A survey of the kinome pharmacopeia reveals multiple scaffolds and targets for the development of novel anthelmintics

AbstractOver one billion people are currently infected with a parasitic nematode. Symptoms can include anemia, malnutrition, developmental delay, and in severe cases, death. Resistance is emerging to the anthelmintics currently used to treat nematode infection, prompting the need to develop new anthelmintics. Towards this end, we identified a set of kinases that may be targeted in a nematode-selective manner. We first screened 2040 inhibitors of vertebrate kinases for those that impair the model nematode Caenorhabditis elegans. By determining whether the terminal phenotype induced by each kinase inhibitor matched that of the predicted target mutant in C. elegans, we identified 17 druggable nematode kinase targets. Of these, we found that nematode EGFR, MEK1, and PLK1 kinases have diverged from vertebrates within their drug-binding pocket. For each of these targets, we identified small molecule scaffolds that may be further modified to develop nematode-selective inhibitors. Nematode EGFR, MEK1, and PLK1 therefore represent key targets for the development of new anthelmintic medicines.

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A Survey of the Kinome Pharmacopeia Reveals Multiple Scaffolds and Targets for the Development of Novel Anthelmintics

10.1101/2020.08.20.259481 ◽

2020 ◽

Author(s):

Jessica Knox ◽

William Zuercher ◽

Peter J. Roy

Keyword(s):

Caenorhabditis Elegans ◽

Developmental Delay ◽

Small Molecule ◽

Parasitic Nematode ◽

Kinase Inhibitor ◽

Binding Pocket ◽

Drug Binding ◽

C Elegans ◽

Specific Manner ◽

Specific Inhibitors

AbstractOver one billion people are currently infected with a parasitic nematode. Symptoms can include anemia, malnutrition, developmental delay, and in severe cases, death. Resistance is emerging to anthelmintic drugs used to treat nematode infection, prompting the need to develop new anthelmintics. Towards this end, we identified a set of kinases that may be targeted in a nematode-specific manner. We first screened 2040 inhibitors of vertebrate kinases for those that impair the model nematode Caenorhabditis elegans. By determining whether the terminal phenotype induced by each kinase inhibitor matched that of the predicted target mutant in C. elegans, we identified 17 druggable nematode kinase targets. Of these, we found that nematode EGFR, MEK1, and PLK1 kinases have diverged from vertebrates within their drug-binding pocket. For each of these targets, we identified small molecule scaffolds that may be further modified to develop nematode-specific inhibitors. Nematode EGFR, MEK1, and PLK1 therefore represent key targets for the development of new anthelmintic medicines.One sentence summaryDruggable Kinases as Anthelmintic Targets

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The Caenorhabditis elegans DEG-3/DES-2 Channel Is a Betaine-Gated Receptor Insensitive to Monepantel

Molecules ◽

10.3390/molecules27010312 ◽

2022 ◽

Vol 27 (1) ◽

pp. 312

Author(s):

Tina V. A. Hansen ◽

Heinz Sager ◽

Céline E. Toutain ◽

Elise Courtot ◽

Cédric Neveu ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Nicotinic Acetylcholine Receptors ◽

Acetylcholine Receptors ◽

Parasitic Nematode ◽

Nematode Species ◽

Xenopus Laevis Oocytes ◽

Allosteric Modulators ◽

C Elegans ◽

Electrode Voltage ◽

Insight Into

Natural plant compounds, such as betaine, are described to have nematocidal properties. Betaine also acts as a neurotransmitter in the free-living model nematode Caenorhabditis elegans, where it is required for normal motility. Worm motility is mediated by nicotinic acetylcholine receptors (nAChRs), including subunits from the nematode-specific DEG-3 group. Not all types of nAChRs in this group are associated with motility, and one of these is the DEG-3/DES-2 channel from C. elegans, which is involved in nociception and possibly chemotaxis. Interestingly, the activity of DEG-3/DES-2 channel from the parasitic nematode of ruminants, Haemonchus contortus, is modulated by monepantel and its sulfone metabolite, which belong to the amino-acetonitrile derivative anthelmintic drug class. Here, our aim was to advance the pharmacological knowledge of the DEG-3/DES-2 channel from C. elegans by functionally expressing the DEG-3/DES-2 channel in Xenopus laevis oocytes and using two-electrode voltage-clamp electrophysiology. We found that the DEG-3/DES-2 channel was more sensitive to betaine than ACh and choline, but insensitive to monepantel and monepantel sulfone when used as direct agonists and as allosteric modulators in co-application with betaine. These findings provide important insight into the pharmacology of DEG-3/DES-2 from C. elegans and highlight the pharmacological differences between non-parasitic and parasitic nematode species.

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Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1608262113 ◽

2016 ◽

Vol 113 (36) ◽

pp. 10055-10060 ◽

Cited By ~ 19

Author(s):

Xinxing Zhang ◽

Kunhua Li ◽

Rachel A. Jones ◽

Steven D. Bruner ◽

Rebecca A. Butcher

Keyword(s):

Caenorhabditis Elegans ◽

Nematode Species ◽

Binding Pocket ◽

Pheromone Biosynthesis ◽

Atp Binding ◽

Metabolic State ◽

C Elegans ◽

Acyl Coa Oxidase ◽

Key Residues ◽

And Behavior

Caenorhabditis elegans secretes ascarosides as pheromones to communicate with other worms and to coordinate the development and behavior of the population. Peroxisomal β-oxidation cycles shorten the side chains of ascaroside precursors to produce the short-chain ascaroside pheromones. Acyl-CoA oxidases, which catalyze the first step in these β-oxidation cycles, have different side chain-length specificities and enable C. elegans to regulate the production of specific ascaroside pheromones. Here, we determine the crystal structure of the acyl-CoA oxidase 1 (ACOX-1) homodimer and the ACOX-2 homodimer bound to its substrate. Our results provide a molecular basis for the substrate specificities of the acyl-CoA oxidases and reveal why some of these enzymes have a very broad substrate range, whereas others are quite specific. Our results also enable predictions to be made for the roles of uncharacterized acyl-CoA oxidases in C. elegans and in other nematode species. Remarkably, we show that most of the C. elegans acyl-CoA oxidases that participate in ascaroside biosynthesis contain a conserved ATP-binding pocket that lies at the dimer interface, and we identify key residues in this binding pocket. ATP binding induces a structural change that is associated with tighter binding of the FAD cofactor. Mutations that disrupt ATP binding reduce FAD binding and reduce enzyme activity. Thus, ATP may serve as a regulator of acyl-CoA oxidase activity, thereby directly linking ascaroside biosynthesis to ATP concentration and metabolic state.

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Characterization and expression of a spliced leader RNA in the parasitic nematode Ascaris lumbricoides var. suum

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3543-3547.1989 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3543-3547

Author(s):

T W Nilsen ◽

J Shambaugh ◽

J Denker ◽

G Chubb ◽

C Faser ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Secondary Structure ◽

Rna Polymerase ◽

Binding Site ◽

Rna Polymerase Ii ◽

Ascaris Lumbricoides ◽

Parasitic Nematode ◽

Secondary Structures ◽

Spliced Leader ◽

C Elegans

The parasitic nematode Ascaris spp. contains a 22-nucleotide spliced-leader (SL) sequence identical to the trans-SL previously described in Caenorhabditis elegans and other nematodes. The SL comprises the first 22 nucleotides of a approximately 110-base RNA and is transcribed by RNA polymerase II. The SL RNA contains a trimethylguanosine cap and a consensus Sm binding site. Furthermore, the Ascaris SL RNA has the potential to adopt a secondary structure which is nearly identical to potential secondary structures of similar SL RNAs in C. elegans and Brugia malayi.

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The use of Caenorhabditis elegans in parasitic nematode research

Parasitology ◽

10.1017/s003118200400647x ◽

2004 ◽

Vol 128 (S1) ◽

pp. S49-S70 ◽

Cited By ~ 39

Author(s):

J. S. GILLEARD

Keyword(s):

Caenorhabditis Elegans ◽

Parasitic Nematode ◽

Expression System ◽

Nematode Species ◽

Current Status ◽

Evolutionary Development ◽

Parasitic Nematodes ◽

Free Living ◽

C Elegans ◽

Free Living Nematode

There is increasing interest in the use of the free-living nematode Caenorhabditis elegans as a tool for parasitic nematode research and there are now a number of compelling examples of its successful application. C. elegans has the potential to become a standard tool for molecular helminthology researchers, just as yeast is routinely used by molecular biologists to study vertebrate biology. However, in order to exploit C. elegans in a meaningful manner, we need a detailed understanding of the extent to which different aspects of C. elegans biology have been conserved with particular groups of parasitic nematodes. This review first considers the current state of knowledge regarding the conservation of genome organisation across the nematode phylum and then discusses some recent evolutionary development studies in free-living nematodes. The aim is to provide some important concepts that are relevant to the extrapolation of information from C. elegans to parasitic nematodes and also to the interpretation of experiments that use C. elegans as a surrogate expression system. In general, examples have been specifically chosen because they highlight the importance of careful experimentation and interpretation of data. Consequently, the focus is on the differences that have been found between nematode species rather than the similarities. Finally, there is a detailed discussion of the current status of C. elegans as a heterologous expression system to study parasite gene function and regulation using successful examples from the literature.

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Developmental strategies during early embryogenesis of Caenorhabditis elegans

Development ◽

10.1242/dev.97.supplement.31 ◽

1986 ◽

Vol 97 (Supplement) ◽

pp. 31-44

Author(s):

Einhard Schierenberg

Keyword(s):

Caenorhabditis Elegans ◽

Parasitic Nematode ◽

Soil Nematode ◽

Developmental Studies ◽

Central Question ◽

Unique Combination ◽

Nematode Caenorhabditis Elegans ◽

Free Living ◽

C Elegans ◽

Multicellular Structure

How the complex, multicellular structure of an organism is generated from the information contained in the uncleaved egg is a central question in developmental studies. Nematodes are particularly suitable for studying this question. A unique combination of favourable properties, including transparent eggshell, normal embryogenesis under the microscope outside the mother, small number of cells and rapid, reproducible development made nematodes classic models for developmental biologists (for reviews see Chitwood & Chitwood, 1974; von Ehrenstein & Schierenberg, 1980). In addition to the attractive features mentioned above, the free-living soil nematode Caenorhabditis elegans (Fig. 1) is also well suited for analysis of the genetic control of development (Brenner, 1974) unlike the classically studied parasitic nematode Parascaris equorum (Ascaris megalocephala). Recently cellular (e.g. Sulston, Schierenberg, White & Thomson, 1983) and genetic (e.g. Sternberg & Horvitz, 1984) aspects of development have been studied extensively in C. elegans.

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Characterization and expression of a spliced leader RNA in the parasitic nematode Ascaris lumbricoides var. suum.

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3543 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3543-3547 ◽

Cited By ~ 47

Author(s):

T W Nilsen ◽

J Shambaugh ◽

J Denker ◽

G Chubb ◽

C Faser ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Secondary Structure ◽

Rna Polymerase ◽

Binding Site ◽

Rna Polymerase Ii ◽

Ascaris Lumbricoides ◽

Parasitic Nematode ◽

Secondary Structures ◽

Spliced Leader ◽

C Elegans

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Caenorhabditis elegans: nature and nurture gift to nematode parasitologists

Parasitology ◽

10.1017/s0031182017002165 ◽

2017 ◽

Vol 145 (8) ◽

pp. 979-987 ◽

Cited By ~ 5

Author(s):

Gustavo Salinas ◽

Gastón Risi

Keyword(s):

Animal Model ◽

Caenorhabditis Elegans ◽

Parasitic Nematode ◽

Model Organism ◽

Parasitic Nematodes ◽

Free Living ◽

C Elegans ◽

Free Living Nematode ◽

Basic Biology ◽

Nature And Nurture

AbstractThe free-living nematode Caenorhabditis elegans is the simplest animal model organism to work with. Substantial knowledge and tools have accumulated over 50 years of C. elegans research. The use of C. elegans relating to parasitic nematodes from a basic biology standpoint or an applied perspective has increased in recent years. The wealth of information gained on the model organism, the use of the powerful approaches and technologies that have advanced C. elegans research to parasitic nematodes and the enormous success of the omics fields have contributed to bridge the divide between C. elegans and parasite nematode researchers. We review key fields, such as genomics, drug discovery and genetics, where C. elegans and nematode parasite research have convened. We advocate the use of C. elegans as a model to study helminth metabolism, a neglected area ready to advance. How emerging technologies being used in C. elegans can pave the way for parasitic nematode research is discussed.

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Imatinib-Resistant BCR-ABL Mutant Cellular Screening Paradigm To Characterize Promising Small-Molecule Inhibitors: T315I-BCR-ABL Targeted Drug Discovery.

Blood ◽

10.1182/blood.v108.11.2181.2181 ◽

2006 ◽

Vol 108 (11) ◽

pp. 2181-2181

Author(s):

Mohammad Azam ◽

William C. Shakespeare ◽

Chester Metcalf ◽

Yihan Wang ◽

Raji Sunderamoorthi ◽

...

Keyword(s):

Drug Discovery ◽

Structural Analysis ◽

Cell Lines ◽

Small Molecule ◽

Kinase Inhibitors ◽

Kinase Inhibitor ◽

Drug Binding ◽

Imatinib Resistance ◽

Inhibition Of Proliferation ◽

Imatinib Resistant

Abstract In patients with chronic myeloid leukemia (CML), kinase domain mutations account for imatinib resistance in the majority of cases. Mutations cause either a direct steric hindrance to drug binding or a conformational change that favors kinase activation, which therefore precludes imatinib binding. We have previously characterized the dual Src-Abl kinase inhibitor AP23464 and found it to effectively suppress the growth of cells expressing native and essentially all imatinib-resistant variants of BCR-ABL, with the notable exception of the gatekeeper T315I mutant (Azam et al., Proc. Natl. Acad. Sci. USA, 103: 9244, 2006). Following this work, we have used mutant panel screening and integrated structural analysis to further characterize key analogs designed to overcome T315I resistance, as exemplified by AP23846 and AP24163. Both molecules effectively inhibit the tyrosine kinase activity of wild type (WT) and T315I variants of BCR-ABL, and inhibit the proliferation of BaF3-derived cell lines expressing these enzymes (see Table below). AP24163 was further characterized against a broader panel of imatinib-resistant BCR-ABL-expressing cell lines and showed a promising profile of proliferation inhibition. Comparison of these data with structural models of the mutants provides insights into the basis for the ability of AP24163 to overcome imatinib resistance. Refinement of small-molecule kinase inhibitors by the integration of sequential screening of panels of mutants coupled with structural analysis is a powerful drug discovery paradigm that is applicable to an increasing number of targeted therapeutic agents. INHIBITION OF PROLIFERATION OF BAF3 CELLS EXPRESSING BCR-ABL AND ITS VARIANTS (IC50 in nM) IMATINIB AP23464 AP23846 AP24163 WT 600 14 500 7 T315I >20000 >1000 500 480 L248R >20000 92 ND 64 G250E 5000 25 ND 63 Q252H 3000 40 ND 42 Y253H 18000 32 ND 44 E255K 12000 74 ND 24 BAF3+IL3 >20000 >1000 500 >10000 Figure Figure

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Conditional Dominant Mutations in the Caenorhabditis elegans Gene act-2 Identify Cytoplasmic and Muscle Roles for a Redundant Actin Isoform

Molecular Biology of the Cell ◽

10.1091/mbc.e05-09-0886 ◽

2006 ◽

Vol 17 (3) ◽

pp. 1051-1064 ◽

Cited By ~ 21

Author(s):

John H. Willis ◽

Edwin Munro ◽

Rebecca Lyczak ◽

Bruce Bowerman

Keyword(s):

Caenorhabditis Elegans ◽

Muscle Cells ◽

Binding Pocket ◽

Embryonic Cell ◽

Temperature Sensitive ◽

Restrictive Temperature ◽

Embryonic Cells ◽

Actin Isoforms ◽

C Elegans ◽

Actin Isoform

Animal genomes each encode multiple highly conserved actin isoforms that polymerize to form the microfilament cytoskeleton. Previous studies of vertebrates and invertebrates have shown that many actin isoforms are restricted to either nonmuscle (cytoplasmic) functions, or to myofibril force generation in muscle cells. We have identified two temperature-sensitive and semidominant embryonic-lethal Caenorhabditis elegans mutants, each with a single mis-sense mutation in act-2, one of five C. elegans genes that encode actin isoforms. These mutations alter conserved and adjacent amino acids predicted to form part of the ATP binding pocket of actin. At the restrictive temperature, both mutations resulted in aberrant distributions of cortical microfilaments associated with abnormal and striking membrane ingressions and protrusions. In contrast to the defects caused by these dominant mis-sense mutations, an act-2 deletion did not result in early embryonic cell division defects, suggesting that additional and redundant actin isoforms are involved. Accordingly, we found that two additional actin isoforms, act-1 and act-3, were required redundantly with act-2 for cytoplasmic function in early embryonic cells. The act-1 and -3 genes also have been implicated previously in muscle function. We found that an ACT-2::GFP reporter was expressed cytoplasmically in embryonic cells and also was incorporated into contractile filaments in adult muscle cells. Furthermore, one of the dominant act-2 mutations resulted in uncoordinated adult movement. We conclude that redundant C. elegans actin isoforms function in both muscle and nonmuscle contractile processes.

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