Differential analysis of 2D NMR spectra: new natural products from a pilot-scale fungal extract library.
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Biological Factors↗
Biomedical subjects
Jon Clardy
Publications and source records attributed to Jon Clardy.
High-throughput screening affords novel and selective trypanothione reductase inhibitors with anti-trypanosomal activity.
Trypanothione reductase (TR), an enzyme that buffers oxidative stress in trypanosomatid parasites, was screened against commercial libraries containing approximately 134,500 compounds. After secondary screening, four chemotypes were identified as screening positives with selectivity for TR over human glutathione reductase. Thirteen compounds from these four chemotypes were purchased, and their in vitro activity against TR and Trypanosoma brucei is described.
Animals↗
High-throughput Plasmodium falciparum growth assay for malaria drug discovery.
New therapeutic agents for the treatment of malaria, the world's most deadly parasitic disease, are urgently needed. Malaria afflicts 300 to 500 million people and results in 1 to 2 million deaths annually, and more than 85% of all malaria-related mortality involves young children and pregnant women in sub-Saharan Africa. The emergence of multidrug-resistant parasites, especially in Plasmodium falciparum, has eroded the efficacy of almost all currently available therapeutic agents. The discovery of new drugs, including drugs with novel cellular targets, could be accelerated with a whole-organism high-throughput screen (HTS) of structurally diverse small-molecule libraries. The standard whole-organism screen is based on incorporation of [3H]hypoxanthine and has liabilities, such as limited throughput, high cost, multiple labor-intensive steps, and disposal of radioactive waste. Recently, screens have been reported that do not use radioactive incorporation, but their reporter signal is not robust enough for HTS. We report a P. falciparum growth assay that is technically simple, robust, and compatible with the automation necessary for HTS. The assay monitors DNA content by addition of the fluorescent dye 4',6-diamidino-2-phenylindole (DAPI) as a reporter of blood-stage parasite growth. This DAPI P. falciparum growth assay was used to measure the 50% inhibitory concentrations (IC50s) of a diverse set of known antimalarials. The resultant IC50s compared favorably with those obtained in the [3H]hypoxanthine incorporation assay. Over 79,000 small molecules have been tested for antiplasmodial activity using the DAPI P. falciparum growth assay, and 181 small molecules were identified as highly active against multidrug-resistant parasites.
Animals↗
Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators.
Although androgen receptor (AR)-mediated signaling is central to prostate cancer, the ability to modulate AR signaling states is limited. Here we establish a chemical genomic approach for discovery and target prediction of modulators of cancer phenotypes, as exemplified by AR signaling. We first identify AR activation inhibitors, including a group of structurally related compounds comprising celastrol, gedunin, and derivatives. To develop an in silico approach for target pathway identification, we apply a gene expression-based analysis that classifies HSP90 inhibitors as having similar activity to celastrol and gedunin. Validating this prediction, we demonstrate that celastrol and gedunin inhibit HSP90 activity and HSP90 clients, including AR. Broadly, this work identifies new modes of HSP90 modulation through a gene expression-based strategy.
Antibiotics, Antineoplastic↗
Preparation of a psammaplysene-based library.
A 28-member focused library, based on the pseudosymmetric template of the marine alkaloids psammaplysenes, was prepared from combinations of components that were, in turn, derived from 4-iodophenol.
Chromatography, Liquid↗
Phaeosphaeride A, an inhibitor of STAT3-dependent signaling isolated from an endophytic fungus.
Phaeosphaeride A, a nitrogen-containing bicyclic compound produced by an endophytic fungus, inhibits signaling by the transcription factor STAT3.
Antineoplastic Agents↗
A biosynthetic gene cluster for the acetyl-CoA carboxylase inhibitor andrimid.
Increasing bacterial resistance to antibiotics with conventional targets has focused attention on antibiotics with unconventional targets. One promising candidate, the acetyl-CoA carboxylase (ACC) inhibitor andrimid, is a potent, broad-spectrum antibiotic with high selectivity for prokaryotic ACC. Here, we report the use of a DNA-based approach to clone the andrimid biosynthetic gene cluster from Pantoea agglomerans, yielding a cosmid that confers robust andrimid production on Escherichia coli. This gene cluster encodes a hybrid nonribosomal peptide/polyketide (NRP/PK) synthase with several unusual features, including three enzymes that form and insert beta-phenylalanine, two transglutaminase-like enzymes that likely serve as condensation catalysts, and four densely hybrid modules that form the succinimide precursor. Unlike most type I NRPSs and PKSs, the andrimid gene cluster is a dissociated system comprised of small proteins. Therefore, future efforts can exploit the genetic manipulability of E. coli to engineer the andrimid synthase with the goal of producing a diverse set of andrimid analogues for clinical evaluation.
Acetyl-CoA Carboxylase↗
Bisandrographolide from Andrographis paniculata activates TRPV4 channels.
Many transient receptor potential (TRP) channels are activated or blocked by various compounds found in plants; two prominent examples include the activation of TRPV1 channels by capsaicin and the activation of TRPM8 channels by menthol. We sought to identify additional plant compounds that are active on other types of TRP channels. We screened a library of extracts from 50 Chinese herbal plants using a calcium-imaging assay to find compounds active on TRPV3 and TRPV4 channels. An extract from the plant Andrographis paniculata potently activated TRPV4 channels. The extract was fractionated further, and the active compound was identified as bisandrographolide A (BAA). We used purified compound to characterize the activity of BAA on certain TRPV channel subtypes. Although BAA activated TRPV4 channels with an EC(50) of 790-950 nm, it did not activate or block activation of TRPV1, TRPV2, or TRPV3 channels. BAA activated a large TRPV4-like current in immortalized mouse keratinocytes (308 cells) that have been shown to express TRPV4 protein endogenously. This compound also activated TRPV4 currents in cell-free outside-out patches from HEK293T cells overexpressing TRPV4 cDNA, suggesting that BAA can activate the channel in a membrane-delimited manner. Another related compound, andrographolide, found in abundance in the plant Andrographis was unable to activate or block activation of TRPV4 channels. These experiments show that BAA activates TRPV4 channels, and we discuss the possibility that activation of TRPV4 by BAA could play a role in some of the effects of Andrographis extract described in traditional medicine.
Andrographis↗
Human methionine aminopeptidase type 2 in complex with L- and D-methionine.
Human methionine aminopeptidase type 2 (hMetAP-2) was identified as the molecular target of anti-angiogenic agents such as fumagillin and its analogues. We describe here the crystal structure of hMetAP-2 in complex with l-methionine and d-methionine at 1.9 and 2.0A resolution, respectively. The comparison of the structure of the two complexes establishes the basis of enantiomer discrimination and provides some considerations for the design of selective MetAP-2 inhibitors.
Aminopeptidases↗
Structure of Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor.
Membrane-associated dihydroorotate dehydrogenase (DHODH) is an antimalarial therapeutic target without an effective inhibitor. Studies on human DHODH (HsDHODH) led to a structural mechanistic model in which respiratory quinones bind in a tunnel formed by the highly variable N-terminus that leads to the flavin mononucleotide-binding site. The therapeutic agents leflunomide (Arava) and brequinar sodium inhibit HsDHODH by binding in this tunnel. Plasmodium falciparum DHODH (PfDHODH) and HsDHODH have markedly different sensitivities to the two drugs. To understand the structural basis of this differential sensitivity and begin a structure-based drug-design cycle for PfDHODH inhibitors, the three-dimensional structure (2.4 Angstroms, R = 20.1%) of PfDHODH bound to the active metabolite of leflunomide was determined by X-ray crystallography. Comparison of the structures of HsDHODH and PfDHODH reveals a completely different binding mode for the same inhibitor in these two catalytically identical enzymes and explains the previously observed species-specific preferential binding. Because no effective inhibitors have been described for PfDHODH, this structure provides critical insight for the design of potential antimalarials.
Algorithms↗
Stopping trouble before it starts.
A recent publication revealing that the cytotoxic marine natural product pateamine A targets eukaryotic initiation factor eIF4A continues a story with lessons for both chemists and biologists, that is, the significance of natural products, the importance of synthetic organic chemistry, the small molecule regulation of eukaryotic translation machinery, and possibly a new approach to cancer chemotherapy.
Antineoplastic Agents↗
Brequinar derivatives and species-specific drug design for dihydroorotate dehydrogenase.
Therapeutic agents brequinar sodium and leflunomide (Arava) work by binding in a hydrophobic tunnel formed by a highly variable N-terminus of family 2 dihydroorotate dehydrogenase (DHODH). The X-ray crystallographic structure of an analog of brequinar bound to human DHODH was determined. In silico screening of a library of compounds suggested another subset of brequinar analogs that do not inhibit human DHODH as potentially effective inhibitors of Plasmodium falciparum DHODH.
Animals↗
FeeM, an N-acyl amino acid synthase from an uncultured soil microbe: structure, mechanism, and acyl carrier protein binding.
Attempts to access antibiotics by capturing biosynthetic genes and pathways directly from environmental DNA, which is overwhelmingly derived from uncultured bacteria, have revealed a large and previously unknown family of N-acyl amino acid synthases (NASs). The structure of the NAS FeeM reveals structural similarity to the GCN5-related N-acyl transferases and acylhomoserine lactone synthases. The overall structure has a central beta sheet with alpha helices on both sides. A bound product at a cleft in the beta sheet identifies the active site and the structural basis for catalysis, and sequence conservation in this region indicates a bias for recognition over speed. FeeM interacts with an acyl carrier protein (FeeL), and the structure, mutagenesis, and enzymatic measurements reveal that a small hydrophobic pocket in alpha helix 5 dominates binding of FeeM to FeeL. The structural and mechanistic analyses suggest that the products of FeeM could be bacterial signaling agents.
Acyl Carrier Protein↗
Isolation and structure assignment of an iminotetrasaccharide from a cultured filamentous cyanobacterium Anabaena sp.
In search of bioactive metabolites in cultured microalgae, a novel acylated iminopseudotetrasaccharide was isolated from a filamentous cyanobacterium Anabaena sp., and its structure was established by NMR, chemical degradation, and X-ray crystallography. The compound consists of glucose, glucuronic acid, arabinose, and 1,4,6-trideoxy-1,4-imino-D-allitol, which is closely related to potent glucosidase inhibitors such as nojirimycin. The tetrasaccharide itself showed moderate inhibitory activity against beta-D-glucuronidase.
1-Deoxynojirimycin↗
A chemical study of cyclic depsipeptides produced by a sponge-derived fungus.
Two novel cyclic depsipeptides, guangomides A (1) and B (2), together with a new destruxin derivative (3) were isolated from the cytotoxic extract obtained from the saltwater culture of an unidentifiable sponge-derived fungus. The new structures were elucidated on the basis of analysis of extensive 1D and 2D NMR data sets, and the absolute configurations of 2S, 9S, 13S, 19S, 24R, 28R of 1 were determined on the basis of the combined X-ray and Marfey's method structure analysis. Identical absolute configurations were assumed for 2. The cytotoxicity of the extract was found to be due to brefeldin A, while 1 and 2 showed weak antibacterial activity against Staphylococcus epidermidis and Enterococcus durans.
Animals↗
New antibiotics from bacterial natural products.
For the past five decades, the need for new antibiotics has been met largely by semisynthetic tailoring of natural product scaffolds discovered in the middle of the 20(th) century. More recently, however, advances in technology have sparked a resurgence in the discovery of natural product antibiotics from bacterial sources. In particular, efforts have refocused on finding new antibiotics from old sources (for example, streptomycetes) and new sources (for example, other actinomycetes, cyanobacteria and uncultured bacteria). This has resulted in several newly discovered antibiotics with unique scaffolds and/or novel mechanisms of action, with the potential to form a basis for new antibiotic classes addressing bacterial targets that are currently underexploited.
Anti-Bacterial Agents↗
Cloning and heterologous expression of isocyanide biosynthetic genes from environmental DNA.
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Anti-Bacterial Agents↗
Systematic investigation of the Escherichia coli metabolome for the biosynthetic origin of an isocyanide carbon atom.
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Anti-Bacterial Agents↗