Human African trypanosomiasis (HAT) is a vector-transmitted tropical disease caused by the protozoan parasite Trypanosoma brucei. High-throughput screening (HTS) of small-molecule libraries in whole-cell assays is one of the most frequently used approaches in drug discovery for infectious diseases. To aid in drug discovery efforts for HAT, the SYBR Green assay was developed for T. brucei in a 384-well format. This semi-automated assay is cost- and time-effective, robust, and reproducible. The SYBR Green assay was compared to the resazurin assay by screening a library of 4000 putative kinase inhibitors, revealing a superior performance in terms of assay time, sensitivity, simplicity, and reproducibility, and resulting in a higher hit confirmation rate. Although the resazurin assay allows for comparatively improved detection of slow-killing compounds, it also has higher false-positive rates that are likely to arise from the assay experimental conditions. The compounds with the most potent antitrypanosomal activity were selected in both screens and grouped into 13 structural clusters, with 11 new scaffolds as antitrypanosomal agents. Several of the identified compounds had IC50 <1 µM coupled with high selectivity toward the parasite. The core structures of the scaffolds are shown, providing promising new starting points for drug discovery for HAT.
Three antifungal xanthones have been isolated from the dichloromethane root extract of Marila laxiflora (Guttiferae). Their structures were established by spectrometric (UV, EI mass spectrometry, 1 H and 13 C nmr) and chemical methods. In addition, other compounds were isolated from the methanol extract: a fourth xanthone, rhamnetin, betulinic acid, and a derivative of benzoic acid.
Modern natural products (NPs) research relies on untargeted liquid chromatography coupled with mass spectrometry metabolomics. Together with cutting-edge processing and computational annotation strategies, such approaches can yield extensive spectral and structural information. However, current processing workflows require feature-alignment steps based on retention time which hinders the comparison of samples originating from different batches or analyzed using different instrumental setups. In addition, there is currently no analytical framework available to efficiently match processed metabolomics data and associated metadata with external resources. To address these limitations, we present a new sample-centric and knowledge-driven framework allowing multi-modal data alignment - e.g. through chemical structures, biological activities, or spectral features - and demonstrate its value in exploring large and chemodiverse natural extract datasets. Here, the experimental data is processed at the sample level, matched with external identifiers where possible, semantically enriched, and integrated into a unified knowledge graph. The use of semantic web technology enables comparison of processed and standardized data, information, and knowledge at the repository scale. We demonstrate the utility of the developed framework, the Experimental Natural Products Knowledge Graph (ENPKG), to leverage the results obtained from screening 1,600 plant extracts against trypanosomatids and streamline the identification of new antiparasitic compounds. Thanks to its versatility, the proposed approach allows for a radically novel exploitation of metabolomics data. Semantic web technologies are a fundamental asset and we anticipate that their adoption will complement the current computational metabolomics pipelines and enable the community to advance in the description of global chemodiversity and drug discovery projects.
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In the absence of drugs to treat or prevent COVID-19, drug repurposing can be a valuable strategy. Despite a substantial number of clinical trials, drug repurposing did not deliver on its promise. While success was observed with some repurposed drugs (e.g., remdesivir, dexamethasone, tocilizumab, baricitinib), others failed to show clinical efficacy. One reason is the lack of clear translational processes based on adequate preclinical profiling before clinical evaluation. Combined with limitations of existing in vitro and in vivo models, there is a need for a systematic approach to urgent antiviral drug development in the context of a global pandemic. We implemented a methodology to test repurposed and experimental drugs to generate robust preclinical evidence for further clinical development. This translational drug development platform comprises in vitro, ex vivo, and in vivo models of SARS-CoV-2, along with pharmacokinetic modeling and simulation approaches to evaluate exposure levels in plasma and target organs. Here, we provide examples of identified repurposed antiviral drugs tested within our multidisciplinary collaboration to highlight lessons learned in urgent antiviral drug development during the COVID-19 pandemic. Our data confirm the importance of assessing in vitro and in vivo potency in multiple assays to boost the translatability of pre-clinical data. The value of pharmacokinetic modeling and simulations for compound prioritization is also discussed. We advocate the need for a standardized translational drug development platform for mild-to-moderate COVID-19 to generate preclinical evidence in support of clinical trials. We propose clear prerequisites for progression of drug candidates for repurposing into clinical trials. Further research is needed to gain a deeper understanding of the scope and limitations of the presented translational drug development platform.
The dicholoromethane extract of Pseudocedrela kotschyi root demonstrated marked antileishmanial properties in preliminary screening of extracts from 21 species commonly used in Malian traditional medicine. Phytochemical investigation of the active extract yielded three novel phragmalin-type limonoid orthoacetates (1-3), named kotschyins A-C, and the known compounds 7-deacetylgedunin (4) and 7-deacetyl-7-oxogedunin (5). The structures of 1-3 were elucidated by analytical methods including 1D- and 2D-NMR spectroscopy together with MS spectroscopy. The relative configurations of 1-3 were assigned on the basis of NOE correlations. The extract and the isolated compounds were tested for their antiprotozoal activities against Leishmania donovani, Trypanosoma brucei rhodesiense, Trypanosoma cruzi, and Plasmodium falciparum as well as for cytotoxicity toward the L-6 cell line. The crude extract and the two gedunin derivatives exhibited good in vitro activity against all of these parasites.
Visceral leishmaniasis is an important parasitic disease of the developing world with a limited arsenal of drugs available for treatment. The existing drugs have significant deficiencies so there is an urgent need for new and improved drugs. In the human host, Leishmania are obligate intracellular parasites which poses particular challenges in terms of drug discovery. To achieve sufficient throughput and robustness, free-living parasites are often used in primary screening assays as a surrogate for the more complex intracellular assays. We and others have found that such axenic assays have a high false positive rate relative to the intracellular assays, and that this limits their usefulness as a primary platform for screening of large compound collections. While many different reasons could lie behind the poor translation from axenic parasite to intracellular parasite, we show here that a key factor is the identification of growth slowing and cytostatic compounds by axenic assays in addition to the more desirable cytocidal compounds. We present a screening cascade based on a novel cytocidal-only axenic amastigote assay, developed by increasing starting density of cells and lowering the limit of detection, and show that it has a much improved translation to the intracellular assay. We propose that this assay is an improved primary platform in a new Leishmania screening cascade designed for the screening of large compound collections. This cascade was employed to screen a diversity-oriented-synthesis library, and yielded two novel antileishmanial chemotypes. The approach we have taken may have broad relevance to anti-infective and anti-parasitic drug discovery.
Human African Trypanosomiasis (HAT) is caused by two trypanosome sub-species, Trypanosoma brucei rhodesiense and Trypanosoma brucei gambiense. Drugs available for the treatment of HAT have significant issues related to difficult administration regimes and limited efficacy across species and disease stages. Hence, there is considerable need to find new alternative and less toxic drugs. An approach to identify starting points for new drug candidates is high throughput screening (HTS) of large compound library collections. We describe the application of an Alamar Blue based, 384-well HTS assay to screen a library of 87,296 compounds against the related trypanosome subspecies, Trypanosoma brucei brucei bloodstream form lister 427. Primary hits identified against T.b. brucei were retested and the IC50 value compounds were estimated for T.b. brucei and a mammalian cell line HEK293, to determine a selectivity index for each compound. The screening campaign identified 205 compounds with greater than 10 times selectivity against T.b. brucei. Cluster analysis of these compounds, taking into account chemical and structural properties required for drug-like compounds, afforded a panel of eight compounds for further biological analysis. These compounds had IC50 values ranging from 0.22 µM to 4 µM with associated selectivity indices ranging from 19 to greater than 345. Further testing against T.b. rhodesiense led to the selection of 6 compounds from 5 new chemical classes with activity against the causative species of HAT, which can be considered potential candidates for HAT early drug discovery. Structure activity relationship (SAR) mining revealed components of those hit compound structures that may be important for biological activity. Four of these compounds have undergone further testing to 1) determine whether they are cidal or static in vitro at the minimum inhibitory concentration (MIC), and 2) estimate the time to kill.
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