Preoperative stereotactic radiosurgery for patients with 1-4 brain metastases: A single-arm phase 2 trial outcome analysis (NCT03398694).

Background: Stereotactic radiosurgery (SRS) following surgical resection is the standard of care for patients with symptomatic oligo brain metastasis (BM), however, it is associated with 10-15% local failure. Targeting a resection cavity is imprecise, thus preoperative radiosurgery where the target is well-defined may be superior, however, the efficacy of preoperative SRS has not yet been tested in a clinical trial. Methods: We conducted a phase 2, single-arm trial of preoperative SRS followed by surgical resection in patients with 1-4 symptomatic oligo BMs (NCT03398694) with the primary objective of measuring 6-month local control (LC). SRS was delivered to all patients utilizing a gamma knife or linear accelerator as per RTOG-9005 dosing criteria [Shaw E, Scott C, Souhami L, et al. Single dose radiosurgical treatment of recurrent previously irradiated primary brain tumors and brain metastases: final report of RTOG protocol 90-05. Int J Radiat Oncol Biol Phys. 2000;47(2):291-298] based on tumor diameter with the exception that the largest lesion diameter treated was 5 cm with 15 Gy with all SRS treatment given in single fraction dosing. Results: The trial screened 50 patients, 48 patients were treated under the protocol and 32 patients completed the entire follow-up period. Of all the patients who completed the follow-up period, the primary endpoint of 6-month LC was 100% (95% CI: 0.891-1.000; P = .005). Secondary endpoints, presented as medians, were overall survival (17.6 months), progression-free survival (5.3 months), distant in-brain failure (40.8% at 1 year), leptomeningeal failure (4.8% at 1 year), and radiation necrosis (7.7% at 1 year). Conclusions: Our data confirms superior local control in patients who received preoperative SRS when compared to historical controls. Further study with a larger randomized cohort of patients is warranted to fully understand the benefits of preoperative SRS.

Genomic analysis of human brain metastases treated with stereotactic radiosurgery reveals unique signature based on treatment failure.

Stereotactic radiosurgery (SRS) has been shown to be efficacious for the treatment of limited brain metastasis (BM); however, the effects of SRS on human brain metastases have yet to be studied. We performed genomic analysis on resected brain metastases from patients whose resected lesion was previously treated with SRS. Our analyses demonstrated for the first time that patients possess a distinct genomic signature based on type of treatment failure including local failure, leptomeningeal spread, and radio-necrosis. Examination of the center and peripheral edge of the tumors treated with SRS indicated differential DNA damage distribution and an enrichment for tumor suppressor mutations and DNA damage repair pathways along the peripheral edge. Furthermore, the two clinical modalities used to deliver SRS, LINAC and GK, demonstrated differential effects on the tumor landscape even between controlled primary sites. Our study provides, in human, biological evidence of differential effects of SRS across BM's.

Genomic Analysis of Human Brain Metastases Treated with Stereotactic Radiosurgery Under the Phase-II Clinical Trial (NCT03398694) Reveals DNA Damage Repair at the Peripheral Tumor Edge.

Stereotactic Radiosurgery (SRS) is one of the leading treatment modalities for oligo brain metastasis (BM), however no comprehensive genomic data assessing the effect of radiation on BM in humans exist. Leveraging a unique opportunity, as part of the clinical trial (NCT03398694), we collected post-SRS, delivered via Gamma-knife or LINAC, tumor samples from core and peripheral-edges of the resected tumor to characterize the genomic effects of overall SRS as well as the SRS delivery modality. Using these rare patient samples, we show that SRS results in significant genomic changes at DNA and RNA levels throughout the tumor. Mutations and expression profiles of peripheral tumor samples indicated interaction with surrounding brain tissue as well as elevated DNA damage repair. Central samples show GSEA enrichment for cellular apoptosis while peripheral samples carried an increase in tumor suppressor mutations. There are significant differences in the transcriptomic profile at the periphery between Gamma-knife vs LINAC.

Neuronal mitochondrial dynamics coordinate systemic mitochondrial morphology and stress response to confer pathogen resistance in C. elegans.

Mitochondrial functions across different tissues are regulated in a coordinated fashion to optimize the fitness of an organism. Mitochondrial unfolded protein response (UPRmt) can be nonautonomously elicited by mitochondrial perturbation in neurons, but neuronal signals that propagate such response and its physiological significance remain incompletely understood. Here, we show that in C. elegans, loss of neuronal fzo-1/mitofusin induces nonautonomous UPRmt through multiple neurotransmitters and neurohormones, including acetylcholine, serotonin, glutamate, tyramine, and insulin-like peptides. Neuronal fzo-1 depletion also triggers nonautonomous mitochondrial fragmentation, which requires autophagy and mitophagy genes. Systemic activation of UPRmt and mitochondrial fragmentation in C. elegans via perturbing neuronal mitochondrial dynamics improves resistance to pathogenic Pseudomonas infection, which is supported by transcriptomic signatures of immunity and stress-response genes. We propose that C. elegans surveils neuronal mitochondrial dynamics to coordinate systemic UPRmt and mitochondrial connectivity for pathogen defense and optimized survival under bacterial infection.

A role of age-dependent DNA methylation reprogramming in regulating the regeneration capacity of Boea hygrometrica leaves.

Plants can regenerate new individuals under appropriate culture conditions. Although the molecular basis of shoot regeneration has steadily been unraveled, the role of age-dependent DNA methylation status in the regulation of explant regeneration remains practically unknown. Here, we established an effective auxin/cytokinin-induced shoot regeneration system for the resurrection plant Boea hygrometrica via direct organogenesis and observed that regeneration was postponed with increasing age of donor plants. Global transcriptome analysis revealed significant upregulation of genes required for hormone signaling and phenylpropanoid biosynthesis and downregulation of photosynthetic genes during regeneration. Transcriptional changes in the positive/negative regulators and cell wall-related proteins involved in plant regeneration, such as ELONGATED HYPOCOTYL5 (HY5), LATERAL ORGAN BOUNDARIES DOMAIN, SHOOT-MERISTEMLESS, and WUSCHEL, were associated with the regeneration process. Comparison of DNA methylation profiling between leaves from young seedlings (YL) and mature plants (ML) revealed increased asymmetrical methylation in ML, which was predominantly distributed in promoter regions of genes, such as HY5 and a member of ABA-responsive element (ABRE) binding protein/ABRE binding factor, as well as genes encoding glycine-rich cell wall structural protein, CENTRORADIALIS-like protein, and beta-glucosidase 40-like essential for shoot meristem and cell wall architecture. Their opposite transcription response in ML explants during regeneration compared with those from YL demonstrated the putative involvement of DNA methylation in regeneration. Moreover, a significant lower expression of DNA glycosylase-lyase required for DNA demethylation in ML was coincident with its postponed regeneration compared with those in YL. Taken together, our results suggest a role of promoter demethylation in B. hygrometrica regeneration.

Weighted Gene Co-expression Network Analysis (WGCNA) Reveals the Hub Role of Protein Ubiquitination in the Acquisition of Desiccation Tolerance in Boea hygrometrica.

Boea hygrometrica can survive extreme drought conditions and has been used as a model to study desiccation tolerance. A genome-wide transcriptome analysis of B. hygrometrica showed that the plant can survive rapid air-drying after experiencing a slow soil-drying acclimation phase. In addition, a weighted gene co-expression network analysis was used to study the transcriptomic datasets. A network comprising 22 modules was constructed, and seven modules were found to be significantly related to desiccation response using an enrichment analysis. Protein ubiquitination was observed to be a common process linked to hub genes in all the seven modules. Ubiquitin-modified proteins with diversified functions were identified using immunoprecipitation coupled with mass spectrometry. The lowest level of ubiquitination was noted at the full soil drying priming stage, which coincided the accumulation of dehydration-responsive gene BhLEA2. The highly conserved RY motif (CATGCA) was identified from the promoters of ubiquitin-related genes that were downregulated in the desiccated samples. An in silico gene expression analysis showed that the negative regulation of ubiquitin-related genes is potentially mediated via a B3 domain-containing transcription repressor VAL1. This study suggests that priming may involve the transcriptional regulation of several major processes, and the transcriptional regulation of genes in protein ubiquitination may play a hub role to deliver acclimation signals to posttranslational level in the acquisition of desiccation tolerance in B. hygrometrica.

Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq.

Bread wheat (Triticum aestivum L.) is an allohexaploid, and the transcriptional characteristics of the wheat embryo and endosperm during grain development remain unclear. To analyze the transcriptome, we performed isoform sequencing (Iso-Seq) for wheat grain and RNA sequencing (RNA-Seq) for the embryo and de-embryonated kernels. The differential regulation between the embryo and de-embryonated kernels was found to be greater than the difference between the two time points for each tissue. Exactly 2264 and 4790 tissue-specific genes were found at 14 days post-anthesis (DPA), while 5166 and 3784 genes were found at 25 DPA in the embryo and de-embryonated kernels, respectively. Genes expressed in the embryo were more likely to be related to nucleic acid and enzyme regulation. In de-embryonated kernels, genes were rich in substance metabolism and enzyme activity functions. Moreover, 4351, 4641, 4516, and 4453 genes with the A, B, and D homoeoloci were detected for each of the four tissues. Expression characteristics suggested that the D genome may be the largest contributor to the transcriptome in developing grain. Among these, 48, 66, and 38 silenced genes emerged in the A, B, and D genomes, respectively. Gene ontology analysis showed that silenced genes could be inclined to different functions in different genomes. Our study provided specific gene pools of the embryo and de-embryonated kernels and a homoeolog expression bias model on a large scale. This is helpful for providing new insights into the molecular physiology of wheat.

Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.).

MAIN CONCLUSION: Totally, 23 and 26 loci for the first count germination ratio and the final germination ratio were detected by quantitative trait loci (QTL) mapping and association mapping, respectively, which could be used to facilitate wheat pre-harvest sprouting breeding. Weak dormancy can cause pre-harvest sprouting in seeds of common wheat which significantly reduces grain yield. In this study, both quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) were used to identify loci controlling seed dormancy. The analyses were based on a recombinant inbred line population derived from Zhou 8425B/Chinese Spring cross and 166 common wheat accessions. Inclusive composite interval mapping detected 8 QTL, while 45 loci were identified in the 166 wheat accessions by GWAS. Among these, four loci (Qbifcgr.cas-3AS/Qfcgr.cas-3AS, Qbifcgr.cas-6AL.1/Qfcgr.cas-6AL.1, Qbifcgr.cas-7BL.2/Qfcgr.cas-7BL.2, and Qbigr.cas-3DL/Qgr.cas-3DL) were detected in both QTL mapping and GWAS. In addition, 41 loci co-located with QTL reported previously, whereas 8 loci (Qfcgr.cas-5AL, Qfcgr.cas-6DS, Qfcgr.cas-7AS, Qgr.cas-3DS.1, Qgr.cas-3DS.2, Qbigr.cas-3DL/Qgr.cas-3DL, Qgr.cas-4B, and Qgr.cas-5A) were likely to be new. Linear regression showed the first count germination ratio or the final germination ratio reduced while multiple favorable alleles increased. It is suggested that QTL pyramiding was effective to reduce pre-harvest sprouting risk. This study could enrich the research on pre-harvest sprouting and provide valuable information of marker exploration for wheat breeding programs.

Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis.

BACKGROUND: Water shortage is a major factor that harms agriculture and ecosystems worldwide. Plants display various levels of tolerance to water deficit, but only resurrection plants can survive full desiccation of their vegetative tissues. Haberlea rhodopensis, an endemic plant of the Balkans, is one of the few resurrection plants found in Europe. We performed transcriptomic analyses of this species under slight, severe and full dehydration and recovery to investigate the dynamics of gene expression and associate them with existing physiological and metabolomics data. RESULTS: De novo assembly yielded a total of 142,479 unigenes with an average sequence length of 1034 nt. Among them, 18,110 unigenes were differentially expressed. Hierarchical clustering of all differentially expressed genes resulted in seven clusters of dynamic expression patterns. The most significant expression changes, involving more than 15,000 genes, started at severe dehydration (~ 20% relative water content) and were partially maintained at full desiccation (< 10% relative water content). More than a hundred pathways were enriched and functionally organized in a GO/pathway network at the severe dehydration stage. Transcriptomic changes in key pathways were analyzed and discussed in relation to metabolic processes, signal transduction, quality control of protein and DNA repair in this plant during dehydration and rehydration. CONCLUSION: Reprograming of the transcriptome occurs during severe dehydration, resulting in a profound alteration of metabolism toward alternative energy supply, hormone signal transduction, and prevention of DNA/protein damage under very low cellular water content, underlying the observed physiological and metabolic responses and the resurrection behavior of H. rhodopensis.

Metastatic Cardiac Angiosarcoma to the Lung, Spine, and Brain: A Case Report and Review of the Literature.

BACKGROUND: Metastatic angiosarcoma to the brain is a rare entity without an established management protocol. CASE DESCRIPTION: A man with primary cardiac angiosarcoma presented with a rare brain metastasis. The patient underwent successful resection of the brain metastasis and was initiated on chemotherapy only for his systemic disease. The patient did not develop local recurrence. A review of primary and metastatic central nervous system angiosarcoma, its pathologic features, clinical disease course, treatment strategies, and genomics is also provided. CONCLUSIONS: Angiosarcomas are rare tumors that are difficult to treat. Gross total resection of a central nervous system metastasis is recommended before initiation of adjuvant chemotherapy or radiation therapy. Close follow-up is still required given the propensity for continued metastasis of these tumors. Future treatments may be developed based on the genomics of angiosarcomas.

Ruptured Mycotic Aneurysm and Cerebral Vasospasm in the Setting of Endocarditis and Heart Failure Requiring Cardiothoracic Surgery: Case Report and Literature Review.

BACKGROUND: Ruptured mycotic aneurysm in the setting of cardiac failure and cerebral vasospasm presents unique management challenges. CASE DESCRIPTION: A patient with a ruptured mycotic aneurysm with subarachnoid hemorrhage, cerebral vasospasm, and endocarditis with heart failure successfully underwent craniotomy, neuroendovascular treatment, and cardiopulmonary bypass for mitral valve replacement while in cerebral vasospasm. This case highlights clinical management strategies for a patient with a ruptured mycotic aneurysm, subarachnoid hemorrhage, cerebral vasospasm, endocarditis, and heart failure. CONCLUSIONS: Open craniotomy, neuroendovascular treatment, and cardiac surgery strategies can be used when treating patients with ruptured mycotic aneurysms and cardiac failure. When the patient also has cerebral vasospasm, maintenance of mean arterial pressure is paramount.

Management of posterior fossa tumors and hydrocephalus in children: a review.

OBJECT: Most pediatric patients that present with a posterior fossa tumor have concurrent hydrocephalus. There is significant debate over the best management strategy of hydrocephalus in this situation. The objectives of this paper were to review the pathophysiology model of posterior fossa tumor hydrocephalus, describe the individual risks factors of persistent hydrocephalus, and discuss the current management options. Specifically, the debate over preresection cerebrospinal fluid diversion is discussed. RESULTS: Only 10-40 % demonstrate persistent hydrocephalus after posterior fossa tumor resection. It appears that young age, moderate to severe hydrocephalus, transependymal edema, the presence of cerebral metastases, and tumor pathology (medulloblastoma and ependymoma) on presentation predict postresection or persistent hydrocephalus. The Canadian Preoperative Prediction Rule for Hydrocephalus (CPPRH), a validated prediction model, can be used to stratify patients at point of first contact into high and low risk for persistent hydrocephalus. CONCLUSIONS: A protocol is proposed for managing hydrocephalus that utilizes the CPPRH. Low-risk patients can be monitored conservatively with or without an intraoperative extraventricular drain, while high-risk patients require the use of an intraoperative extraventricular drain, higher postoperative hydrocephalus surveillance, and even consideration for a preoperative endoscopic third ventriculostomy.

Survival following Ommaya reservoir placement for neoplastic meningitis.

The objective of this study was to evaluate the outcomes of patients with neoplastic meningitis (NM) following Ommaya reservoir placement in order to determine whether any patient factors are associated with longer survival. NM is a devastating late manifestation of cancer, and given its dismal prognosis, identifying appropriate patients for Ommaya reservoir placement is difficult. The authors performed a retrospective review of 80 patients who underwent Ommaya reservoir placement at three medical centers from September 2001 through September 2012. The primary outcome was death. Differences in survival were assessed with Kaplan-Meier survival analyses. The Cox proportional hazards and logistic regression modeling were performed to identify factors associated with survival. The primary diagnoses were solid organ, hematologic, and primary central nervous system tumors in 53.8%, 41.3%, and 5%, respectively. The median overall survival was 72.5 days (95% confidence interval 36-122) with 30% expiring within 30 days and only 13.8% surviving more than 1 year. There were no differences in median overall survival between sites (p=0.37) despite differences in time from diagnosis of NM to Ommaya reservoir placement (p<0.001). Diagnosis of hematologic malignancy was inversely associated with death within 90 days (p=0.04; odds ratio 0.34), older age was associated with death within 90 days (p=0.05; odds ratio 1.5, per 10 year increase in age). The prognosis of NM remains poor despite the available treatment with intraventricular chemotherapy. There exists significant variability in treatment algorithms among medical centers and consideration of this variability is crucial when interpreting existing series of Ommaya reservoir use in the treatment of patients with NM.

Anchor-based classification and type-C inhibitors for tyrosine kinases.

Tyrosine kinases regulate various biological processes and are drug targets for cancers. At present, the design of selective and anti-resistant inhibitors of kinases is an emergent task. Here, we inferred specific site-moiety maps containing two specific anchors to uncover a new binding pocket in the C-terminal hinge region by docking 4,680 kinase inhibitors into 51 protein kinases, and this finding provides an opportunity for the development of kinase inhibitors with high selectivity and anti-drug resistance. We present an anchor-based classification for tyrosine kinases and discover two type-C inhibitors, namely rosmarinic acid (RA) and EGCG, which occupy two and one specific anchors, respectively, by screening 118,759 natural compounds. Our profiling reveals that RA and EGCG selectively inhibit 3% (EGFR and SYK) and 14% of 64 kinases, respectively. According to the guide of our anchor model, we synthesized three RA derivatives with better potency. These type-C inhibitors are able to maintain activities for drug-resistant EGFR and decrease the invasion ability of breast cancer cells. Our results show that the type-C inhibitors occupying a new pocket are promising for cancer treatments due to their kinase selectivity and anti-drug resistance.

Module organization and variance in protein-protein interaction networks.

A module is a group of closely related proteins that act in concert to perform specific biological functions through protein-protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores and interface evolution scores to describe the module elements, including core and ring components. Functions of core components were highly correlated with those of essential genes. In comparison with ring components, core proteins/PPIs were conserved across multiple species. Subsequently, protein/module variance of PPI networks confirmed that core components form dynamic network hubs and play key roles in various biological functions. Based on the analyses of gene essentiality, module variance, and gene co-expression, we summarize the observations of module organization and variance as follows: 1) a module consists of core and ring components; 2) core components perform major biological functions and collaborate with ring components to execute certain functions in some cases; 3) core components are more conserved and essential during organizational changes in different biological states or conditions.

Homopharma: a new concept for exploring the molecular binding mechanisms and drug repurposing.

BACKGROUND: Drugs that simultaneously target multiple proteins often improve efficacy, particularly in the treatment of complex diseases such as cancers and central nervous system disorders. Many approaches have been proposed to identify the potential targets of a drug. Recently, we have introduced Space-Related Pharmamotif (SRPmotif) method to recognize the proteins that share similar binding environments. In addition, compounds with similar topology may bind to similar proteins and have similar protein-compound interactions. However, few studies have focused on exploring the relationships between binding environments and protein-compound interactions, which is important for understanding molecular binding mechanisms and helpful to be used in discovering drug repurposing. RESULTS: In this study, we propose a new concept of "Homopharma", combining similar binding environments and protein-compound interaction profiles, to explore the molecular binding mechanisms and drug repurposing. A Homopharma consists of a set of proteins which have the conserved binding environment and a set of compounds that share similar structures and functional groups. These proteins and compounds present conserved interactions and similar physicochemical properties. Therefore, these compounds are often able to inhibit the proteins in a Homopharma. Our experimental results show that the proteins and compounds in a Homopharma often have similar protein-compound interactions, comprising conserved specific residues and functional sites. Based on the Homopharma concept, we selected four flavonoid derivatives and 32 human protein kinases for enzymatic profiling. Among these 128 bioassays, the IC50 of 56 and 25 flavonoid-kinase inhibitions are less than 10 µM and 1 µM, respectively. Furthermore, these experimental results suggest that these flavonoids can be used as anticancer compounds, such as oral and colorectal cancer drugs. CONCLUSIONS: The experimental results show that the Homopharma is useful for identifying key binding environments of proteins and compounds and discovering new inhibitory effects. We believe that the Homopharma concept can have the potential for understanding molecular binding mechanisms and providing new clues for drug development.

Pseudarthrosis failures of anterior subaxial cervical spine fusion using a plate with a single screw per vertebral body: a case series.

INTRODUCTION: The UNIPLATE was developed to improve operative times and limit dissection at the lateral margins of the vertebral bodies. The distinguishing character of this plate is its thin design, which requires only one screw per vertebral level (monovertebral screw plate). Most cervical spine plates, in contrast, are designed for two screws per vertebral level (bivertebral screw plate). Limited reports of the biomechanical efficacy of the UNIPLATE are available, and to the authors' knowledge, this report represents the largest clinical study of its use. METHODS: This is a retrospective chart-review study of consecutively treated patients without previous cervical spine surgery undergoing anterior cervical diskectomy and fusion at one or two levels. The primary end point was symptomatic pseudarthrosis requiring revision surgery. Pseudarthrosis is defined as a failure of bony fusion on the operated level seen on thin-cut computed tomography scans performed on symptomatic patients. The rate of revision surgery caused by symptomatic pseudarthrosis was compared between patients undergoing one- and two-level fusion surgeries treated with UNIPLATE compared with other plates with two screws per vertebral level. The minimum follow-up was 18 months. RESULTS: A total of 162 patients were identified, including 125 patients with one-level fusion and 37 patients with two-level fusion surgery. The median follow-up period was 3.3 years. A significantly greater incidence (odds ratio 10.2, P = 0.042) of reoperation for symptomatic pseudarthrosis was noted for patients treated with the UNIPLATE (4 of 13, 31%) compared with patients treated with bivertebral screw plates (1 of 24, 2.5%). No significant difference in reoperation attributable to symptomatic pseudarthrosis was noted for different plating systems for one-level fusion surgeries. CONCLUSIONS: There is an increased rate of reoperation for symptomatic pseudarthrosis after anterior cervical diskectomy and fusion surgery with the use of a monovertebral screw semiconstrained plate, particularly in two-level fusion surgeries. Use of the UNIPLATE system has since been abandoned at our institution in favor of bivertebral screw plating systems.

Total synthetic protoapigenone WYC02 inhibits cervical cancer cell proliferation and tumour growth through PIK3 signalling pathway.

Flavonoids have been intensively explored for their anticancer activity. In this study, a total synthetic flavonoid protoapigenone, known as WYC02, was analysed for its potential anticancer activity on human cervical cancer cells as well as the underlying mechanisms for these effects. The site-moiety maps are used to explore the binding site similarity, pharmacophore and docking pose similarity. The effect of WYC02 on cell viability, migration, invasion and apoptosis as well as the underlying mechanisms was analysed in vitro using human cervical cancer cells. The effect of WYC02 on in vivo tumour growth was assessed in a tumour xenograft study. WYC02 inhibited cell proliferation, MMPs activity, migration and invasion in cervical cancer cells. We speculated that WYC02 might inhibit the activities of PIK3 family proteins, including PIK3CA, PIK3CB, PIK3CD and PIK3CG. Indeed, WYC02 decreased the expression of PIK3 family proteins, especially PIK3CG, through ubiquitination and inhibited the activities of PIK3CG and PIK3 downstream molecules AKT1 and MTOR in cervical cancer cells. Furthermore, PIK3 signalling pathway was involved in the inhibitory effect of WYC02 on cervical cancer cell proliferation and tumour growth in vitro and in vivo. WYC02 inhibits cervical cancer cell proliferation and tumourigenesis via PIK3 signalling pathway and has the potential to be developed as a chemotherapeutic agent in cervical cancer.

KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms.

Kinases play central roles in signaling pathways and are promising therapeutic targets for many diseases. Designing selective kinase inhibitors is an emergent and challenging task, because kinases share an evolutionary conserved ATP-binding site. KIDFamMap (http://gemdock.life.nctu.edu.tw/KIDFamMap/) is the first database to explore kinase-inhibitor families (KIFs) and kinase-inhibitor-disease (KID) relationships for kinase inhibitor selectivity and mechanisms. This database includes 1208 KIFs, 962 KIDs, 55 603 kinase-inhibitor interactions (KIIs), 35 788 kinase inhibitors, 399 human protein kinases, 339 diseases and 638 disease allelic variants. Here, a KIF can be defined as follows: (i) the kinases in the KIF with significant sequence similarity, (ii) the inhibitors in the KIF with significant topology similarity and (iii) the KIIs in the KIF with significant interaction similarity. The KIIs within a KIF are often conserved on some consensus KIDFamMap anchors, which represent conserved interactions between the kinase subsites and consensus moieties of their inhibitors. Our experimental results reveal that the members of a KIF often possess similar inhibition profiles. The KIDFamMap anchors can reflect kinase conformations types, kinase functions and kinase inhibitor selectivity. We believe that KIDFamMap provides biological insights into kinase inhibitor selectivity and binding mechanisms.

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

BACKGROUND: To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. RESULTS: We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. CONCLUSIONS: SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.