Chatbot responses suggest that hypothetical biology questions are harder than realistic ones

The biology education literature includes compelling assertions that unfamiliar problems are especially useful for revealing students' true understanding of biology. However, there is only limited evidence that such novel problems have different cognitive requirements than more familiar problems. Here, we sought additional evidence by using chatbots based on large language models as models of biology students. For human physiology and cell biology, we developed sets of realistic and hypothetical problems matched to the same lesson learning objectives (LLOs). Problems were considered hypothetical if (i) known biological entities (molecules and organs) were given atypical or counterfactual properties (redefinition) or (ii) fictitious biological entities were introduced (invention). Several chatbots scored significantly worse on hypothetical problems than on realistic problems, with scores declining by an average of 13%. Among hypothetical questions, redefinition questions appeared especially difficult, with many chatbots scoring as if guessing randomly. These results suggest that, for a given LLO, hypothetical problems may have different cognitive demands than realistic problems and may more accurately reveal students' ability to apply biology core concepts to diverse contexts. The Test Question Templates (TQT) framework, which explicitly connects LLOs with examples of assessment questions, can help educators generate problems that are challenging (due to their novelty), yet fair (due to their alignment with pre-specified LLOs). Finally, ChatGPT's rapid improvement toward expert-level answers suggests that future educators cannot reasonably expect to ignore or outwit chatbots but must do what we can to make assessments fair and equitable.

Teaching science with the "universal language" of music: alignment with the Universal Design for Learning framework

The idea of teaching science through music has undeniable appeal in implying that learning can be engaging and fun while also covering content efficiently. Indeed, there is little doubt that songs can be uniquely memorable, suggesting mnemonic options for core content. However, many classroom implementations of science music have limitations such as an overemphasis on rote memorization, rather than a constructivist building of understanding. In this brief review, we ask how music might facilitate the learning of science content in a manner consistent with the well-known pedagogical framework of Universal Design for Learning (UDL). In our view, UDL suggests certain distinct possible benefits of incorporating music into curricula, leading us to propose four models of practice. These four models are as follows: 1) students enjoy music together, 2) students critically analyze songs as texts, 3) students creatively augment existing songs, and 4) students create new songs. Model 1 can contribute to an inclusive learning environment, while models 2-4 can encourage cognitively rich active learning, and models 3-4 can additionally help students channel scientific understanding into the creation of authentic products. We conclude with comments on logistical issues that arise in implementing these four models, including the use of appropriate rubrics and the prioritization of artistic quality.NEW & NOTEWORTHY Instructors and students often find it fun to incorporate music into science classes. However, the casual usage of music in this context can unintentionally convey that science courses are mostly about memorizing scientific facts. In this article, the authors argue for a more nuanced approach to teaching science with music, rooted in Universal Design for Learning (UDL).

Using Test Question Templates to teach physiology core concepts

The past ∼15 years have seen increasing interest in defining disciplinary core concepts. Within the field of physiology, Michael, McFarland, Modell, and colleagues have published studies that defined physiology core concepts and have elaborated many of these as detailed conceptual frameworks. With such helpful definitions now in place, attention is turning to the related issue of how to maximize student understanding of the core concepts by linking these "big ideas" to concrete student-facing resources for active learning and assessment. Our practitioner-based view begins with the recognition that in many if not most undergraduate physiology courses assessment drives learning. We have therefore linked published conceptual frameworks to Test Question Templates (TQTs), whose structure promotes transparent assessments as well as the active learning needed to prepare for such assessments. We provide examples of conceptual framework-linked TQTs for the physiology core concepts of Homeostasis, Flow Down Gradients, the Cell Membrane, and Cell-Cell Communication. We argue that this deployment of TQTs has at least two distinct benefits for the teaching and learning of core concepts. First, documenting the connections between conceptual frameworks and TQTs may clarify coverage and assessment of the core concepts for both instructors and students. Second, misconceptions about core concepts may be directly targeted and dispelled via thoughtful construction, arrangement, and iteration of TQTs. We propose that the TQT framework or similar approaches may be applied fruitfully to any sufficiently articulated physiology core concept for high school, undergraduate, or graduate students.NEW & NOTEWORTHY Our students often focus on the grades they need to advance through academic programs. How can instructors harness this understandable interest in grades to help students gain a true understanding of core concepts? The new framework of Test Question Templates (TQTs) shows promise in linking student priorities like test scores to instructor priorities like core concepts.

Student Perceptions of a Framework for Facilitating Transfer from Lessons to Exams, and the Relevance of This Framework to Published Lessons

A main goal of academic courses is to help students acquire knowledge and skills that they can transfer to multiple contexts. In this article, we (i) examine students' responses to test question templates (TQTs), a framework intended to facilitate transfer, and (ii) determine whether similar transfer-promoting strategies are commonly embedded in published biology lessons. In study 1, in surveys administered over several academic quarters, students consistently reported that TQTs helped them transfer course content to exams and the real world; that multiple (two to five) examples were generally needed to understand a given TQT, leading >40% students to create their own additional examples; and that TQTs would be helpful in other science courses. In study 2, among 100 peer-reviewed lessons published by CourseSource or the National Center for Case Study Teaching in Science (NCCSTS), less than 5% of lessons gave students advice about exams or helped students create additional practice problems. The latter finding is not meant as criticism of these excellent lessons, which are a boon to the biology education community. However, with TQT-like prescriptions generally absent from peer-reviewed lessons, biology instructors may wish to supplement the lessons with TQT-like strategies to explicitly connect the material to subsequent exams.

Tunes in the Zoom Room: Remote Learning via Videoconference Discussions of Physiology Songs

As most instruction has been forced online, biology instructors have become acutely aware of the many advantages and limitations of online teaching. Here, we investigate one possible advantage of online education: the ease of allowing remote guest speakers to interact with students in real time. In particular, we piloted a model in which guest speakers could facilitate direct music-related interactions with students, possibly benefiting students' content knowledge and sense of community. In the context of an undergraduate animal physiology course, face-to-face lessons on arterial blood gases and the renal system were supplemented with videoconferences with a guest speaker who presented relevant content-rich songs and led class discussions of the lyrics. Survey and test data suggested that, after each of the lessons, the students (i) had increased confidence in their understanding of the material, (ii) performed better on objective test questions, and (iii) attributed their learning chiefly to the musical intervention. While our approach awaits further exploration and testing, this report provides preliminary evidence of its feasibility and offers practical suggestions for others who may wish to give it a try.

Is memorization the name of the game? Undergraduates' perceptions of the usefulness of physiology songs

The possible benefits of using music to enhance learning of STEM content are numerous, diverse, and largely unproven. We sought to determine which (if any) of these possible benefits are commonly experienced by undergraduate students and are thus especially worthy of further investigation. Four hundred ninety-three students in nine physiology courses at two midsized American universities rated the usefulness of short instructor-penned mathematical physiology songs and explained in their own words why each song would or would not be a useful study aid. The students collectively perceived the usefulness of each song to depend on both academic factors (e.g., the lyrics' clarity or relevance to the course) and aesthetic values (e.g., the appeal of the rhythm or the quality of the singing). Most strikingly, although students' free responses were brief (median length: 18 words in study phase 1, 16 words in study phase 2), nearly one-half of them (1,039 of 2,191) concerned memory, suggesting that many students see educational songs primarily as mnemonic devices. A second major theme of students' comments concerned the conciseness and information density of the songs. Though all 10 songs were brief, lasting 17-54 s, students seemed to prefer shorter songs (perhaps better called "jingles"). This first-of-its-kind data set on student perceptions of educational songs should inform the creation and usage of such songs, as well as further research on their possible value.

Fragment-Based Screening of a Natural Product Library against 62 Potential Malaria Drug Targets Employing Native Mass Spectrometry

Natural products are well known for their biological relevance, high degree of three-dimensionality, and access to areas of largely unexplored chemical space. To shape our understanding of the interaction between natural products and protein targets in the postgenomic era, we have used native mass spectrometry to investigate 62 potential protein targets for malaria using a natural-product-based fragment library. We reveal here 96 low-molecular-weight natural products identified as binding partners of 32 of the putative malarial targets. Seventy-nine (79) fragments have direct growth inhibition on Plasmodium falciparum at concentrations that are promising for the development of fragment hits against these protein targets. This adds a fragment library to the published HTS active libraries in the public domain.

Teaching the Core Concepts of Physiology: What, Why, and How

In a new book, Joel Michael and colleagues argue that we can teach physiology better by infusing our curricula with specific core concepts developed and refined in faculty workshops and surveys. After defining the 15 core concepts and unpacking some of them, they discuss the integration of these core concepts into the teaching of physiology.

Bioaffinity Mass Spectrometry Screening

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS or ESI-FTMS) was used to screen 192 natural product extracts and a 659-member natural product-based fragment library for bindings to a potential malaria drug target, Plasmodium falciparum Rab11a (PfRab11a, PF13_0119). One natural product extract and 11 fragments showed binding activity. A new natural product, arborside E, was identified from the active extract of Psydrax montigena as a weak binder. Its binding activity and inhibitory activity against PfRab11a were confirmed by ESI-FTMS titration experiments and an orthogonal enzyme assay.

Biochemical Screening of Five Protein Kinases from Plasmodium falciparum against 14,000 Cell-Active Compounds

In 2010 the identities of thousands of anti-Plasmodium compounds were released publicly to facilitate malaria drug development. Understanding these compounds' mechanisms of action--i.e., the specific molecular targets by which they kill the parasite--would further facilitate the drug development process. Given that kinases are promising anti-malaria targets, we screened ~14,000 cell-active compounds for activity against five different protein kinases. Collections of cell-active compounds from GlaxoSmithKline (the ~13,000-compound Tres Cantos Antimalarial Set, or TCAMS), St. Jude Children's Research Hospital (260 compounds), and the Medicines for Malaria Venture (the 400-compound Malaria Box) were screened in biochemical assays of Plasmodium falciparum calcium-dependent protein kinases 1 and 4 (CDPK1 and CDPK4), mitogen-associated protein kinase 2 (MAPK2/MAP2), protein kinase 6 (PK6), and protein kinase 7 (PK7). Novel potent inhibitors (IC50 < 1 μM) were discovered for three of the kinases: CDPK1, CDPK4, and PK6. The PK6 inhibitors are the most potent yet discovered for this enzyme and deserve further scrutiny. Additionally, kinome-wide competition assays revealed a compound that inhibits CDPK4 with few effects on ~150 human kinases, and several related compounds that inhibit CDPK1 and CDPK4 yet have limited cytotoxicity to human (HepG2) cells. Our data suggest that inhibiting multiple Plasmodium kinase targets without harming human cells is challenging but feasible.

High-throughput screening against thioredoxin glutathione reductase identifies novel inhibitors with potential therapeutic value for schistosomiasis

BACKGROUND

Schistosomiasis, a parasitic disease also known as bilharzia and snail fever, is caused by different species of flatworms, such as Schistosoma mansoni (S. mansoni). Thioredoxin glutathione reductase (TGR) from S. mansoni (SmTGR) is a well-characterized drug target for schistosomiasis, yet no anti-SmTGR compounds have reached clinical trials, suggesting that therapeutic development against schistosomiasis might benefit from additional scaffolds targeting this enzyme.

METHODS

A high-throughput screening (HTS) assay in vitro against SmTGR was developed and applied to a diverse compound library. SmTGR activity was quantified with ThioGlo®, a reagent that fluoresces upon binding to the free sulfhydryl groups of the reaction product GSH (reduced glutathione).

RESULTS

We implemented an HTS effort against 59,360 synthetic compounds. In the primary screening, initial hits (928 or 1.56 %) showing greater than 90 % inhibition on SmTGR activity at a final concentration of 10 μM for each compound were identified. Further tests were carried out to confirm the effects of these hits and to explore the concentration-dependent response characteristics. As a result, 74 of them (0.12 %) representing 17 chemical scaffolds were confirmed and showed a great concentration-dependent inhibitory trend against SmTGR, including structures previously shown to be lethal to schistosomal growth. Of these, two scaffolds displayed a limited structure-activity relationship. When tested in cultured larvae, 39 compounds had cidal activity in 48 h, and five of them killed larvae completely at 3.125 μM. Of these, three compounds also killed adult worms ex vivo at concentrations between 5 μM and 10 μM.

CONCLUSION

These confirmed hits may serve as starting points for the development of novel therapeutics to combat schistosomiasis.

The Bacterial Sec Pathway of Protein Export: Screening and Follow-Up

Most noncytoplasmic bacterial proteins are exported through the SecYEG channel in the cytoplasmic membrane. This channel and its associated proteins, collectively referred to as the Sec pathway, have strong appeal as a possible antibiotic drug target, yet progress toward new drugs targeting this pathway has been slow, perhaps due partly to many researchers' focus on a single component, the SecA ATPase. Here we report on a pathway-based screen in which beta-galactosidase (β-gal) activity is trapped in the cytoplasm of Escherichia coli cells if translocation through SecYEG is impaired. Several hit compounds passed a counterscreen distinguishing between β-gal overexpression and impaired β-gal export. However, the most extensively characterized hit gave limited E. coli growth inhibition (EC(50) ≥ 400 µM), and growth inhibition could not be unambiguously linked to the compound's effect on the Sec pathway. Our study and others underscore the challenges of finding potent druglike hits against this otherwise promising drug target.

Cofactor-independent phosphoglycerate mutase from nematodes has limited druggability, as revealed by two high-throughput screens

Cofactor-independent phosphoglycerate mutase (iPGAM) is essential for the growth of C. elegans but is absent from humans, suggesting its potential as a drug target in parasitic nematodes such as Brugia malayi, a cause of lymphatic filariasis (LF). iPGAM's active site is small and hydrophilic, implying that it may not be druggable, but another binding site might permit allosteric inhibition. As a comprehensive assessment of iPGAM's druggability, high-throughput screening (HTS) was conducted at two different locations: ∼220,000 compounds were tested against the C. elegans iPGAM by Genzyme Corporation, and ∼160,000 compounds were screened against the B. malayi iPGAM at the National Center for Drug Screening in Shanghai. iPGAM's catalytic activity was coupled to downstream glycolytic enzymes, resulting in NADH consumption, as monitored by a decline in visible-light absorbance at 340 nm. This assay performed well in both screens (Z′-factor >0.50) and identified two novel inhibitors that may be useful as chemical probes. However, these compounds have very modest potency against the B. malayi iPGAM (IC₅₀ >10 µM) and represent isolated singleton hits rather than members of a common scaffold. Thus, despite the other appealing properties of the nematode iPGAMs, their low druggability makes them challenging to pursue as drug targets. This study illustrates a “druggability paradox” of target-based drug discovery: proteins are generally unsuitable for resource-intensive HTS unless they are considered druggable, yet druggability is often difficult to predict in the absence of HTS data.

Parasitic worms like Brugia malayi cause widespread lymphatic filariasis (LF) in southeast Asia and sub-Saharan Africa. The adult worms causing most of the symptoms of LF are difficult to treat with existing drugs. As a possible step toward new LF drugs, we searched for inhibitors of the B. malayi cofactor-independent phosphoglycerate mutase (iPGAM), an enzyme thought to be critical to survival and development of this parasite. Despite testing over 100,000 compounds at each of two screening centers, we found only two compounds that consistently inhibited the B. malayi enzyme more strongly than the cofactor-dependent enzyme found in humans. These compounds have limited potency and are not especially great starting points for drug development. The 3-dimensional structure of iPGAM suggests that the active site is difficult to access from the surrounding solvent, which may partly explain our very low yield of inhibitors. We conclude that iPGAM may not be an ideal drug target in B. malayi or related organisms because it is difficult to inhibit with druglike compounds.

Re: misconceptions are "so yesterday!"

A response to Maskiewicz and Lineback's essay in the September 2013 issue of CBE-Life Sciences Education.

Plasmodium gametocyte inhibition identified from a natural-product-based fragment library

Fragment-based screening is commonly used to identify compounds with relatively weak but efficient localized binding to protein surfaces. We used mass spectrometry to study fragment-sized three-dimensional natural products. We identified seven securinine-related compounds binding to Plasmodium falciparum 2'-deoxyuridine 5'-triphosphate nucleotidohydrolase (PfdUTPase). Securinine bound allosterically to PfdUTPase, enhancing enzyme activity and inhibiting viability of both P. falciparum gametocyte (sexual) and blood (asexual) stage parasites. Our results provide a new insight into mechanisms that may be applicable to transmission-blocking agents.

A mechanism-based whole-cell screening assay to identify inhibitors of protein export in Escherichia coli by the Sec pathway

More than 20% of bacterial proteins are noncytoplasmic, and most of these pass through the SecYEG channel en route to the periplasm, cell membrane, or surrounding environment. The Sec pathway, encompassing SecYEG and several associated proteins (SecA, SecB, YidC, SecDFYajC), is of interest as a potential drug target because it is distinct from targets of current drugs, is essential for bacterial growth, and exhibits dissimilarities in eukaryotes and bacteria that increase the likelihood of selectively inhibiting the microbial pathway. As a step toward validating the pathway as a drug target, we have adapted a mechanism-based whole-cell assay in a manner suitable for high-throughput screening (HTS). The assay uses an engineered strain of Escherichia coli that accumulates beta-galactosidase (β-gal) in its cytoplasm if translocation through SecYEG is blocked. The assay should facilitate rapid identification of compounds that specifically block the Sec pathway because widely, toxic compounds and nonspecific protein synthesis inhibitors prevent β-gal production and thus do not register as hits. Testing of current antibiotics confirmed that they do not generally act through the Sec pathway. A mini-screen of 800 compounds indicated the assay's readiness for larger screening projects.

TDR Targets: a chemogenomics resource for neglected diseases

The TDR Targets Database (http://tdrtargets.org) has been designed and developed as an online resource to facilitate the rapid identification and prioritization of molecular targets for drug development, focusing on pathogens responsible for neglected human diseases. The database integrates pathogen specific genomic information with functional data (e.g. expression, phylogeny, essentiality) for genes collected from various sources, including literature curation. This information can be browsed and queried using an extensive web interface with functionalities for combining, saving, exporting and sharing the query results. Target genes can be ranked and prioritized using numerical weights assigned to the criteria used for querying. In this report we describe recent updates to the TDR Targets database, including the addition of new genomes (specifically helminths), and integration of chemical structure, property and bioactivity information for biological ligands, drugs and inhibitors and cheminformatic tools for querying and visualizing these chemical data. These changes greatly facilitate exploration of linkages (both known and predicted) between genes and small molecules, yielding insight into whether particular proteins may be druggable, effectively allowing the navigation of chemical space in a genomics context.

Expression of proteins in Escherichia coli as fusions with maltose-binding protein to rescue non-expressed targets in a high-throughput protein-expression and purification pipeline

Despite recent advances, the expression of heterologous proteins in Escherichia coli for crystallization remains a nontrivial challenge. The present study investigates the efficacy of maltose-binding protein (MBP) fusion as a general strategy for rescuing the expression of target proteins. From a group of sequence-verified clones with undetectable levels of protein expression in an E. coli T7 expression system, 95 clones representing 16 phylogenetically diverse organisms were selected for recloning into a chimeric expression vector with an N-terminal histidine-tagged MBP. PCR-amplified inserts were annealed into an identical ligation-independent cloning region in an MBP-fusion vector and were analyzed for expression and solubility by high-throughput nickel-affinity binding. This approach yielded detectable expression of 72% of the clones; soluble expression was visible in 62%. However, the solubility of most proteins was marginal to poor upon cleavage of the MBP tag. This study offers large-scale evidence that MBP can improve the soluble expression of previously non-expressing proteins from a variety of eukaryotic and prokaryotic organisms. While the behavior of the cleaved proteins was disappointing, further refinements in MBP tagging may permit the more widespread use of MBP-fusion proteins in crystallographic studies.

A systems biology approach uncovers cellular strategies used by Methylobacterium extorquens AM1 during the switch from multi- to single-carbon growth

Background

When organisms experience environmental change, how does their metabolic network reset and adapt to the new condition? Methylobacterium extorquens is a bacterium capable of growth on both multi- and single-carbon compounds. These different modes of growth utilize dramatically different central metabolic pathways with limited pathway overlap.

Methodology/Principal Findings

This study focused on the mechanisms of metabolic adaptation occurring during the transition from succinate growth (predicted to be energy-limited) to methanol growth (predicted to be reducing-power-limited), analyzing changes in carbon flux, gene expression, metabolites and enzymatic activities over time. Initially, cells experienced metabolic imbalance with excretion of metabolites, changes in nucleotide levels and cessation of cell growth. Though assimilatory pathways were induced rapidly, a transient block in carbon flow to biomass synthesis occurred, and enzymatic assays suggested methylene tetrahydrofolate dehydrogenase as one control point. This “downstream priming” mechanism ensures that significant carbon flux through these pathways does not occur until they are fully induced, precluding the buildup of toxic intermediates. Most metabolites that are required for growth on both carbon sources did not change significantly, even though transcripts and enzymatic activities required for their production changed radically, underscoring the concept of metabolic setpoints.

Conclusions/Significance

This multi-level approach has resulted in new insights into the metabolic strategies carried out to effect this shift between two dramatically different modes of growth and identified a number of potential flux control and regulatory check points as a further step toward understanding metabolic adaptation and the cellular strategies employed to maintain metabolic setpoints.

Identification of inhibitors for putative malaria drug targets among novel antimalarial compounds

The efficacy of most marketed antimalarial drugs has been compromised by evolution of parasite resistance, underscoring an urgent need to find new drugs with new mechanisms of action. We have taken a high-throughput approach toward identifying novel antimalarial chemical inhibitors of prioritized drug targets for Plasmodium falciparum, excluding targets which are inhibited by currently used drugs. A screen of commercially available libraries identified 5655 low molecular weight compounds that inhibit growth of P. falciparum cultures with EC(50) values below 1.25μM. These compounds were then tested in 384- or 1536-well biochemical assays for activity against nine Plasmodium enzymes: adenylosuccinate synthetase (AdSS), choline kinase (CK), deoxyuridine triphosphate nucleotidohydrolase (dUTPase), glutamate dehydrogenase (GDH), guanylate kinase (GK), N-myristoyltransferase (NMT), orotidine 5'-monophosphate decarboxylase (OMPDC), farnesyl pyrophosphate synthase (FPPS) and S-adenosylhomocysteine hydrolase (SAHH). These enzymes were selected using TDRtargets.org, and are believed to have excellent potential as drug targets based on criteria such as their likely essentiality, druggability, and amenability to high-throughput biochemical screening. Six of these targets were inhibited by one or more of the antimalarial scaffolds and may have potential use in drug development, further target validation studies and exploration of P. falciparum biochemistry and biology.

Identification of attractive drug targets in neglected-disease pathogens using an in silico approach

Background

The increased sequencing of pathogen genomes and the subsequent availability of genome-scale functional datasets are expected to guide the experimental work necessary for target-based drug discovery. However, a major bottleneck in this has been the difficulty of capturing and integrating relevant information in an easily accessible format for identifying and prioritizing potential targets. The open-access resource TDRtargets.org facilitates drug target prioritization for major tropical disease pathogens such as the mycobacteria Mycobacterium leprae and Mycobacterium tuberculosis; the kinetoplastid protozoans Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi; the apicomplexan protozoans Plasmodium falciparum, Plasmodium vivax, and Toxoplasma gondii; and the helminths Brugia malayi and Schistosoma mansoni.

Methodology/Principal Findings

Here we present strategies to prioritize pathogen proteins based on whether their properties meet criteria considered desirable in a drug target. These criteria are based upon both sequence-derived information (e.g., molecular mass) and functional data on expression, essentiality, phenotypes, metabolic pathways, assayability, and druggability. This approach also highlights the fact that data for many relevant criteria are lacking in less-studied pathogens (e.g., helminths), and we demonstrate how this can be partially overcome by mapping data from homologous genes in well-studied organisms. We also show how individual users can easily upload external datasets and integrate them with existing data in TDRtargets.org to generate highly customized ranked lists of potential targets.

Conclusions/Significance

Using the datasets and the tools available in TDRtargets.org, we have generated illustrative lists of potential drug targets in seven tropical disease pathogens. While these lists are broadly consistent with the research community's current interest in certain specific proteins, and suggest novel target candidates that may merit further study, the lists can easily be modified in a user-specific manner, either by adjusting the weights for chosen criteria or by changing the criteria that are included.

In cell-based drug development, researchers attempt to create drugs that kill a pathogen without necessarily understanding the details of how the drugs work. In contrast, target-based drug development entails the search for compounds that act on a specific intracellular target—often a protein known or suspected to be required for survival of the pathogen. The latter approach to drug development has been facilitated greatly by the sequencing of many pathogen genomes and the incorporation of genome data into user-friendly databases. The present paper shows how the database TDRtargets.org can identify proteins that might be considered good drug targets for diseases such as African sleeping sickness, Chagas disease, parasitic worm infections, tuberculosis, and malaria. These proteins may score highly in searches of the database because they are dissimilar to human proteins, are structurally similar to other “druggable” proteins, have functions that are easy to measure, and/or fulfill other criteria. Researchers can use the lists of high-scoring proteins as a basis for deciding which potential drug targets to pursue experimentally.

Chemical genetics of Plasmodium falciparum

Malaria caused by Plasmodium falciparum is a catastrophic disease worldwide (880,000 deaths yearly). Vaccine development has proved difficult and resistance has emerged for most antimalarials. In order to discover new antimalarial chemotypes, we have employed a phenotypic forward chemical genetic approach to assay 309,474 chemicals. Here we disclose structures and biological activity of the entire library, many of which exhibited potent in vitro activity against drug resistant strains, and detailed profiling of 172 representative candidates. A reverse chemical genetic study identified 19 new inhibitors of 4 validated drug targets and 15 novel binders among 61 malarial proteins. Phylochemogenetic profiling in multiple organisms revealed similarities between Toxoplasma gondii and mammalian cell lines and dissimilarities between P. falciparum and related protozoans. One exemplar compound displayed efficacy in a murine model. Overall, our findings provide the scientific community with new starting points for malaria drug discovery.

Buffer optimization of thermal melt assays of Plasmodium proteins for detection of small-molecule ligands

In the past decade, thermal melt/thermal shift assays have become a common tool for identifying ligands and other factors that stabilize specific proteins. Increased stability is indicated by an increase in the protein's melting temperature (Tm). In optimizing the assays for subsequent screening of compound libraries, it is important to minimize the variability of Tm measurements so as to maximize the assay's ability to detect potential ligands. The authors present an investigation of Tm variability in recombinant proteins from Plasmodium parasites. Ligands of Plasmodium proteins are particularly interesting as potential starting points for drugs for malaria, and new drugs are urgently needed. A single standard buffer (100 mM HEPES [pH 7.5], 150 mM NaCl) permitted estimation of Tm for 58 of 61 Plasmodium proteins tested. However, with several proteins, Tm could not be measured with a consistency suitable for high-throughput screening unless alternative protein-specific buffers were employed. The authors conclude that buffer optimization to minimize variability in Tm measurements increases the success of thermal melt screens involving proteins for which a standard buffer is suboptimal.

Genomic-scale prioritization of drug targets: the TDR Targets database

The increasing availability of genomic data for pathogens that cause tropical diseases has created new opportunities for drug discovery and development. However, if the potential of such data is to be fully exploited, the data must be effectively integrated and be easy to interrogate. Here, we discuss the development of the TDR Targets database (http://tdrtargets.org), which encompasses extensive genetic, biochemical and pharmacological data related to tropical disease pathogens, as well as computationally predicted druggability for potential targets and compound desirability information. By allowing the integration and weighting of this information, this database aims to facilitate the identification and prioritization of candidate drug targets for pathogens.

Poem: A is for alanine

The poem below presents a brief review of amino acid abbreviations and structures. Among the featured facts are the following: histidine has a pK(a) close to the normal pH of the cytosol and therefore is an effective intracellular buffer, the R group of isoleucine is hydrophobic, and many protein kinases add a phosphate at the -OH site of tyrosine. This work is just one of many science songs and poems that may be used for educational purposes. A comprehensive database of over 2,000 songs is available online at www.science-groove.org/MASSIVE/.

Acidosis inhibits oxidative phosphorylation in contracting human skeletal muscle in vivo

This study tested the hypothesis that acidic pH inhibits oxidative ATP supply during exercise in hand (first dorsal interosseus, FDI) and lower limb (leg anterior compartment, LEG) muscles. We measured oxidative flux and estimated mitochondrial capacity using the changes in creatine phosphate concentration ([PCr]) and pH as detected by 31P magnetic resonance (MR) spectroscopy during isometric exercise and recovery. The highest oxidative ATP flux in sustained exercise was about half the estimated mitochondrial capacity in the LEG (0.38 +/- 0.06 vs. 0.90 +/- 0.14 mM ATP s(-1), respectively), but at the estimated capacity in the FDI (0.61 +/- 0.05 vs. 0.61 +/- 0.09 mM ATP s(-1), respectively). During sustained exercise at a higher contraction rate, intracellular acidosis (pH < 6.88) prevented a rise in oxidative flux in the LEG and FDI despite significantly increased [ADP]. We tested whether oxidative flux could increase above that achieved in sustained exercise by raising [ADP] (> 0.24 mM) and avoiding acidosis using burst exercise. This exercise raised oxidative flux (0.69 +/- 0.05 mM ATP s(-1)) to nearly twice that found with sustained exercise in the LEG and matched (0.65 +/- 0.11 mM ATP s(-1)) the near maximal flux seen during sustained exercise in the FDI. Thus both muscles reached their highest oxidative fluxes in the absence of acidosis. These results show that acidosis inhibits oxidative phosphorylation in vivo and can limit ATP supply in exercising muscle to below the mitochondrial capacity.

Altered energetic properties in skeletal muscle of men with well-controlled insulin-dependent (type 1) diabetes

This study asked whether the energetic properties of muscles are changed by insulin-dependent diabetes mellitus (or type 1 diabetes), as occurs in obesity and type 2 diabetes. We used (31)P magnetic resonance spectroscopy to measure glycolytic flux, oxidative flux, and contractile cost in the ankle dorsiflexor muscles of 10 men with well-managed type 1 diabetes and 10 age- and activity-matched control subjects. Each subject performed sustained isometric muscle contractions lasting 30 and 120 s while attempting to maintain 70-75% of maximal voluntary contraction force. An altered glycolytic flux in type 1 diabetic subjects relative to control subjects was apparent from significant differences in pH in muscle at rest and at the end of the 120-s bout. Glycolytic flux during exercise began earlier and reached a higher peak rate in diabetic patients than in control subjects. A reduced oxidative capacity in the diabetic patients' muscles was evident from a significantly slower phosphocreatine recovery from a 30-s exercise bout. Our findings represent the first characterization of the energetic properties of muscle from type 1 diabetic patients. The observed changes in glycolytic and oxidative fluxes suggest a diabetes-induced shift in the metabolic profile of muscle, consistent with studies of obesity and type 2 diabetes that point to common muscle adaptations in these diseases.

A "functional biopsy" of muscle properties in sprinters and distance runners

PURPOSE

Fast- and slow-twitch human muscle fibers exhibit large (two- to threefold) differences in metabolic enzyme activities and contractile economy. We asked whether comparable flux differences are evident in the muscles of athletes specializing in extremely different (i.e., sprint and long-distance) running events.

METHODS

We took an in vivo "functional biopsy" of the ankle dorsiflexor muscles of 17 members of a university track team by using (31)P magnetic resonance spectroscopy. Ten sprinters (SPR) and seven distance runners (DIS) performed rapid isometric dorsiflexions against the resistance of a plastic foot holder. The contractile cost of exercise and glycolytic flux were calculated from changes in pH, [PCr], and [P(i)] during ischemic exercise, and oxidative capacity was calculated from PCr recovery kinetics after aerobic exercise.

RESULTS

Contractile costs were 47% higher in SPR than in DIS, whereas oxidative capacities were 52% higher in DIS than in SPR. Surprisingly, glycolytic ATP production was similar in the two groups.

CONCLUSION

The muscles of SPR and DIS exhibit clear differences in energetic properties, but these differences are smaller than the two- to three-fold variations seen in the properties of individual muscle fibers.

Fiber recruitment affects oxidative recovery measurements of human muscle in vivo

PURPOSE

Fast-twitch and slow-twitch muscle fibers are known to have distinct metabolic properties. However, it has not been clearly established whether such heterogeneity within mixed-fiber muscles can influence measurements of energy metabolism in vivo. We therefore tested the hypothesis that differences in muscle fiber recruitment can cause differences in whole-muscle oxidative recovery from exercise.

METHODS

We used (31)P magnetic resonance spectroscopy to measure oxidative ATP synthesis in the ankle dorsiflexor muscles of eight healthy volunteers under a variety of recruitment conditions. Oxidative ATP synthesis after isometric exercise was quantified as the rate constant k(PCr), the reciprocal of the time constant of PCr recovery.

RESULTS

k(PCr) was 37% higher after low-force ramp contractions (which primarily recruit slow-twitch fibers) than after ballistic contractions to the same peak force (which recruit both fast- and slow-twitch fibers). k(PCr) was also 24% higher after low-force ramp contractions than after high-force ramp contractions, presumably reflecting the recruitment of fast-twitch fibers at high forces.

CONCLUSION

Our results indicate that the muscle fibers recruited first in voluntary contractions have a higher oxidative capacity than those recruited last. Such metabolic differences among fibers can confound whole-muscle measurements and thus need to be taken into account when studying voluntary exercise.

Control of glycolysis in contracting skeletal muscle. I. Turning it on

Why does the onset of glycolytic flux in muscle lag the start of exercise? We tested the hypothesis that both elevated metabolite levels and muscle activity are required for flux to begin. Glycolytic flux was determined from changes in muscle pH, phosphocreatine concentration, and P(i) concentration ([P(i)]) as measured by 31P magnetic resonance spectroscopy. Eight subjects performed rapid ankle dorsiflexions to approximately 45% of maximal voluntary contraction force under ischemia at a rate of 1 contraction/s. Subjects completed two bouts of exercise separated by 1 min of ischemic rest. Glycolytic flux was activated by 27 s in the first bout, ceased during the ischemic rest period, and was activated more quickly in the second bout. Because the onset in both bouts occurred at approximately the same [P(i)], ADP concentration, and AMP concentration, the activation of glycolysis appears to be related to the elevation of these metabolite concentrations. However, because no glycolytic flux occurred at rest, even when metabolite levels were high, both muscle activity and elevated metabolites are needed to turn on this pathway. We conclude that the delayed onset of glycolytic flux during exercise reflects the time needed to raise metabolites to flux-activating levels.

Control of glycolysis in contracting skeletal muscle. II. Turning it off

Glycolytic flux in muscle declines rapidly after exercise stops, indicating that muscle activation is a key controller of glycolysis. The mechanism underlying this control could be 1) a Ca(2+)-mediated modulation of glycogenolysis, which supplies substrate (hexose phosphates, HP) to the glycolytic pathway, or 2) a direct effect on glycolytic enzymes. To distinguish between these possibilities, HP levels were raised by voluntary 1-Hz exercise, and glycolytic flux was measured after the exercise ceased. Glycolytic H(+) and ATP production were quantified from changes in muscle pH, phosphocreatine concentration, and P(i) concentration as measured by 31P magnetic resonance spectroscopy. Substrate (HP) and metabolite (P(i), ADP, and AMP) levels remained high when exercise stopped because of the occlusion of blood flow with a pressure cuff. Glycolytic flux declined to basal levels within approximately 20 s of the end of exercise despite elevated levels of HP and metabolites. Therefore, this flux does not subside because of insufficient HP substrate; rather, glycolysis is controlled independently of glycogenolytic HP production. We conclude that the inactivation of glycolysis after exercise reflects the cessation of contractile activity and is mediated within the glycolytic pathway rather than via the control of glycogen breakdown.

Limits to sustainable muscle performance: interaction between glycolysis and oxidative phosphorylation

This paper proposes a mechanism responsible for setting the sustainable level of muscle performance. Our contentions are that the sustainable work rate is determined (i) at the muscle level, (ii) by the ability to maintain ATP supply and (iii) by the products of glycolysis that may inhibit the signal for oxidative phosphorylation. We argue below that no single factor ‘limits’ sustainable performance, but rather that the flux through and the interaction between glycolysis and oxidative phosphorylation set the level of sustainable ATP supply. This argument is based on magnetic resonance spectroscopy measurements of the sources and sinks for energy in vivo in human muscle and rattlesnake tailshaker muscle during sustained contractions. These measurements show that glycolysis provides between 20% (human muscle) and 40% (tailshaker muscle) of the ATP supply during sustained contractions in these muscles. We cite evidence showing that this high glycolytic flux does not reflect an O2 limitation or mitochondria operating at their capacity. Instead, this flux reflects a pathway independent of oxidative phosphorylation for ATP supply during aerobic exercise. The consequence of this high glycolytic flux is accumulation of H+, which we argue inhibits the rise in the signal activating oxidative phosphorylation, thereby restricting oxidative ATP supply to below the oxidative capacity. Thus, both glycolysis and oxidative phosphorylation play important roles in setting the highest steady-state ATP synthesis flux and thereby determine the sustainable level of work by exercising muscle.

Characterization of sphinganine kinase activity in corn shoot microsomes

The activity of sphinganine kinase, the enzyme catalyzing the first step in the breakdown of the sphingoid long-chain base sphinganine by converting it to sphinganine 1-phosphate, was characterized in microsomes isolated from corn shoots. Activity was assayed by monitoring the conversion of [3H]sphinganine to [3H]sphinganine 1-phosphate, which was recovered in the aqueous phase following lipid extraction. Sphinganine kinase was found to utilize D-erythro-sphinganine and ATP as substrates. Maximum product formation required the presence of Mg2+. The apparent Km for ATP was 0.81 mM. GTP also served as a source of phosphate, whereas CTP and UTP were not effective substrates in this assay. Maximum product formation was observed at sphinganine concentrations of approximately 100 microM. Results of competition experiments suggested that the enzyme could also phosphorylate D-erythro-sphingosine but not DL-threo-sphinganine or D-phytosphingosine. Enzyme activity was greatest in the microsomal fraction obtained by differential centrifugation and was localized to the Golgi and endoplasmic reticulum using marker enzymes. The specific activity of the enzyme under optimal conditions was 1.08 nmol/min x mg protein, a value 25-fold higher than that reported for preparations from brain tissue. Fumonisin, a mycotoxin that disrupts sphingolipid metabolism, did not alter sphinganine kinase activity in vivo or in vitro. The results of this study demonstrate, for the first time, the presence of sphinganine kinase activity in plant tissue and suggest that the properties of the kinase from corn microsomes are distinct from those of the mammalian and protistan enzymes in some respects.