period. Computed tomography (CT), magnetic resonance (MR) imaging, and conventional and CT angiography could not establish the differential diagnosis. Open craniotomy revealed the mass as thrombosed giant aneurysm from the pericallosal artery. Direct clipping with thrombectomy was performed successfully with an uneventful postoperative course. Thrombosed giant aneurysm of the distal anterior cerebral artery should be considered in the differential diagnosis of an unusual mass in the mid-frontal area, particularly in the presence of inconclusive angiographic and MR imaging findings.

ASIA SPINE: The Past, Present, and Future.

The sharing of international academic accomplishment and friendship is important; furthermore, to better understand and anticipate the future, we should look back and remember where we started. Regarding ASIA SPINE, the authors aimed to record how the pioneers of Asian spinal surgery started this spine meeting series more than 20 years ago and that later developed into the present state of the conference. The authors will also explore the possible future of this conference. In June 1996, when Professor Hiroshi Nakagawa organized the 11th Annual Meeting of the Japanese Society of Spinal Surgery, spinal neurosurgeons from Korea and Japan including Professor Young Soo Kim, Professor Jung Keun Suh, and Professor Nakagawa discussed the establishment of a multinational conference on spinal surgery via a partnership between the 2 countries. Finally, from September 18 to 20, 1997, the First Biennial Meeting of the Japan-Korea Conference on Spinal Surgery was held in Nagoya, Japan, with Professor Hiroshi Nakagawa as the first organizing President. From then, a biennial meeting was held every other year in Korea or Japan until 2009. In September 2010, the next generation of spinal neurosurgeons decided to organize the first meeting of ASIA SPINE in Incheon, Korea, in order to represent all Asian spine specialists. This meeting has been since held annually around the region including in Taiwan. Remembering the pioneers in the field of spinal surgery is invaluable and extremely important. The authors hope that interest in ASIA SPINE will further expand to other nations in Asia who have advanced philosophies and refined technologies. We wish ASIA SPINE continued success and the ability to promote prolonged international friendship among the Asian countries .

Sulfonanilide Derivatives in Identifying Novel Aromatase Inhibitors by Applying Docking, Virtual Screening, and MD Simulations Studies.

Breast cancer is one of the leading causes of death noticed in women across the world. Of late the most successful treatments rendered are the use of aromatase inhibitors (AIs). In the current study, a two-way approach for the identification of novel leads has been adapted. 81 chemical compounds were assessed to understand their potentiality against aromatase along with the four known drugs. Docking was performed employing the CDOCKER protocol available on the Discovery Studio (DS v4.5). Exemestane has displayed a higher dock score among the known drug candidates and is labeled as reference. Out of 81 ligands 14 have exhibited higher dock scores than the reference. In the second approach, these 14 compounds were utilized for the generation of the pharmacophore. The validated four-featured pharmacophore was then allowed to screen Chembridge database and the potential Hits were obtained after subjecting them to Lipinski's rule of five and the ADMET properties. Subsequently, the acquired 3,050 Hits were escalated to molecular docking utilizing GOLD v5.0. Finally, the obtained Hits were consequently represented to be ideal lead candidates that were escalated to the MD simulations and binding free energy calculations. Additionally, the gene-disease association was performed to delineate the associated disease caused by CYP19A1.

PreSPI: a domain combination based prediction system for protein-protein interaction.

With the accumulation of protein and its related data on the Internet, many domain-based computational techniques to predict protein interactions have been developed. However, most techniques still have many limitations when used in real fields. They usually suffer from low accuracy in prediction and do not provide any interaction possibility ranking method for multiple protein pairs. In this paper, we propose a probabilistic framework to predict the interaction probability of proteins and develop an interaction possibility ranking method for multiple protein pairs. Using the ranking method, one can discern the protein pairs that are more likely to interact with each other in multiple protein pairs. The validity of the prediction model was evaluated using an interacting set of protein pairs in yeast and an artificially generated non-interacting set of protein pairs. When 80% of the set of interacting protein pairs in the DIP (Database of Interacting Proteins) was used as a learning set of interacting protein pairs, high sensitivity (77%) and specificity (95%) were achieved for the test groups containing common domains with the learning set of proteins within our framework. The stability of the prediction model was also evident when tested over DIP CORE, HMS-PCI and TAP data. In the validation of the ranking method, we reveal that some correlations exist between the interacting probability and the accuracy of the prediction.

Molecular interactions of UvrB protein and DNA from Helicobacter pylori: Insight into a molecular modeling approach.

Helicobacter pylori (H. pylori) persevere in the human stomach, an environment in which they encounter many DNA-damaging conditions, including gastric acidity. The pathogenicity of H. pylori is enhanced by its well-developed DNA repair mechanism, thought of as 'machinery,' such as nucleotide excision repair (NER). NER involves multi-enzymatic excinuclease proteins (UvrABC endonuclease), which repair damaged DNA in a sequential manner. UvrB is the central component in prokaryotic NER, essential for damage recognition. Therefore, molecular modeling studies of UvrB protein from H. pylori are carried out with homology modeling and molecular dynamics (MD) simulations. The results reveal that the predicted structure is bound to a DNA hairpin with 3-bp stem, an 11-nucleotide loop, and 3-nt 3' overhang. In addition, a mutation of the Y96A variant indicates reduction in the binding affinity for DNA. Free-energy calculations demonstrate the stability of the complex and help identify key residues in various interactions based on residue decomposition analysis. Stability comparative studies between wild type and mutant protein-DNA complexes indicate that the former is relatively more stable than the mutant form. This predicted model could also be useful in designing new inhibitors for UvrB protein, as well as preventing the pathogenesis of H. pylori.

QSAR modeling to design selective histone deacetylase 8 (HDAC8) inhibitors.

HDAC8 inhibitors have become an attractive treatment for cancer. This study aimed to facilitate the identification of potential chemical scaffolds for the selective inhibition of histone deacetylase 8 (HDAC8) using in silico approaches. Non-linear QSAR classification and regression models of HDAC8 inhibitors were developed with support vector machine. Mean impact value-based sequential forward feature selection and grid search strategy were used for molecular descriptor selection and parameter optimization, respectively. The generated QSAR models were validated by leave-one-out cross validation and an external test set. The best QSAR classification model yielded 84 % of accuracy on the external test prediction and Matthews correlation coefficient is 0.69. The best QSAR regression model showed low root-mean-square error (0.63) and high squared correlation coefficient (0.53) for the test set. The validated QSAR models together with various drug-like properties, molecular docking and molecular dynamics simulation were sequentially used as a multi-step query in chemical database virtual screening. Finally, two hit compounds were discovered as new structural scaffolds which can be used for further in vitro and in vivo activity analyses. The strategy used in this study could be a promising computational strategy which can be utilized for other target drug design.

Structural Identification of a Non-Glycosylated Variant at Ser126 for O-Glycosylation Site from EPO BRP, Human Recombinant Erythropoietin by LC/MS Analysis.

A variant peak was detected in the analysis of RP-HPLC of rHu-EPO, which has about 7% relative content. Fractions of the main and the variant peaks were pooled separately and further analyzed to identify the molecular structure of the variant peak. Total mass analysis for each peak fraction using ESI-TOF MS shows differences in molecular mass. The fraction of the main peak tends to result in higher molecular masses than the fraction of the variant. The detected masses for the variant are about 600-1000 Da smaller than those for the main peak. Peptide mapping analysis for each peak fraction using Asp-N and Glu-C shows differences in O-glycopeptide profiles at Ser126. The O-glycopeptides were not detected in the fraction of the variant. It is concluded that the variant peak is non-O-glycosylated rHu-EPO and the main peak is fully O-glycosylated rHu-EPO at Ser126.

Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition.

Ribosome inhibiting proteins, RIPs, are a widespread family of toxic enzymes. Ricin is a plant toxin used as a poison and biological warfare agent; shiga toxin is a homologue expressed by pathogenic strains of E. coli. There is interest in creating effective antidote inhibitors to this class of enzymes. RIPs act by binding and hydrolyzing a specific adenine base from rRNA. Previous virtual screens revealed that pterins could bind in the specificity pocket of ricin and inhibit the enzyme. In this paper we explore a range of compounds that could serve as better platforms for inhibitor design. This establishes the importance of key hydrogen bond donors and acceptors for active-site complementarity. 8-Methyl-9-oxoguanine is a soluble compound that has the best inhibitory properties of any platform tested. The X-ray structure of this complex revealed that the inhibitor binds in an unexpected way that provides insight for future design. Several inhibitors of ricin were also shown to be inhibitors of shiga toxin, suggesting this program has the potential to develop effective antidotes to an important form of food poisoning.

Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair.

Protein-protein interaction plays a critical role in biological processes. The identification of interacting proteins by computational methods can provide new leads in functional studies of uncharacterized proteins without performing extensive experiments. We developed a database for the potentially interacting domain pairs (PID) extracted from a dataset of experimentally identified interacting protein pairs (DIP: database of interacting proteins) with InterPro, an integrated database of protein families, domains and functional sites. In developing protein interaction databases and predictive methods, sensitive statistical scoring systems is critical to provide a reliability index for accurate functional analysis of interaction networks. We present a statistical scoring system, named "PID matrix score" as a measure of the interaction probability (interactability) between domains. This system provided a valuable tool for functional prediction of unknown proteins. For the evaluation of PID matrix, cross validation was performed with subsets of DIP data. The prediction system gives about 50% sensitivity and more than 98% specificity, which implies that the information for interacting proteins pairs could be enriched about 30 fold with the PID matrix. It is demonstrated that mapping of the genome-wide interaction network can be achieved by using the PID matrix.

Microsurgical midline approach for the decompression of extraforaminal stenosis in L5-S1.

OBJECT: When performing surgery, the extraforaminal window is very narrow at the L5-S1 level. The authors describe a microsurgical method for decompression of the L-5 nerve root trapped between a marginal osteophyte of the vertebral body and the transverse process. The procedure was performed in 16 patients with extraforaminal stenosis. METHODS: The cranial part of the L5-S1 facet joint and the caudal portion of the pedicle and transverse process of L-5 were removed via a midline skin incision and partial resection of the pars interarticularis; a high-speed drill was used as was a surgical microscope. The affected nerve root was decompressed and mobilized cranially. Postoperatively all patients reported excellent relief of their sciatic pain, and there were no technique-associated complications. There was no recurrence during the follow-up period, that ranged from 14 to 70 months. CONCLUSIONS: The authors recommend this technique for the effective decompression of symptomatic extraforaminal L5-S1 stenosis. The need for a dangerous and tedious removal of the vertebral osteophyte together with spinal fusion is avoided.

PreSPI: design and implementation of protein-protein interaction prediction service system.

With the recognition of the importance of computational approach for protein-protein interaction prediction, many techniques have been developed to computationally predict protein-protein interactions. However, few techniques are actually implemented and announced in service form for general users to readily access and use the techniques. In this paper, we design and implement a protein interaction prediction service system based on the domain combination based protein-protein interaction prediction technique, which is known to show superior accuracy to other conventional computational protein-protein interaction prediction methods. In the prediction accuracy test of the method, high sensitivity (77%) and specificity (95%) are achieved for test protein pairs containing common domains with learning sets of proteins in a Yeast. The stability of the method is also manifested through the testing over DIP CORE, HMS-PCI, and TAP data. The functions of the system are divided into core, subsidiary, and general service function categories. The core function category includes the functions that can be provided only by using the domain combination based protein-protein interaction prediction method. Interaction prediction for a single protein pair and visualization of interaction probability distributions are the functions in this category. The subsidiary function category includes the functions that can be derived from the core functions. Domain combination pair search with high appearance probability and construction of protein interaction network are the functions in this category. Lastly, the general service function category includes the functions that can be implemented by collecting and organizing the protein and domain data in the Internet. Performance, openness and flexibility are the major design goals and they are achieved by adopting parallel execution techniques, Web Services standards, and layered architecture respectively. In this paper, several representative user interfaces of the system are also introduced with comprehensive usage guides.

Structural identification of modified amino acids on the interface between EPO and its receptor from EPO BRP, human recombinant erythropoietin by LC/MS analysis.

Protein modifications of recombinant pharmaceuticals have been observed both in vitro and in vivo. These modifications may result in lower efficacy, as well as bioavailability changes and antigenicity among the protein pharmaceuticals. Therefore, the contents of modification should be monitored for the quality and efficacy of protein pharmaceuticals. The interface of EPO and its receptor was visualized, and potential amino acids interacting on the interface were also listed. Two different types of modifications on the interface were identified in the preparation of rHu-EPO BRP. A UPLC/Q-TOF MS method was used to evaluate the modification at those variants. The modification of the oxidized variant was localized on the Met54 and the deamidated variants were localized on the Asn47 and Asn147. The extent of oxidation at Met54 was 3.0% and those of deamidation at Asn47 and Asn147 were 2.9% and 4.8%, respectively.

Multi-conformation dynamic pharmacophore modeling of the peroxisome proliferator-activated receptor γ for the discovery of novel agonists.

Activation of the peroxisome proliferator-activated receptor γ (PPARγ) is important for the treatment of type 2 diabetes and obesity through the regulation of glucose metabolism and fatty acid accumulation. Hence, the discovery of novel PPARγ agonists is necessary to overcome these diseases. In this study, a newly developed approach, multi-conformation dynamic pharmacophore modeling (MCDPM), was used for screening candidate compounds that can properly bind PPARγ. Highly populated structures obtained from molecular dynamics (MD) simulations were selected by clustering analysis. Based on these structures, pharmacophore models were generated from the ligand-binding pocket and then validated to check the rationality. Consequently, two hits were retrieved as final candidates by utilizing virtual screening and molecular docking simulations. These compounds can be used in the design of novel PPARγ agonists.

Remote cerebral and cerebellar hemorrhage after massive cerebrospinal fluid leakage.

Dural tears can occur during spinal surgery and may lead to cerebrospinal fluid (CSF) leakage which is rarely involved in remote cerebellar hemorrhage. Only a few of cases of simultaneous cerebral and cerebellar hemorrhage have been reported in the English literature. We experienced a case of multiple remote cerebral and cerebellar hemorrhages in a 63-year-old man who exhibited no significant neurologic deficits after spinal surgery. Magnetic resonance imaging (MRI) performed 4 days after the surgery showed a large amount of CSF leakage in the lumbosacral space. The patient underwent the second surgery for primary repair of the dural defect, but complained of headache after dural repair surgery. Brain MRI taken 6 days after the dural repair surgery revealed multifocal remote intracerebral and cerebellar hemorrhages in the right temporal lobe and both cerebellar hemispheres. We recommend diagnostic imaging to secure early identification and treatment of this complication in order to prevent serious neurologic deficits.

Increased Vascular Endothelial Growth Factor in the Ventricular Cerebrospinal Fluid as a Predictive Marker for Subsequent Ventriculoperitoneal Shunt Infection : A Comparison Study among Hydrocephalic Patients.

OBJECTIVE: The aim of this study is to determine the association between the cerebrospinal fluid (CSF) biomarkers and inflammation, and the predictive value of these CSF biomarkers for subsequent shunt associated infection. METHODS: We obtained CSF samples from the patients with hydrocephalus during ventriculoperitoneal (VP) shunt operations. Twenty-two patients were enrolled for this study and divided into 3 groups: subarachnoid hemorrhage (SAH)-induced hydrocephalus, idiopathic normal pressure hydrocephalus (INPH) and hydrocephalus with a subsequent shunt infection. We analyzed the transforming growth factor-ß1, tumor necrosis factor-α, vascular endothelial growth factor (VEGF) and total tau in the CSF by performing enzyme-linked immunosorbent assay. The subsequent development of shunt infection was confirmed by the clinical presentations, the CSF parameters and CSF culture from the shunt devices. RESULTS: The mean VEGF concentration (±standard deviation) in the CSF of the SAH-induced hydrocephalus, INPH and shunt infection groups was 236±138, 237±80 and 627±391 pg/mL, respectively. There was a significant difference among the three groups (p=0.01). Between the SAH-induced hydrocephalus and infection groups and between the INPH and infection groups, there was a significant difference of the VEGF levels (p<0.01). However, the other marker levels did not differ among them. CONCLUSION: The present study showed that only the CSF VEGF levels are associated with the subsequent development of shunt infection. Our results suggest that increased CSF VEGF could provide a good condition for bacteria that are introduced at the time of surgery to grow in the brain, rather than reflecting a sequel of bacterial infection before VP shunt.