- 3-Hydroxypyrimidine-2,4-dione-5-N-benzylcarboxamides Potently Inhibit HIV-1 Integrase and RNase H
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Resistance selection by human immunodeficiency virus (HIV) toward known drug regimens necessitates the discovery of structurally novel antivirals with a distinct resistance profile. On the basis of our previously reported 3-hydroxypyrimidine-2,4-dione (HPD) core, we have designed and synthesized a new integrase strand transfer (INST) inhibitor type featuring a 5-N-benzylcarboxamide moiety. Significantly, the 6-alkylamino variant of this new chemotype consistently conferred low nanomolar inhibitory activity against HIV-1. Extended antiviral testing against a few raltegravir-resistant HIV-1 clones revealed a resistance profile similar to that of the second generation INST inhibitor (INSTI) dolutegravir. Although biochemical testing and molecular modeling also strongly corroborate the inhibition of INST as the antiviral mechanism of action, selected antiviral analogues also potently inhibited reverse transcriptase (RT) associated RNase H, implying potential dual target inhibition. In vitro ADME assays demonstrated that this novel chemotype possesses largely favorable physicochemical properties suitable for further development.
- Wu, Bulan,Tang, Jing,Wilson, Daniel J.,Huber, Andrew D.,Casey, Mary C.,Ji, Juan,Kankanala, Jayakanth,Xie, Jiashu,Sarafianos, Stefan G.,Wang, Zhengqiang
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- 6-Arylthio-3-hydroxypyrimidine-2,4-diones potently inhibited HIV reverse transcriptase-associated RNase H with antiviral activity
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Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function not targeted by current drugs. Although a few chemotypes have been reported to inhibit HIV RNase H in biochemical assays, their general lack of significant antiviral activity in cell culture necessitates continued efforts in identifying highly potent RNase H inhibitors to confer antiviral activity. We report herein the design, synthesis, biochemical and antiviral evaluations of a new 6-arylthio subtype of the 3-hydroxypyrimidine-2,4-dione (HPD) chemotype. In biochemical assays these new analogues inhibited RT RNase H in single-digit nanomolar range without inhibiting RT polymerase (pol) at concentrations up to 10 μM, amounting to exceptional biochemical inhibitory selectivity. Many analogues also inhibited integrase strand transfer (INST) activity in low to sub micromolar range. More importantly, most analogues inhibited HIV in low micromolar range without cytotoxicity. In the end, compound 13j (RNase H IC50 = 0.005 μM; RT pol IC50 = 10 μM; INST IC50 = 4.0 μM; antiviral EC50 = 7.7 μM; CC50 > 100 μM) represents the best analogues within this series. These results characterize the new 6-arylthio-HPD subtype as a promising scaffold for HIV RNase H inhibitor discovery.
- Wang, Lei,Tang, Jing,Huber, Andrew D.,Casey, Mary C.,Kirby, Karen A.,Wilson, Daniel J.,Kankanala, Jayakanth,Xie, Jiashu,Parniak, Michael A.,Sarafianos, Stefan G.,Wang, Zhengqiang
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- Double-Winged 3-Hydroxypyrimidine-2,4-diones: Potent and Selective Inhibition against HIV-1 RNase H with Significant Antiviral Activity
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Human immunodeficiency virus (HIV) reverse transcriptase (RT)-Associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function yet to be exploited as an antiviral target. One of the possible challenges may be that targeting HIV RNase H is confronted with a steep substrate barrier. We have previously reported a 3-hydroxypyrimidine-2,4-dione (HPD) subtype that potently and selectively inhibited RNase H without inhibiting HIV in cell culture. We report herein a critical redesign of the HPD chemotype featuring an additional wing at the C5 position that led to drastically improved RNase H inhibition and significant antiviral activity. Structure-Activity relationship (SAR) concerning primarily the length and flexibility of the two wings revealed important structural features that dictate the potency and selectivity of RNase H inhibition as well as the observed antiviral activity. Our current medicinal chemistry data also revealed that the RNase H biochemical inhibition largely correlated the antiviral activity.
- Vernekar, Sanjeev Kumar V.,Tang, Jing,Wu, Bulan,Huber, Andrew D.,Casey, Mary C.,Myshakina, Nataliya,Wilson, Daniel J.,Kankanala, Jayakanth,Kirby, Karen A.,Parniak, Michael A.,Sarafianos, Stefan G.,Wang, Zhengqiang
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- Ammonium Chloride-Promoted Rapid Synthesis of Monosubstituted Ureas under Microwave Irradiation
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Monosubstituted ureas are important scaffolds in organic chemistry. They appear in various biologically active compounds and serve as versatile precursors in synthesis. Monosubstituted ureas were originally prepared using toxic and hazardous phosgene equivalents. Modern methods include transamidation of urea and nucleophilic addition to cyanate salts, both of which suffer from a narrow substrate scope due to the need for a strong acid and prolonged reaction times. We hereby report that ammonium chloride can promote the reaction between amines and potassium cyanate to generate monosubstituted ureas in water. This method proceeds rapidly under microwave irradiation and tolerates a broad range of functional groups. Unlike previous strategies, it is compatible with other nucleophiles, acid-labile moieties, and most of the common protecting groups. The products precipitate out of solution, allowing facile isolation without column chromatography.
- Lan, Chunling Blue,Auclair, Karine
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supporting information
p. 5135 - 5146
(2021/10/19)
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- Metal binding 6-arylthio-3-hydroxypyrimidine-2,4-diones inhibited human cytomegalovirus by targeting the pUL89 endonuclease of the terminase complex
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The genome packaging of human cytomegalovirus (HCMV) requires a divalent metal-dependent endonuclease activity localized to the C-terminus of pUL89 (pUL89-C), which is reminiscent of RNase H-like enzymes in active site structure and catalytic mechanism. Our previous work has shown that metal-binding small molecules can effectively inhibit pUL89-C while conferring significant antiviral activities. In this report we generated a collection of 43 metal-binding small molecules by repurposing analogs of the 6-arylthio-3-hydroxypyrimidine-2,4-dione chemotype previously synthesized for targeting HIV-1 RNase H, and by chemically synthesizing new N-1 analogs. The analogs were subjected to two parallel screening assays: the pUL89-C biochemical assay and the HCMV antiviral assay. Compounds with significant inhibition from each assay were further tested in a dose-response fashion. Single dose cell viability and PAMPA cell permeability were also conducted and considered in selecting compounds for the dose-response antiviral testing. These assays identified a few analogs displaying low μM inhibition against pUL89-C in the biochemical assay and HCMV replication in the antiviral assay. The target engagement was further evaluated via a thermal shift assay using recombinant pUL89-C and molecular docking. Overall, our current work identified novel inhibitors of pUL89-C with significant antiviral activities and further supports targeting pUL89-C with metal-binding small molecules as an antiviral approach against HCMV.
- Wang, Lei,Edwards, Tiffany C.,Sahani, Rajkumar Lalji,Xie, Jiashu,Aihara, Hideki,Geraghty, Robert J.,Wang, Zhengqiang
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supporting information
(2021/06/21)
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- 3-Hydroxypyrimidine-2,4-diones as Selective Active Site Inhibitors of HIV Reverse Transcriptase-Associated RNase H: Design, Synthesis, and Biochemical Evaluations
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Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains an unvalidated antiviral target. A major challenge of specifically targeting HIV RNase H arises from the general lack of selectivity over RT polymerase (pol) and integrase (IN) strand transfer (ST) inhibitions. We report herein the synthesis and biochemical evaluations of three novel 3-hydroxypyrimidine-2,4-dione (HPD) subtypes carefully designed to achieve selective RNase H inhibition. Biochemical studies showed the two subtypes with an N-1 methyl group (9 and 10) inhibited RNase H in low micromolar range without siginificantly inhibiting RT polymerase, whereas the N-1 unsubstituted subtype 11 inhibited RNase H in submicromolar range and RT polymerase in low micromolar range. Subtype 11 also exhibited substantially reduced inhibition in the HIV-1 INST assay and no significant cytotoxicity in the cell viability assay, suggesting that it may be amenable to further structure-activity relationship (SAR) for identifying RNase H inhibitors with antiviral activity.
- Tang, Jing,Liu, Feng,Nagy, Eva,Miller, Lena,Kirby, Karen A.,Wilson, Daniel J.,Wu, Bulan,Sarafianos, Stefan G.,Parniak, Michael A.,Wang, Zhengqiang
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supporting information
p. 2648 - 2659
(2016/04/10)
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- Synthesis, antitumor evaluation and crystal structure of hydroxyurea derivatives
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A series of hydroxyurea derivatives have been synthesized and elucidated by means of FT-IR, 1H-, 13C-NMR and MS. The exact stereostructures of representative compounds have been determined by X-ray crystal structure analysis. In the crystals, inversion dimers linked by pairs of N-H...O hydrogen bonds occurred, and further N-H...O links led to chains of molecules. In vitro antitumor activities against Tca8113 human tongue cancer cells and L1210 murine leukemia cells were evaluated. A total of 8 of the 12 compounds had higher inhibitory activities than hydroxyurea against L1210 cells. Among them, the most promising compounds were 3e, 3d, 3a and 2d.
- Mai, Xi,Lu, Xiaosan,Xia, Hongying,Cao, Yusheng,Liao, Yijing,Lv, Xiaolan
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experimental part
p. 94 - 97
(2010/04/26)
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- Coordination chemistry based approach to lipophilic inhibitors of 1-deoxy-D-xylulose-5-phosphate reductoisomerase
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1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) in the non-mevalonate pathway found in most bacteria is a validated anti-infective drug target. Fosmidomycin, a potent DXR inhibitor, is active against Gram-negative bacteria. A coordination chemistry and structure based approach was used to discover a novel, lipophilic DXR inhibitor with an IC50 of 1.4 μM. It exhibited a broad spectrum of activity against Gram-negative and -positive bacteria with minimal inhibition concentrations of 20-100 μM (or 3.7-19 μg/mL).
- Deng, Lisheng,Sundriyal, Sandeep,Rubio, Valentina,Shi, Zheng-Zheng,Song, Yongcheng
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supporting information; experimental part
p. 6539 - 6542
(2010/04/04)
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- Thrombin inhibitors
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This application relates to novel compounds of formula I (and their pharmaceutically acceptable salts), as defined herein, processes and intermediates for their preparation, pharmaceutical formulations comprising the novel compounds of formula I, and the use of defined compounds of formula I as thrombin inhibitors.
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- Synthesis of N-1-oxypyrimidine 1,3-dioxolane and 1,3-oxathiolane nucleosides
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Two series of 1,3-dioxolanes and 1,3-oxathiolane nucleosides containing N-1-oxypyrimidine were synthesized as potential antiviral agents.
- Nguyen-Ba,Lee,Chan,Zacharie
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p. 2311 - 2312
(2007/10/03)
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