ACID: a free tool for drug repurposing using consensus inverse docking strategy.

Drug repurposing offers a promising alternative to dramatically shorten the process of traditional de novo development of a drug. These efforts leverage the fact that a single molecule can act on multiple targets and could be beneficial to indications where the additional targets are relevant. Hence, extensive research efforts have been directed toward developing drug based computational approaches. However, many drug based approaches are known to incur low successful rates, due to incomplete modeling of drug-target interactions. There are also many technical limitations to transform theoretical computational models into practical use. Drug based approaches may, thus, still face challenges for drug repurposing task. Upon this challenge, we developed a consensus inverse docking (CID) workflow, which has a ~ 10% enhancement in success rate compared with current best method. Besides, an easily accessible web server named auto in silico consensus inverse docking (ACID) was designed based on this workflow (http://chemyang.ccnu.edu.cn/ccb/server/ACID).

PADFrag: A Database Built for the Exploration of Bioactive Fragment Space for Drug Discovery.

Structural analyses of drugs and pesticides can enable the identification of new bioactive compounds with novel and diverse scaffolds as well as improve our understanding of the bioactive fragment space. The Pesticide And Drug Fragments (PADFrag) database is a unique bioinformatic-cheminformatic cross-referencing resource that combines detailed bioactive fragment data and potential targets with a strong focus on quantitative, analytic, and molecular-scale information for the exploration of bioactive fragment space for drug discovery ( http://chemyang.ccnu.edu.cn/ccb/database/PADFrag/ ). The main applications of PADFrag are the analysis of the privileged structures within known bioactive molecules, ab initio molecule library design, and core fragment discovery for fragment-based drug design. Other potential applications include prediction of fragment interactions and general pharmaceutical research.

[Effect of Beclin-1 shRNA on hypoxia-induced autophagy in SH-SY5Y cells].

OBJECTIVE: To observe the effect of hypoxia on autophagy in Beclin-1-knockdown SH-SY5Y cells by constructing a stable transfected SH-SY5Y cell lines of silencing Beclin-1 gene. METHODS: Beclin-1shRNA lentiviral vector and negative control lentiviral vector were constructed; the vector was transfected into SH-SY5Y cells; then the expression of Beclin-1 mRNA was detected by RT-PCR, the level of Beclin-1 protein was detected by Western blot. CCK-8 method was used to determine the effect of Beclin-1 knockdown on the viability of SH-SY5Y cells. Next, the blank control, negative control and transfected cells were cultured under 21% normoxia and 5% hypoxia conditions. The expression of LC3 protein in each group was detected by Western blot and the autophagic bodies were observed by electron microscopy. RESULTS: Beclin-1 shRNA significantly inhibited the expression of Beclin-1 mRNA and protein in SH-SY5Y cells; after silencing Beclin 1 gene, the survival rate of Beclin-1 shRNA group cells was no different from that of negative control (NC) group. After 5% hypoxia treatment, compared with NC group, the ratio of LC3Ⅱ/LC3Ⅰand the number of autophagy bodies were all decreased in Beclin-1 shRNA group. CONCLUSIONS: Beclin-1 knockdown SH-SY5Y cell lines and negative control cell lines were successfully established. Lentivirus-mediated Beclin-1 shRNA has no effect on the viability of SH-SY5Y cells, but can inhibit hypoxia-induced autophagy.

High glucose improves healing of periodontal wound by inhibiting proliferation and osteogenetic differentiation of human PDL cells.

Periodontal ligament (PDL) cells play an important role in wound healing of periodontal tissues. Response of PDL cells' cellular activity to high-glucose concentration levels may be the key in understanding the relationship between periodontal disease and diabetes mellitus. We studied the effect of high-glucose medium on proliferation of PDL cells in vitro. PDL cells were cultured for 1, 4, 7, 10, 14 and 17 days in normal (1100 mg/l) glucose or in high (4500 mg/l) glucose medium. The 3-(4,5-dimethylithiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay for proliferation was performed. In order to evaluate the osteogenetic differentiation of human PDL cells, the cells were induced with normal- or high-glucose medium for 1, 7, 14, 21 and 28 days. The results indicated that high glucose significantly inhibited proliferation of PDL cells. Concerning the mineralised nodule formation, the percentage of calcified area to total culture dish of PDL cells in high glucose level was lower than that in normal glucose medium. The increase in alkaline phosphatase activity and collagen expression could be observed in high-glucose-containing osteogenetic factor. In conclusion, high glucose improves healing of periodontal wound by inhibiting proliferation and differentiation of PDL cells, which could explain for delayed periodontal regeneration and healing in diabetic patients.

[Protective effect of hypoxic preconditioning on SH-SY5Y cells injured by oxygen-glucose deprivation].

OBJECTIVE: To investigate the protection effects of hypoxic preconditioning(HPC) on the SH-SY5Y cell injured by oxygen-glu-cose deprivation(OGD),and to discuss the possible mechanism. METHODS: SH-SY5Y cells were randomly divided into 4 groups. In normal group,the cells were cultured without OGD treatment. In HPC group,the cultured SH-SY5Y cells were treated for 5 days by intermittently ex-posing to hypoxic gas mixture (2% O2,5% CO2) for 30 min in every day. In OGD group,the culture medium was replaced by glucose-free medium and the cells were transferred to a humidified incubation chamber flushed by a gas mixture of 1% O2 and 5% CO2 for 10 h. After that, the cells were fed with glucose-supplemented medium and cultured under normoxic condition for 24 h. In HPC+OGD group,the cultured SH-SY5Y cells were treated for 5 days by intermittently exposing to hypoxic gas mixture for 30 min in each day, then the cells were given the same treatments as those in OGD group. The cell viability was assessed by MTT assay. The degree of the cell damage was evaluated by deter-mining lactate dehydrogenase (LDH) leakage. TUNEL staining were used to detect the variation of cell apoptosis. The expression of Caspase 3 and hypoxia inducible factor-1α(HIF-1α) at protein levels was examined by Western blot. RESULTS: Hypoxic preconditioning relieved the cells apoptosis,decreased the amount of LDH leakage and improved the viability of SH-SY5Y cells injured by OGD (P<0.05). Western blot showed that the expression of Caspase 3 protein in HPC+OGD group was significantly lower than that in OGD group (P<0.05); HIF-1α protein expression was significantly higher than that of OGD group (P<0.05). CONCLUSIONS: Hypoxic preconditioning has protective effect on in vitro cultured SH-SY5Y cells injured by OGD. The mechanism may be related to the increase of HIF-1a protein.

[Development and effectiveness evaluation of time-resolved fluoroimmunoassay kit for detection of Schistosoma japonicum].

OBJECTIVE: To develop a kit of time-resolved fluoroimmunoassay (TRFIA) for detection of Schistosoma japonicum protein SjP38, and evaluate its effectiveness. METHODS: The anti 9G7 SjP38 monoclonal antibody was used as the capture anti-body coated with 96-hole plate, and the Eu3+ labeled 1A6 monoclonal antibody was used as the detection antibody to establish the TRFIA SjP38 kit. In addition, the accuracy, sensitivity, precision, stability and coincidence rate to pathogenic diagnosis of the kit were evaluated. RESULTS: This established kit possessed high accuracy, wide linear range from 2 to 1 250 ng/ml, high sensitivity with the minimum detectable concentration of 0.14 ng/ml, and good precision (the coefficient variation of the intra- and inter-assay were 3.6% to 4.6% and 5.1% to 6.7%, respectively). The stability tests showed that the reagents could be stable for six months at 4 ℃, 7 d at 37 ℃. The positive and negative corresponding rates to the pathogen detection method were 95% and 100% respectively. CONCLUSIONS: All the performance and detection indicators of the kit have reached the requirements of clinical test, but its clinical application still needs further validation.

Volar locking plate versus external fixation for the treatment of unstable distal radial fractures: a meta-analysis of randomized controlled trials.

BACKGROUND: The choice between volar locking plates (VLP) and external fixation (EF) for unstable distal radius fractures have not reached a consensus. The meta-analysis of randomized controlled trials was performed to compare VLP with EF to determine the dominant strategy. MATERIALS AND METHODS: Meta-analysis was performed with a systematic search of studies conducted by using the PubMed, Embase, and Cochrane Central Register of Controlled Trials databases. The randomized controlled trials that compared VLP with EF was identified. Characteristics, functional outcomes, radiological results, and complications were manually extracted from all the selected studies. RESULTS: Six studies encompassing 445 patients met the inclusion criteria. There was significant difference between two procedures in disabilities of the arm shoulder and hand scores at 3,6, and 12 mo, visual analogue scale at 6 mo, grip strength at 3 mo, supination at 3 and 6 mo, extension at 3 mo, ulnar variance at 12 mo, and reoperation rate at 12 mo, postoperatively. However, there was no significant difference between flexion, pronation, radial deviation, and ulnar deviation at all follow-up points postoperatively and overall complications at 12 mo, postoperatively. CONCLUSIONS: EF had less reoperative rate due to complications, however, VLP had advantages in functional recovery in the early period after surgery, but two methods had similar functional recovery at 12 mo, postoperatively. Clinician should make the treatment decision with great caution for the patients who sustained unstable distal radial fractures.

Nicotine induction of theta frequency oscillations in rodent medial septal diagonal band in vitro.

AIM: This study aimed to examine the role of the nicotinic receptor (nAChR) in the generation of theta oscillations (4-12 Hz) in vitro. METHODS: Electrophysiological studies were performed on medial septal diagonal band area (MSDB) slices to measure theta oscillation. Immunofluorescence and confocal microscopy studies were carried out to detect α4 nAChR and ß2 nAChR subunits in perfused-fixed tissue from VGluT2-GFP and GAD67-GFP transgenic mice. RESULTS: Application of nicotine to MSDB slices produced persistent theta oscillations in which area power increased in a dose-responsive manner. This activity was inhibited by GABAA receptor antagonists and partially by ionotropic glutamate receptor antagonists, indicating the involvement of local GABAergic and glutamatergic neurons in the production of the rhythmic activity. The nicotine-induced theta activity was also inhibited selectively by non-α7*nAChR antagonists, suggesting the presence of these receptor types on GABAergic and glutamatergic neuron populations in the MSDB. This was confirmed by immunofluorescence and confocal microscopy studies in transgenic mice in which the GABAergic and glutamatergic neurons express green fluorescent protein (GFP), showing localisation of ß2 nAChR and α4 nAChR subunits, the most common constituents of non-α7*nAChRs, in both cell types in the MSDB. CONCLUSION: Theta activity in the MSDB may be generated by tonic stimulation of non-α7*nAChRs.

[Long-term results of dual anti-collagen membrane in guided tissue regeneration].

OBJECTIVE: To evaluate the long-term clinical effect of dual anti-collagen membranes in guided tissue regeneration (GTR). METHODS: This randomized clinical trial included 26 teeth in 24 patients, presenting a total of 31 lesions consisting of intrabony defects and furcation defects. Twenty-six teeth were divided into two groups and treated by GTR with dual anti-collagen membranes and atelocollagen membranes, respectively. At baseline, 6 months, 1, 3 and 6 years, the following parameters were recorded: clinical attachment level, probing depth, gingival recession and the quantity of alveolar bone analyzed by computer assisted densitometry image analysis (CADIA). RESULTS: At 1 year after GTR surgery, the gain of clinical attachment in dual anti-collagen membranes group was (3.93 ± 1.74) mm, compared with (2.25 ± 1.90) mm in atelocollagen group (P = 0.044). The increasing of the value of CADIA in dual anti-collagen membrane and atelocollagen group were (53.14 ± 21.35) and (32.96 ± 17.97), P = 0.031. At 3 and 6 years, clinical parameters remained basically stable in both groups, compared to that at 1 year after surgery. CONCLUSIONS: The regeneration of periodontal tissues obtained by GTR with dual anti-collagen membranes could be maintained on a long-term basis.

[Establishment and application of an intact natural model of human dental plaque biofilm].

PURPOSE: Human dental plaque is implicated in a number of oral diseases. Collection of its undisturbed intact structure facilitates observing the formation and the effect of treatment. This study established a model in vivo to collect intact natural dental plaque biofilm, and observed the features and evaluated the immediate penetration and bactericidal effect of an essential oil (EO) mouthrinse on it at different periods. METHODS: Three 500 microm wide grooves were cut into hydroxyapatite (HA) discs. The discs were worn by six volunteers for 6, 24 and 48 hours, then broken into halves, one served as control, while the other received a one-minute extra-oral EO mouthrinse treatment. 5, 15 and 30 minutes later, the plaque was visualized with a vitality staining technique to observe the sustained changes of biofilm structure in situ and the effect of EO on intact biofilm. The biofilm thickness and fluorescent density of vital and total bacteria were obtained through diagram analysis, assessing the percentage of thickness and fluorescent density of vital to total bacteria. All data analysis was performed using SPSS 13.0 software package. One-way ANOVA and Student-Neuman-Keuls tests were used. RESULTS: The thickness of 6h, 24h and 48 h biofilm was (11.92 + or - 4.63) microm, (18.63 + or - 4.66)microm, (27.55 + or - 6.35) microm, respectively, which increased significantly within 48 hours (P<0.05), especially those within 6 hours. The percentages of thickness and fluorescent density of vital to total bacteria at different periods showed no significant changes (P>0.05). For 6-hour samples, plaque vitality for thickness and fluorescent density decreased significantly within 5 minutes after exposure to the EO (P<0.05). Meanwhile, for 24, 48-hour samples, plaque vitality decreased significantly within 15 minutes (P<0.05). CONCLUSIONS: This study successfully establishes a model for collecting natural undisturbed plaque biofilm in situ, showing the changes constantly within 48 hours. EO mouthrinse has an immediate penetration and antimicrobial effect on the sustained dental plaque biofilm, especially 15 minutes later.

[Protective effect of baicalin on experimental periodontitis in rats and its possible mechanisms].

OBJECTIVE: To investigate the effect of baicalin on the experimental periodontitis in rats, as well as the expression of MMP-1, MMP-2, MMP-9. METHODS: Twenty-seven adult male Sprague-Dawley rats were divided into three groups, with 9 rats in each group. A nylon thread was placed around the lower first molars of rats, which were sacrificed after 7 days. Baicalin (200 mg/kg) was administered to the experimental group by oral gavage, starting one day before the induction of periodontitis. The negative control group received vehicle (0.5% carboxymethylcellulose) alone. The blank control group did not get induction of periodontitis. The alveolar bone loss (ABL) and the area fraction (AA% ) occupied by collagen fibers were assessed. MMP-1, MMP-2 and MMP-9 protein expressions in the gingiva were detected by immunohistochemistry. RESULTS: Baicalin treatment significantly decreased ABL compared with the negative control group (P = 0.009). AA% of collagen fibers was significantly higher in baicalin-treated group than in the negative control group (P = 0.047). Baicalin treatment significantly down-regulated the protein expression for MMP-1 (P = 0.023) and MMP-9 (P = 0.042) and decreased the expression for MMP-2 (P = 0.099) compared with the negative control group. CONCLUSIONS: Baicalin protects against tissue damage in ligature-induced periodontitis in rats, which might be mediated in part by its inhibitory effect on the expression of MMP-1, MMP-2 and MMP-9.

[Effect of hypoxic preconditioning on the learning and memory ability and expressions of survivin and HSP-70 proteins in rats with focal cerebral ischemia/reperfusion injury].

OBJECTIVE: To study the neuroprotective effect of hypoxic preconditioning on reperfusion injury following ischemia and its molecular mechanism. METHODS: Forty-eight rats were randomized into 3 groups, namely the sham operated group, ischemia/reperfusion (I/R) group, and I/R following hypoxic preconditioning group (HP+I/R). In the latter two groups, the rats were subjected to middle cerebral artery occlusion (MACO) for 3 h followed by reperfusion for 24 h to induce cerebral I/R injury. The learning and memory ability of the rats 24 h after reperfusion was assessed using Y-maze test. Immunohistochemistry was performed to quantify the expressions of survivin and HSP-70 proteins in the rat brain tissues. RESULTS: The number of survivin- and HSP-70-positive cells in the brain tissues was significantly different between HP+I/R group and IR and the sham operated groups (P<0.05), and following I/R injury, the rats in HP+I/R group showed much better performance in the Y-maze test than those in I/R group. CONCLUSION: Hypoxic preconditioning can protect the ischemic brain against reperfusion injury, promote recovery of the learning and memory ability and neurological functions following the injury. Up-regulation of the expressions of survivin and HSP-70 proteins might be one of the molecular mechanisms for this neuroprotective effect.

Rose bengal staining in detection of oral precancerous and malignant lesions with colorimetric evaluation: a pilot study.

Early detection of oral precancerous and malignant lesions is still a diagnostic challenge for most of clinicians, and ideal adjuncts for detection of these lesions are currently unavailable. Our preliminary study has indicated that rose bengal (RB) staining might have the potency as a diagnostic aid; however, its clinical significance and reliability in hospital-based population are still not clear. In the present study, we investigated the efficacy of RB staining in detection of oral precancerous and malignant lesions. RB staining was conducted in 132 patients, and staining results were determined by a 4-graded shade guide, which had been quantitatively measured in the 1976 CIEL*a*b* space by instrumental colorimetry. Histological examination was performed in 128 of 132 patients after RB staining. The sensitivity and specificity to detect epithelial dysplasia (DP) and oral squamous cell carcinoma were 93.9 and 73.7%, respectively. The positive and negative likelihood ratios were 3.570 and 0.082, respectively. Moreover, RB staining seemed promising to detect DP in oral leukoplakia, lichen planus and leukokeratosis. In this study, 5 of 6 DP or oral squamous cell carcinoma were identified by RB staining before histological examination. In conclusion, RB staining may be a valuable diagnostic test in detection of oral precancerous and malignant lesions.

[Expression of Scleraxis in human periodontal ligament cells and gingival fibroblasts].

OBJECTIVE: To study if Scleraxis, a basic helix-loop-helix type transcription factor, could be expressed in human periodontal ligament cells (hPDLC), bone marrow cells (hBMSC) and gingival fibroblasts (hGF), and to investigate if Scleraxis was involved in hPDLC differentiation. METHODS: hPDLC, hBMSC and hGF were cultured. Expression of Scleraxis in hPDLC from different passages and in hBMSC and hGF was analyzed by reverse transcription polymerase chain reaction (RT-PCR). RESULTS: Scleraxis expression in hPDLC, hBMSC and hGF were significantly different (P < 0.05). The A values of Scleraxis/beta-actin in these kinds of cells were 0.877 +/- 0.024, 0.438 +/- 0.031, 0.313 +/- 0.083, respectively. The expression of Scleraxis was the highest in hPDLC and lowest in hGF. Scleraxis expression of hPDLC decreased with increase of passages in culture. CONCLUSIONS: Scleraxis was expressed in hPDLC, hBMSC and hGF in vitro, and may play an important role in differentiation of hPDLC.

A single nucleotide polymorphism in the matrix metalloproteinase-1 promoter enhances oral squamous cell carcinoma susceptibility in a Chinese population.

We genotyped 96 oral squamous cell carcinoma (OSCC) patients for the 1G/2G polymorphism of matrix metalloproteinase-1 (MMP-1) promoter -1607 bp using PCR-RFLP. A control population of 120 frequency-matched subjects was also genotyped for the same polymorphism. The detection frequency of 2G allele was significantly higher in OSCC subjects (76%) than in the control group (56.7%). The frequency of 2G allele had a significant difference between the OSCC and controls group (p = 0.00, Odds Ratio, OR = 2.232, 95% CI = 1.477-3.372). The genotype 2G/2G was found in 57.3% of the OSCC, and 34.2% in the controls. The proportion of 2G homozygote (2G/2G) was significantly higher in the OSCC group when compared to controls (p = 0.001, OR = 2.585, 95% CI = 1.487-4.494). OSCC patients were stratified by clinicopathological parameters including gender, smoking, clinical stage and lymph node metastasis, but the only statistically significant association with MMP-1 genotype was with smoking. The results showed that a SNP in the MMP-1 promoter -1607 bp was associated with OSCC susceptibility in a Chinese population.

[Effects of baicalin on the expression of pro-MMP-1 and MMP-3 in human gingival fibroblasts and periodontal ligament cells].

OBJECTIVE: To investigate the influence of baicalin on the IL-1beta induced pro-MMP-1 in HGF and the effects of baicalin on MMP-3 expression in periodontal ligament cells (PDLCs). METHODS: The amount of secreted pro-MMP-1 and MMP-3 expression was detected by ELISA and cell immunochemistry. RESULTS: (1) The amount of secreted pro-MMP-1 (3.333 +/- 0.123) microg/L increased significantly following 1 microg/L of IL-1beta, compared with control group (1.960 +/- 0.180) microg/L. Addition of baicalin to cell culture medium for 1 hour following IL-1beta decreased pro-MMP-1 secretion in a dose-dependent manner in the range of 10 approximately 1,000 microg/L. (2) 1 microg/L IL-1beta could significantly stimulate the synthesis and secretion of MMP-3 in PDLCs. (3) The baicalin could not interfere the synthesis of MMP-3, but could inhibit the release of MMP-3 from PDLCs. CONCLUSIONS: Baicalin could inhibit the secretion of pro-MMP-1 and MMP-3 expression in IL-1beta induced HGF and PDLCs, which suggests that baicalin may play an important role in preventing and treating periodontal disease.