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.

e Borrelia burgdorferi, the Lyme disease spirochete, couples environmental sensing and gene regulation primarily via the Hk1/ Rrp1 two-component system (TCS) and Rrp2/RpoN/RpoS pathways. Beginning with acquisition, we reevaluated the contribution of these pathways to spirochete survival and gene regulation throughout the enzootic cycle. Live imaging of B. burgdorferi caught in the act of being acquired revealed that the absence of RpoS and the consequent derepression of tick-phase genes impart a Stay signal required for midgut colonization. In addition to the behavioral changes brought on by the RpoS-off state, acquisition requires activation of cyclic di-GMP (c-di-GMP) synthesis by the Hk1/Rrp1 TCS; B. burgdorferi lacking either component is destroyed during the blood meal. Prior studies attributed this dramatic phenotype to a metabolic lesion stemming from reduced glycerol uptake and utilization. In a head-to-head comparison, however, the B. burgdorferi ⌬glp mutant had a markedly greater capacity to survive tick feeding than B. burgdorferi ⌬hk1 or ⌬rrp1 mutants, establishing unequivocally that glycerol metabolism is only one component of the protection afforded by c-di-GMP. Data presented herein suggest that the protective response mediated by c-di-GMP is multifactorial, involving chemotactic responses, utilization of alternate substrates for energy generation and intermediary metabolism, and remodeling of the cell envelope as a means of defending spirochetes against threats engendered during the blood meal. Expression profiling of c-di-GMP-regulated genes through the enzootic cycle supports our contention that the Hk1/Rrp1 TCS functions primarily, if not exclusively, in ticks. These data also raise the possibility that c-di-GMP enhances the expression of a subset of RpoS-dependent genes during nymphal transmission. Borrelia burgdorferi, the causative agent of Lyme disease, is maintained in nature within an enzootic cycle that involves an arthropod vector and vertebrate reservoir hosts, typically, small rodents and birds (1). In the northeastern United States, the primary vector for B. burgdorferi is the black-legged deer tick, Ixodes scapularis (2, 3). Because B. burgdorferi cannot be passaged transovarially, naive larvae acquire spirochetes by feeding on infected reservoir hosts. Successful colonization of the vector requires B. burgdorferi to establish an intimate association with rapidly differentiating, highly endocytic midgut epithelial cells (4-6). In order to accomplish this feat, spirochetes must resist deleterious substances within the midgut lumen, such as host-and tick-derived innate immune effector molecules, reactive oxygen species (ROS), and salivary enzymes imbibed from the feeding site (4, 7-11). At the same time, B. burgdorferi also must alter its metabolic machinery to exploit the availability of alternative carbon sources (e.g., glycerol, N-acetylglucosamine [GlcNAc], chitobiose) as the supply of ingested glucose diminishes (12-15). During nymphal transmission, spirochetes are almost certai...

Background: The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistance can also assist in identifying the mode of action of uncharacterized but potent antimalarial compounds identified in high-throughput chemical screening campaigns against Plasmodium falciparum.

cMalaria remains a significant infectious disease that causes millions of clinical cases and >800,000 deaths per year. The Malaria Box is a collection of 400 commercially available chemical entities that have antimalarial activity. The collection contains 200 drug-like compounds, based on their oral absorption and the presence of known toxicophores, and 200 probe-like compounds, which are intended to represent a broad structural diversity. These compounds have confirmed activities against the asexual intraerythrocytic stages of Plasmodium falciparum and low cytotoxicities, but their mechanisms of action and their activities in other stages of the parasite's life cycle remain to be determined. The apicoplast is considered to be a promising source of malaria-specific targets, and its main function during intraerythrocytic stages is to provide the isoprenoid precursor isopentenyl diphosphate, which can be used for phenotype-based screens to identify compounds targeting this organelle. We screened 400 compounds from the Malaria Box using apicoplast-targeting phenotypic assays to identify their potential mechanisms of action. We identified one compound that specifically targeted the apicoplast. Further analyses indicated that the molecular target of this compound may differ from those of the current antiapicoplast drugs, such as fosmidomycin. Moreover, in our efforts to elucidate the mechanisms of action of compounds from the Malaria Box, we evaluated their activities against other stages of the life cycle of the parasite. Gametocytes are the transmission stage of the malaria parasite and are recognized as a priority target in efforts to eradicate malaria. We identified 12 compounds that were active against gametocytes with 50% inhibitory concentration values of <1 M.

Malaria is one of the leading causes of morbidity and mortality in the tropics, with 300 to 500 million clinical cases and 1.5 to 2.7 million deaths per year. Nearly all fatal cases are caused by Plasmodium falciparum. The resistance of this parasite to conventional antimalarial drugs such as chloroquine is growing at an alarming rate and therefore new efficient drugs are urgently needed (1-3).In all organisms studied so far, the biosynthesis of isoprenoids such as dolichol, cholesterol, and ubiquinones depends on the condensation of the different numbers of isopentenyl diphosphate (IPP) 1 and dimethylallyl diphosphate units. In mammals and fungi, these units are derived from the classical mevalonate pathway (4). However, in higher plants, in several algae, in some eubacteria, and in P. falciparum the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway was described as the alternative non-mevalonate pathway for the synthesis of IPP (for reviews, see Refs. 5-10). This pathway starts with the condensation of pyruvate and glyceraldehyde 3-phosphate, which yields 1-deoxy-D-xylulose-5-phosphate (DOXP) as a key metabolite (11-17). The DOXP reductoisomerase then catalyzes the simultaneous intramolecular rearrangement and reduction of DOXP to form MEP (18 -22). The activity of this enzyme is specifically inhibited by fosmidomycin (23). Several reaction steps are necessary for the conversion of MEP to IPP. The downstream intermediates of MEP for this pathway are: 4-(cytidine-5-diphospho)-2-C-methyl-D-erythritol (CDP-ME) (24), 4-(cytidine-5-diphospho)-2-C-methyl-D-erythritol-2-phosphate (CDP-MEP), 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (ME-2,4-cPP) (25, 26), and 4-hydroxy-3-methylbut-2-enyl pyrophosphate (27-31). IPP and dimethylallyl diphosphate are synthesized through independent routes in the late steps of the non-mevalonate pathway (32). These units are used for the biosynthesis of ubiquinones and dolichols, and for the prenylation of proteins and other products (33)(34)(35).Based on the sequence data provided by the malaria genome project (plasmodb.org), Jomaa and co-workers (21) identified two genes in P. falciparum that encode key enzymes of the MEP pathway: 1-deoxy-D-xylulose-5-phosphate synthase and 1-deoxy-D-xylulose-5-phosphate reductoisomerase. They also demonstrated that an amino-terminal signal sequence in 1-de- 1 The abbreviations and trivial names used are: IPP, isopentenyl diphosphate; MEP, 2-C-methyl-D-erythritol-4-phosphate; DOXP, 1-deoxy-D-xylulose-5-phosphate; DOX, 1-deoxy-D-xylulose; CDP-ME, 4-(cytidine-5-diphospho)-2-C-methyl-D-erythritol; CDP-MEP, 4-(cytidine-5-diphospho)-2-C-methyl-D-erythritol-2-phosphate; ME-2,4-cPP, 2-Cmethyl-D-erythritol-2,4-cyclodiphosphate; HPLC, high-performance liquid chromatography; ESI-QTOF-MS, ESI-quadrupole time-of-flight mass spectrometry; Q n , Coenzyme Q n .

Summary Plasmodium falciparum, the primary cause of deaths from malaria, is a purine auxotroph and relies on hypoxanthine salvage from the host purine pool. Purine starvation as an antimalarial target has been validated by inhibition of purine nucleoside phosphorylase. Hypoxanthine depletion kills Plasmodium falciparum in cell culture and in Aotus monkey infections. Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from P. falciparum is required for hypoxanthine salvage by forming inosine 5′-monophosphate, a branchpoint for all purine nucleotide synthesis in the parasite. Here we present a new class of HGXPRT inhibitors, the acyclic Immucillin phosphonates (AIPs), and cell permeable AIP prodrugs. The AIPs are simple, potent, selective and biologically stable inhibitors. The AIP prodrugs block proliferation of cultured parasites by inhibiting the incorporation of hypoxanthine into the parasite nucleotide pool and validates HGXPRT as a target in malaria.

Malaria is a leading cause of morbidity and mortality in the tropics. Chemotherapeutic and vector control strategies have been applied for more than a century but have not been efficient in disease eradication. Increased resistance of malaria parasites to drug treatment and of mosquito vectors to insecticides requires the development of novel chemotherapeutic agents. Malaria parasites exhibit rapid nucleic acid synthesis during their intraerythrocytic growth phase. Plasmodium purine and pyrimidine metabolic pathways are distinct from those of their human hosts. Thus, targeting purine and pyrimidine metabolic pathways provides a promising route for novel drug development. Recent developments in enzymatic transition state analysis have provided an improved route to inhibitor design targeted to specific enzymes, including those of purine and pyrimidine metabolism. Modern transition state analogue drug discovery has resulted in transition state analogues capable of binding to target enzymes with unprecedented affinity and specificity. These agents can provide specific blocks in essential pathways. The combination of tight binding with the high specificity of these logically designed inhibitors, results in low toxicity and minor side effects. These features reduce two of the major problems with the current antimalarials. Transition state analogue design is being applied to generate new lead compounds to treat malaria by targeting purine and pyrimidine pathways.

The S-adenosylmethionine (AdoMet) salvage enzyme 5 -methylthioadenosine phosphorylase (MTAP) has been implicated as both a cancer target and a tumor suppressor. We tested these hypotheses in mouse xenografts of human lung cancers. AdoMet recycling from 5 -methylthioadenosine (MTA) was blocked by inhibition of MTAP with methylthioDADMe-Immucillin-A (MTDIA), an orally available, nontoxic, picomolar transition state analogue. Blood, urine, and tumor levels of MTA increased in response to MTDIA treatment. Disruption of pathways linked to polyamine synthesis and S-adenosylmethionine (AdoMet) 2 salvage provides metabolic targets in anticancer therapy based on the essential roles of these metabolites in cell growth. AdoMet is the major methyl donor for biosynthetic methylation reactions, a precursor for polyamine synthesis, and the source of methyl groups for DNA methylation. Targeting polyamine metabolism directly at L-ornithine decarboxylase by ␣,␣-difluoromethylornithine has had limited anticancer success (1). Two AdoMet molecules are converted to 5Ј-methylthioadenosine (MTA) in spermine synthesis, and 5Ј-methylthioadenosine phosphorylase (MTAP) recycles MTA by phosphorolysis to permit subsequent resynthesis of AdoMet (Fig. 1). Our working hypothesis was that inhibition of MTAP would affect cellular MTA and AdoMet metabolism with downstream effects on protein, DNA methylation, polyamine synthesis, and polyamine-dependent enzyme reactions. We targeted MTAP by transition state analysis and developed methylthio-DADMe-Immucillin-A (MTDIA), an orally available transition state analogue inhibitor of MTAP (2). Others have proposed that MTAP is a tumor suppressor gene (3), and experiments here explore the effects of MTAP inhibition in human lung cancer xenografts.We previously demonstrated that treatment of human FaDu head and neck tumors in mouse xenografts with MT-DIA prevented tumor growth with no apparent toxicity to the mice (4). Here, we report that both MTAP-positive (H358) and MTAP-deleted (A549) human lung cancer cell lines are also sensitive to MTAP inhibition in mouse xenografts. The mechanism is probed by the metabolic and genetic consequences of MTDIA administration. In culture, MTDIA in combination with MTA slows A549 cell growth but induces apoptosis in H358 cells.Lung cancer is the leading cause of cancer-related deaths worldwide (5). Patients diagnosed at an advanced stage have a median survival of less than 12 months (6 -8). Thus, development of novel therapeutics for lung cancer is a research priority. MTDIA demonstrated significant suppression of tumor growth with human lung cancer A549 and H358 cells in mouse xenografts. Low toxicity, oral availability, and significant tumor suppression by MTDIA all support additional evaluation as an agent for the treatment of lung cancers. EXPERIMENTAL PROCEDURESCell Lines-Human non-small cell lung adenocarcinoma (NSCLC) cell line A549 and prostate carcinoma cell line PC3 were obtained from the American Type Culture Collection (Manassas, VA). Human bronchioloalveolar ...