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Flaviviruses comprise major emerging pathogens such as dengue virus (DENV) or Zika virus (ZIKV). The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase (RdRp) domain of non-structural protein 5 (NS5). This essential enzymatic activity renders the RdRp attractive for antiviral therapy. NS5 synthesizes viral RNA via a “de novo” initiation mechanism. Crystal structures of the flavivirus RdRp revealed a “closed” conformation reminiscent of a pre-initiation state, with a well ordered priming loop that extrudes from the thumb subdomain into the dsRNA exit tunnel, close to the “GDD” active site. To-date, no allosteric pockets have been identified for the RdRp, and compound screening campaigns did not yield suitable drug candidates. Using fragment-based screening via X-ray crystallography, we found a fragment that bound to a pocket of the apo-DENV RdRp close to its active site (termed “N pocket”). Structure-guided improvements yielded DENV pan-serotype inhibitors of the RdRp de novo initiation activity with nano-molar potency that also impeded elongation activity at micro-molar concentrations. Inhibitors exhibited mixed inhibition kinetics with respect to competition with the RNA or GTP substrate. The best compounds have EC50 values of 1–2 μM against all four DENV serotypes in cell culture assays. Genome-sequencing of compound-resistant DENV replicons, identified amino acid changes that mapped to the N pocket. Since inhibitors bind at the thumb/palm interface of the RdRp, this class of compounds is proposed to hinder RdRp conformational changes during its transition from initiation to elongation. This is the first report of a class of pan-serotype and cell-active DENV RdRp inhibitors. Given the evolutionary conservation of residues lining the N pocket, these molecules offer insights to treat other serious conditions caused by flaviviruses.

Cyanobacteria from a diversity of marine and freshwater habitats are known to produce neurotoxic secondary metabolites. 1 Herein, we describe the complete stereostructure, synthesis, and biological properties of kalkitoxin (1), a novel neurotoxic lipopeptide from a Caribbean collection of Lyngbya majuscula.The organic extract of this L. majuscula exhibited potent brine shrimp and fish toxicity. 2 Using these assays, the toxic metabolite kalkitoxin (1), was isolated by sequential silica gel VLC, CC, and normal-phase HPLC (12.8 mg, 0.3% of extract). Subsequently, bioassay-guided fractionation using a primary cell culture of rat neurons in a microphysiometer 3 or inhibition of IL-1 stimulation of sPLA 2 in hepatocarcinoma cells 4 led to re-isolation of 1 in small yield from various Caribbean collections of L. majuscula.Kalkitoxin (1) analyzed for C 21 H 38 N 2 OS indicated four degrees of unsaturation; from 13 C NMR analysis in DMSO-d 6 two were due to double bonds, one to a carbonyl group, and the remaining one to a ring system. 5 Data from E.COSY, HSQC, and a modified HSQMBC 6 experiments in benzene-d 6 allowed deduction of six partial structures for 1 (Supporting Information). One partial structure was composed of a sec-butyl group in which the methine component was deshielded to a chemical shift (δ 2.28) consistent with its being adjacent to a carbonyl. A second partial structure was composed of a methylated tertiary amide group which existed in two conformations (Supporting Information). A third partial structure possessed a deshielded methylene (δ 3.35) that could be sequentially connected by E.COSY to a second methylene group, and by HSQMBC to a methine and high-field methyl group. By E.COSY, an additional high-field methylene group (δ 1.10, 1.02) was adjacent to a methine which also bore a methyl group. The fifth partial structure was composed of a similar -CH 2 -CH-CH 3 grouping; however, in this case, the methylene group protons were deshielded to δ2 .31 and δ 2.55. The final partial structure, based on E.COSY correlations, HSQMBC, and chemical shift models, 7 was composed of a thiazoline ring with an ethylene appendage; this was further substantiated by EIMS fragmentations (Supporting Information). HSQMBC data were used to connect these partial structures and gave the full planar structural assignment of 1.The C3 stereochemistry of kalkitoxin was determined by Marfey's analysis. Kalkitoxin was ozonized and then hydrolyzed in 6 N HCl to obtain cysteic acid. Marfey's analysis of this hydrolysate yielded L-cysteic acid, defining C3 as R. The limited amount of kalkitoxin precluded determination of the C2′ stereochemistry. The relative stereochemistry of the three chiral centers within the aliphatic chain of kalkitoxin (C7, C8, C10) was determined using the J-based configuration analysis method. 8 The 3 J CH values were measured by a modification of the recently reported HSQMBC pulse sequence, 6 and the 3 J HH values were determined utilizing the E.COSY pulse sequence. 9 To overcome the limited sample size...

M arine cyanobacteria represent a particularly rich source of structurally unique neurotoxic secondary metabolites (1-5). Lyngbya majuscula is a pantropical marine cyanobacterium that is the source of antillatoxin (ATX), a structurally unusual lipopeptide (1) (Fig. 1). Blooms of L. majuscula have been associated with adverse effects on human health. These blooms have been reported to cause respiratory irritation, eye inflammation, and severe contact dermatitis in exposed fishermen and swimmers (6). ATX has been shown to be among the most ichthyotoxic metabolites isolated to date from a marine microalga (1) and, more recently, has been demonstrated to be neurotoxic in primary cultures of rat cerebellar granule cells (4). In the latter study, morphologic evidence of ATX-induced neurotoxicity included swelling of neuronal somata, thinning of neurites, and blebbing of neurite membranes. ATX also induced a concentration-dependent cytotoxicity in cerebellar granule neurons as monitored by lactate dehydrogenase efflux (ATX EC 50 ϭ 20.1 Ϯ 6.4 nM) (4). This neurotoxic response of ATX was prevented by coexposure with noncompetitive antagonists of the N-methyl-D-aspartate (NMDA) receptor such as MK-801 and dextrorphan.Voltage-gated sodium channels are responsible for generation of the rising phase of the action potential in membranes of neurons as well as in most other electrically excitable cells. Sodium channels consist of a pore-forming ␣ subunit of 260 kDa associated with auxiliary ␤ subunits of 33-36 kDa (7,8). Voltagegated sodium channels represent the molecular target for an array of natural products including marine neurotoxins. Marine neurotoxins such as tetrodotoxin (TTX), saxitoxin, conotoxins, sea anemone toxins, brevetoxin, and ciguatoxin all bind with high affinity and specificity to at least six distinct receptor sites on sodium channel ␣ subunits (8). Collectively, these toxins have served as important tools to explore the structure and function of voltage-dependent sodium channels. These marine neurotoxins produce characteristic alterations in the two major properties of sodium channels, namely ion permeation and gating (8).The objective of the present study was to test the hypothesis that ATX acts as an activator of voltage-dependent sodium channels. This hypothesis emanated from our previous studies which were consistent with ATX acting as an autocrine excitotoxic agent in cerebellar granule neurons. In this study we have used a combination of neurochemical and pharmacological approaches to show that ATX is a structurally unusual lipopeptide activator of neuronal voltage-gated sodium channels. Materials and MethodsMaterials. Tritiated batrachotoxin A 20-␣-benzoate ([ 3 H]BTX) and 22 Na ϩ were obtained from DuPont͞NEN. Deltamethrin was purchased from Biomol (Plymouth Meeting, PA). Veratridine, brevetoxin-1 (PbTx-1), and ouabain were obtained from Sigma. Sea anemone toxin was purchased from Calbiochem. Fluo-3 AM and pluronic acid were obtained from Molecular Probes. ATX was either authentic natural (Ϫ)-ant...

We performed a fragment screen on the dengue virus serotype 3 RNA-dependent RNA polymerase using x-ray crystallography. A screen of 1,400 fragments in pools of eight identified a single hit that bound in a novel pocket in the protein. This pocket is located in the polymerase palm subdomain and conserved across the four serotypes of dengue virus. The compound binds to the polymerase in solution as evidenced by surface plasmon resonance and isothermal titration calorimetry analyses. Related compounds where a phenyl is replaced by a thiophene show higher affinity binding, indicating the potential for rational design. Importantly, inhibition of enzyme activity correlated with the binding affinity, showing that the pocket is functionally important for polymerase activity. This fragment is an excellent starting point for optimization through rational structurebased design.Dengue virus (DENV) 3 is the most widespread mosquitoborne viral infection. Disease symptoms of DENV-infected patients range from a mild fever to severe plasma leakage and hemorrhagic shock (1). There are four serotypes of DENV (DENV-1 to -4) that concurrently circulate around the world in tropical and subtropical regions. The vast majority of clinical cases are not reported, and there are estimated to be approximately 390 million human cases of dengue worldwide per year (2). There is currently no licensed vaccine or antiviral to treat DENV infection, underlining the urgency for the development of safe therapeutics (3). DENV is a member of the Flavivirus genus that also includes other viruses that are pathogenic to humans such as West Nile virus (WNV), yellow fever virus, Japanese encephalitis virus (JEV), and tick-borne encephalitis virus.One of the most attractive antiviral targets is the DENV RNA-dependent RNA polymerase (RdRp) because (i) viral polymerases are clinically proven therapeutic targets and (ii) the RdRp is the most conserved viral protein among the four serotypes of DENV so that the likelihood of a single compound with pan-serotype activity is higher than compounds targeting other viral proteins. The DENV RdRp activity resides in the C-terminal two-thirds of the viral nonstructural protein 5 (NS5) (reviewed in Ref. 4), whereas the N-terminal one-third of DENV NS5 encodes a methyltransferase (5).Crystal structures of the RdRp domain and full-length NS5 have been determined (6, 7). The overall architecture of the polymerase resembles a right hand with fingers, palm, and thumb subdomains. DENV RdRp catalyzes de novo initiation, as well as elongation. Like other RdRps that perform de novo RNA synthesis, DENV RdRp has a fully encircled active site (8). These polymerases undergo a conformational change from a closed to an open conformation during the transition from de novo initiation to elongation. During this process, the initiation loop (also known as the priming loop) is thought to move out of the active site, in a manner similar to the hepatitis C virus polymerase (9).A number of in vitro enzyme assays have been developed for DENV Rd...

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The discovery and optimization of non-nucleoside dengue viral RNA-dependent-RNA polymerase (RdRp) inhibitors are described. An X-ray-based fragment screen of Novartis' fragment collection resulted in the identification of a biphenyl acetic acid fragment 3, which bound in the palm subdomain of RdRp. Subsequent optimization of the fragment hit 3, relying on structure-based design, resulted in a >1000-fold improvement in potency in vitro and acquired antidengue activity against all four serotypes with low micromolar EC50 in cell-based assays. The lead candidate 27 interacts with a novel binding pocket in the palm subdomain of the RdRp and exerts a promising activity against all clinically relevant dengue serotypes.

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