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Journal ArticleDOI

A novel approach for the discovery of chemically diverse anti-malarial compounds targeting the Plasmodium falciparum Coenzyme A synthesis pathway

31 Aug 2014-Malaria Journal (BioMed Central)-Vol. 13, Iss: 1, pp 343-343
TL;DR: A novel high throughput approach for the identification of chemically diverse inhibitors of the CoA synthesis pathway is reported, substantiates the suitability of this approach to identify novel starting points for future anti-malarial drug development.
Abstract: Malaria is a devastating parasitic disease, causing more than 600,000 deaths annually. Drug resistance has rendered previous generation anti-malarials ineffective and is also rapidly emerging against the current therapeutics of choice, artemisinin and its derivatives, making the discovery of new anti-malarials with novel mechanisms of action a priority. The Coenzyme A (CoA) synthesis pathway, a well-known anti-microbial drug target that is also essential for the malaria parasite Plasmodium falciparum, has not yet been exploited in anti-malarial drug development. A novel high throughput approach for the identification of chemically diverse inhibitors of the CoA synthesis pathway is reported. To identify novel CoA synthesis pathway inhibitors, a chemical rescue screening approach was developed. In short, a test compound was considered likely to inhibit the P. falciparum CoA synthesis pathway, if addition of the end product of the pathway, CoA, was able to negate the growth-inhibitory action of the compound on P. falciparum parasites. The chemical rescue approach was employed to screen the Medicines for Malaria Venture malaria box and a small focussed compound library. This resulted in the identification of 12 chemically diverse potential inhibitors of the CoA pathway. To ascertain accurate potency and selectivity, the half-maximal inhibitory concentration (IC50 value) of these compounds was determined for both P. falciparum and a human cell line. Seven compounds showed submicromolar activity against the parasite, with selectivity indices ranging between six and greater than 300. CoA supplementation was confirmed to alleviate the effects on parasite growth and cell viability in a dose dependent manner. Microscopic investigation into the stage of effect and phenotype of treated parasites was performed on a selection of the active compounds. The chemical rescue approach described resulted in the identification of a set of chemically diverse CoA synthesis pathway inhibitors with IC50 values ranging between 120 nM and 6 μM. The identified compounds will be utilized as tools for further investigating the parasite CoA synthesis pathway to define their exact mechanism of action. Furthermore, the chemical diversity of the compounds identified substantiates the suitability of this approach to identify novel starting points for future anti-malarial drug development.

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Citations
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Journal ArticleDOI
TL;DR: The results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications.
Abstract: A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts.

377 citations

01 Jul 2016
TL;DR: The Medicines for Malaria Venture Malaria Box as mentioned in this paper is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite.
Abstract: A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts.

258 citations

Journal ArticleDOI
TL;DR: The Pathogen Box collection is tested against kinetoplastid parasites and malaria life cycle stages in vitro and chemical starting points for malaria, human African trypanosomiasis, Chagas disease, and leishmaniasis drug discovery efforts have been identified.
Abstract: Open-access drug discovery provides a substantial resource for diseases primarily affecting the poor and disadvantaged. The open-access Pathogen Box collection is comprised of compounds with demonstrated biological activity against specific pathogenic organisms. The supply of this resource by the Medicines for Malaria Venture has the potential to provide new chemical starting points for a number of tropical and neglected diseases, through repurposing of these compounds for use in drug discovery campaigns for these additional pathogens. We tested the Pathogen Box against kinetoplastid parasites and malaria life cycle stages in vitro Consequently, chemical starting points for malaria, human African trypanosomiasis, Chagas disease, and leishmaniasis drug discovery efforts have been identified. Inclusive of this in vitro biological evaluation, outcomes from extensive literature reviews and database searches are provided. This information encompasses commercial availability, literature reference citations, other aliases and ChEMBL number with associated biological activity, where available. The release of this new data for the Pathogen Box collection into the public domain will aid the open-source model of drug discovery. Importantly, this will provide novel chemical starting points for drug discovery and target identification in tropical disease research.

98 citations

Journal ArticleDOI
TL;DR: A new class of drugs, hexahydroquinolines, inhibits host haemoglobin endocytosis by Plasmodium falciparum and displays both therapeutic and transmission-blocking activities.
Abstract: Antimalarial compounds with dual therapeutic and transmission-blocking activity are desired as high-value partners for combination therapies. Here, we report the identification and characterization of hexahydroquinolines (HHQs) that show low nanomolar potency against both pathogenic and transmissible intra-erythrocytic forms of the malaria parasite Plasmodium falciparum. This activity translates into potent transmission-blocking potential, as shown by in vitro male gamete formation assays and reduced oocyst infection and prevalence in Anopheles mosquitoes. In vivo studies illustrated the ability of lead HHQs to suppress Plasmodium berghei blood-stage parasite proliferation. Resistance selection studies, confirmed by CRISPR–Cas9-based gene editing, identified the digestive vacuole membrane-spanning transporter PfMDR1 (P. falciparum multidrug resistance gene-1) as a determinant of parasite resistance to HHQs. Haemoglobin and haem fractionation assays suggest a mode of action that results in reduced haemozoin levels and might involve inhibition of host haemoglobin uptake into intra-erythrocytic parasites. Furthermore, parasites resistant to HHQs displayed increased susceptibility to several first-line antimalarial drugs, including lumefantrine, confirming that HHQs have a different mode of action to other antimalarials drugs for which PfMDR1 is known to confer resistance. This work evokes therapeutic strategies that combine opposing selective pressures on this parasite transporter as an approach to countering the emergence and transmission of multidrug-resistant P. falciparum malaria. A new class of drugs, hexahydroquinolines, inhibits host haemoglobin endocytosis by Plasmodium falciparum and displays both therapeutic and transmission-blocking activities.

34 citations

Journal ArticleDOI
TL;DR: Pantothenamides inhibit blood-stage Plasmodium falciparum with potencies similar to that of chloroquine, and are identified as a pantothenamide resistant to degradation, with excellent antiplasmodial activity, target specificity, and low toxicity.
Abstract: Pantothenamides inhibit blood-stage Plasmodium falciparum with potencies (50% inhibitory concentration [IC50], ∼20 nM) similar to that of chloroquine. They target processes dependent on pantothenate, a precursor of the essential metabolic cofactor coenzyme A. However, their antiplasmodial activity is reduced due to degradation by serum pantetheinase. Minor modification of the pantothenamide structure led to the identification of α-methyl-N-phenethyl-pantothenamide, a pantothenamide resistant to degradation, with excellent antiplasmodial activity (IC50, 52 ± 6 nM), target specificity, and low toxicity.

31 citations


Cites background from "A novel approach for the discovery ..."

  • ...Furthermore, a recent study showed that CoA biosynthesis can be targeted by a chemically diverse set of inhibitors that do not resemble pantothenate, the most potent of which had a 50% inhibitory concentration (IC50; the concentration that inhibits parasite proliferation by 50%) of 120 nM against blood-stage parasites (12)....

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References
More filters
Journal ArticleDOI
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Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

70,111 citations

Journal ArticleDOI
TL;DR: A screening window coefficient, called "Z- factor," is defined, which is reflective of both the assay signal dynamic range and the data variation associated with the signal measurements, and therefore is suitable for assay quality assessment.
Abstract: The ability to identify active compounds (³hits²) from large chemical libraries accurately and rapidly has been the ultimate goal in developing high-throughput screening (HTS) assays. The ability to identify hits from a particular HTS assay depends largely on the suitability or quality of the assay used in the screening. The criteria or parameters for evaluating the ³suitability² of an HTS assay for hit identification are not well defined and hence it still remains difficult to compare the quality of assays directly. In this report, a screening window coefficient, called ³Z-factor,² is defined. This coefficient is reflective of both the assay signal dynamic range and the data variation associated with the signal measurements, and therefore is suitable for assay quality assessment. The Z-factor is a dimensionless, simple statistical characteristic for each HTS assay. The Z-factor provides a useful tool for comparison and evaluation of the quality of assays, and can be utilized in assay optimization and validation.

6,474 citations

Journal ArticleDOI
TL;DR: Different in vitro and in vivo screens for antimalarial drug discovery are suggested and a streamlined process for evaluating new compounds on the path from drug discovery to development is recommended.
Abstract: Increased efforts in antimalarial drug discovery are urgently needed. The goal must be to develop safe and affordable new drugs to counter the spread of malaria parasites that are resistant to existing agents. Drug efficacy, pharmacology and toxicity are important parameters in the selection of compounds for development, yet little attempt has been made to review and standardize antimalarial drug-efficacy screens. Here, we suggest different in vitro and in vivo screens for antimalarial drug discovery and recommend a streamlined process for evaluating new compounds on the path from drug discovery to development.

823 citations


"A novel approach for the discovery ..." refers background in this paper

  • ...This clearly demonstrates the need for anti-malarial drugs with novel mechanisms of action and/or of different chemical origin to effectively counteract the development of resistance, thus reinforcing the current defense against malaria [3,4]....

    [...]

Journal ArticleDOI
20 May 2010-Nature
TL;DR: A phenotypic forward chemical genetic approach to discover new antimalarial chemotypes and structures and biological activity of the entire library are disclosed, many of which showed potent in vitro activity against drug-resistant P. falciparum strains.
Abstract: Malaria caused by Plasmodium falciparum is a disease that is responsible for 880,000 deaths per year worldwide. Vaccine development has proved difficult and resistance has emerged for most antimalarial drugs. To discover new antimalarial chemotypes, we have used 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 showed potent in vitro activity against drug-resistant P. falciparum 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 several 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. Our findings provide the scientific community with new starting points for malaria drug discovery.

535 citations


"A novel approach for the discovery ..." refers methods in this paper

  • ...falciparum strain 3D7 was independently assessed using an established imagebased growth inhibition assay [14,15]....

    [...]

Journal ArticleDOI
TL;DR: Previous knowledge is integrated with the most recent findings in the genetics, enzymology and regulation of CoA biosynthesis in bacteria, plants and mammals to integrate previous knowledge with the latest findings.

513 citations


"A novel approach for the discovery ..." refers background in this paper

  • ...For pantothenate kinase, the enzyme catalysing the first and rate-limiting step of CoA synthesis [11], the maximal amino acid sequence homology between the known human isotypes and the two putative P....

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  • ...Despite the conservation of the five enzymatic steps involved in CoA synthesis in eukaryotes [11], the amino acid sequence of the enzymes involved are not highly conserved between species [7]....

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