Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Small-molecule inhibition of pyruvate phosphate dikinase targeting the nucleotide binding site

Pyruvate phosphate dikinase (PPDK) is an essential enzyme of C4 photosynthesis in plants, catalyzing the ATP-driven conversion of pyruvate to phosphoenolpyruvate ( PEP). It is further used by some bacteria and unicellular protists in the reverse, ATP-forming direction. Many weed species use C4 photosynthesis in contrast to world's major crops, which are C3 plants. Hence inhibitors of PPDK may be used as C4-specific herbicides. By screening a library of 80 commercially available kinase inhibitors, we identified compounds derived from bisindolylmaleimide (bisindolylmaleimide IV, IC50 = 0.76 +/- 0.13 mu M) and indirubin (indirubin3'- monoxime, IC50 = 4.2 +/- 0.9 mu M) that showed high inhibitory potency towards PPDK and are among the most effective PPDK inhibitors described today. Physiological studies on leaf tissues of a C4 model plant confirmed in vivo inhibition of C4-driven photosynthesis by these substances. Moreover, comparative docking studies of non-inhibitory bisindolylmaleimide derivatives suggest that the selectivity towards PPDK may be increased by addition of functional groups to the core structure

Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism

Pyruvate phosphate dikinase (PPDK) is an essential enzyme of both the C-4 photosynthetic pathway and cellular energy metabolism of some bacteria and unicellular protists. In C-4 plants, it catalyzes the ATP- and P-i-dependent formation of phosphoenolpyruvate (PEP) while in bacteria and protozoa the ATP-forming direction is used. PPDK is composed out of three distinct domains and exhibits one of the largest single domain movements known today during its catalytic cycle. However, little information about potential intermediate steps of this movement was available. A recent study resolved a discrete intermediate step of PPDK's swiveling movement, shedding light on the details of this intriguing mechanism. Here we present an additional structural intermediate that possibly represents another crucial step in the catalytic cycle of PPDK, providing means to get a more detailed understanding of PPDK's mode of function

Oxygen evolution <i>in vivo</i> in the presence of putative PPDK inhibitors.

<p>The rate of O₂ evolution of <i>Zea mays</i> leaf slices was measured in solution with a Clark-type electrode. PPDK inhibitors identified in the <i>in vitro</i> screening assay were added to the leaf slices in a final concentration of 20 μg mL⁻¹. A significant decrease (<i>p</i> ≤ 0.05) was observed for BIM IV, IO, BIO and PP242. Rates were normalized to the total amount of chlorophyll in the leaf samples and corrected for electrode drift. O₂ evolution rates relative to the respective controls are given in percent. Noteworthy, the O₂ evolution rate in the presence of IO and BIO was negative, hence representing a consumption of O₂. Errors shown are SEM.</p

Dose-response curves of selected inhibitors of C₄ plant PPDK.

<p>The PPDK concentration is kept constant at 0.2 μM, while the inhibitor concentrations are varied between 0 μM and 200 μM. The mean activity from three experiments relative to the control is plotted for bisindolylmaleimide IV (a), Go6983 (b), indirubin-3’-monoxime (c), 6-bromoindirubin-3’-monoxime (d), ABT-869 (e), PP242 (f) and the PPDK specific inhibitor ilimaquinone (g). The <i>IC</i>₅₀ values were calculated from these data by non-linear regression using log-logistic dose-response functions. Errors shown are standard errors of the mean (SEM).</p

Mean activity of PPDK at inhibitor concentrations of 100 μM.

<p>Depicted from left to right are the most potent inhibitors identified in the initial screening assay with the known PPDK inhibitor ilimaquinone. Inhibitors colored red were further analyzed for their <i>IC</i>₅₀ values. Errors shown are standard deviations (SD).</p

Efficient In Vivo Screening Method for the Identification of C-4 Photosynthesis Inhibitors Based on Cell Suspensions of the Single-Cell C-4 Plant Bienertia sinuspersici

The identification of novel herbicides is of crucial importance to modern agriculture. We developed an efficient in vivo assay based on oxygen evolution measurements using suspensions of chlorenchyma cells isolated from the single-cell C-4 plant Bienertia sinuspersici to identify and characterize inhibitors of C4 photosynthesis. This novel approach fills the gap between conventional in vitro assays for inhibitors targeting C-4 key enzymes and in vivo experiments on whole plants. The assay addresses inhibition of the target enzymes in a plant context thereby taking care of any reduced target inhibition due to metabolization or inadequate uptake of small molecule inhibitors across plant cell walls and membranes. Known small molecule inhibitors targeting C-4 photosynthesis were used to validate the approach. To this end, we tested pyruvate phosphate dikinase inhibitor bisindolylmaleimide IV and phosphoenolpyruvate carboxylase inhibitor okanin. Both inhibitors show inhibition of plant photosynthesis at half-maximal inhibitory concentrations in the sub-mM range and confirm their potential to act as a new class of C-4 selective inhibitors

Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase

Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP-and P-i-dependent formation of phosphoenolpyruvate from pyruvate in C-4-plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C-4-enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme

Ensemble- and Rigidity Theory-Based Perturbation Approach To Analyze Dynamic Allostery

Allostery describes the functional coupling between sites in biomolecules. Recently, the role of changes in protein dynamics for allosteric communication has been highlighted. A quantitative and predictive description of allostery is fundamental for understanding biological processes. Here, we integrate an ensemble-based perturbation approach with the analysis of biomolecular rigidity and flexibility to construct a model of dynamic allostery. Our model, by definition, excludes the possibility of conformational changes, evaluates static, not dynamic, properties of molecular systems, and describes allosteric effects due to ligand binding in terms of a novel free-energy measure. We validated our model on three distinct biomolecular systems: eglin c, protein tyrosine phosphatase 1B, and the lymphocyte function-associated antigen 1 domain. In all cases, it successfully identified key residues for signal transmission in very good agreement with the experiment. It correctly and quantitatively discriminated between positively or negatively cooperative effects for one of the systems. Our model should be a promising tool for the rational discovery of novel allosteric drugs