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Volkova Y, Zavarzin I. Synthesis of Phosphorus(V)-Substituted Six-Membered N-Heterocycles: Recent Progress and Challenges. Molecules 2023; 28:molecules28062472. [PMID: 36985443 PMCID: PMC10054050 DOI: 10.3390/molecules28062472] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023] Open
Abstract
Heterocycles functionalized with pentavalent phosphorus are of great importance since they include a great variety of biologically active compounds and pharmaceuticals, advanced materials, and valuable reactive intermediates for organic synthesis. Significant progress in synthesis of P(O)R2-substituted six-membered heterocycles has been made in the past decade. This review covers the synthetic strategies towards aromatic monocyclic six-membered N-heterocycles, such as pyridines, pyridazines, pyrimidines, and pyrazines bearing phosphonates and phosphine oxides, which were reported from 2012 to 2022.
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2
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Wei Y, Li W, Du T, Hong Z, Lin J. Targeting HIV/HCV Coinfection Using a Machine Learning-Based Multiple Quantitative Structure-Activity Relationships (Multiple QSAR) Method. Int J Mol Sci 2019; 20:ijms20143572. [PMID: 31336592 PMCID: PMC6678913 DOI: 10.3390/ijms20143572] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/13/2019] [Accepted: 07/21/2019] [Indexed: 12/11/2022] Open
Abstract
Human immunodeficiency virus type-1 and hepatitis C virus (HIV/HCV) coinfection occurs when a patient is simultaneously infected with both human immunodeficiency virus type-1 (HIV-1) and hepatitis C virus (HCV), which is common today in certain populations. However, the treatment of coinfection is a challenge because of the special considerations needed to ensure hepatic safety and avoid drug–drug interactions. Multitarget inhibitors with less toxicity may provide a promising therapeutic strategy for HIV/HCV coinfection. However, the identification of one molecule that acts on multiple targets simultaneously by experimental evaluation is costly and time-consuming. In silico target prediction tools provide more opportunities for the development of multitarget inhibitors. In this study, by combining Naïve Bayes (NB) and support vector machine (SVM) algorithms with two types of molecular fingerprints, MACCS and extended connectivity fingerprints 6 (ECFP6), 60 classification models were constructed to predict compounds that were active against 11 HIV-1 targets and four HCV targets based on a multiple quantitative structure–activity relationships (multiple QSAR) method. Five-fold cross-validation and test set validation were performed to measure the performance of the 60 classification models. Our results show that the 60 multiple QSAR models appeared to have high classification accuracy in terms of the area under the ROC curve (AUC) values, which ranged from 0.83 to 1 with a mean value of 0.97 for the HIV-1 models and from 0.84 to 1 with a mean value of 0.96 for the HCV models. Furthermore, the 60 models were used to comprehensively predict the potential targets of an additional 46 compounds, including 27 approved HIV-1 drugs, 10 approved HCV drugs and nine selected compounds known to be active against one or more targets of HIV-1 or HCV. Finally, 20 hits, including seven approved HIV-1 drugs, four approved HCV drugs, and nine other compounds, were predicted to be HIV/HCV coinfection multitarget inhibitors. The reported bioactivity data confirmed that seven out of nine compounds actually interacted with HIV-1 and HCV targets simultaneously with diverse binding affinities. The remaining predicted hits and chemical-protein interaction pairs with the potential ability to suppress HIV/HCV coinfection are worthy of further experimental investigation. This investigation shows that the multiple QSAR method is useful in predicting chemical-protein interactions for the discovery of multitarget inhibitors and provides a unique strategy for the treatment of HIV/HCV coinfection.
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Affiliation(s)
- Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Wei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
- Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin 300000, China
| | - Tengfei Du
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China
| | - Zhangyong Hong
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China.
- Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin 300000, China.
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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3
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Lacbay CM, Menni M, Bernatchez JA, Götte M, Tsantrizos YS. Pharmacophore requirements for HIV-1 reverse transcriptase inhibitors that selectively "Freeze" the pre-translocated complex during the polymerization catalytic cycle. Bioorg Med Chem 2018; 26:1713-1726. [PMID: 29478802 DOI: 10.1016/j.bmc.2018.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/06/2018] [Accepted: 02/13/2018] [Indexed: 12/20/2022]
Abstract
Reverse transcriptase (RT) is responsible for replicating the HIV-1 genome and is a validated therapeutic target for the treatment of HIV infections. During each cycle of the RT-catalyzed DNA polymerization process, inorganic pyrophosphate is released as the by-product of nucleotide incorporation. Small molecules were identified that act as bioisosteres of pyrophosphate and can selectively freeze the catalytic cycle of HIV-1 RT at the pre-translocated stage of the DNA- or RNA-template-primer-enzyme complex.
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Affiliation(s)
- Cyrus M Lacbay
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Michael Menni
- Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
| | - Jean A Bernatchez
- Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada; Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada; Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada.
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4
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Chapman TM, Wallace C, Gillen KJ, Bakrania P, Khurana P, Coombs PJ, Fox S, Bureau EA, Brownlees J, Melton DW, Saxty B. N-Hydroxyimides and hydroxypyrimidinones as inhibitors of the DNA repair complex ERCC1-XPF. Bioorg Med Chem Lett 2015; 25:4104-8. [PMID: 26321360 DOI: 10.1016/j.bmcl.2015.08.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/06/2015] [Accepted: 08/07/2015] [Indexed: 11/19/2022]
Abstract
A high throughput screen allowed the identification of N-hydroxyimide inhibitors of ERCC1-XPF endonuclease activity with micromolar potency, but they showed undesirable selectivity profiles against FEN-1. A scaffold hop to a hydroxypyrimidinone template gave compounds with similar potency but allowed selectivity to be switched in favour of ERCC1-XPF over FEN-1. Further exploration of the structure-activity relationships around this chemotype gave sub-micromolar inhibitors with >10-fold selectivity for ERCC1-XPF over FEN-1.
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Affiliation(s)
- Timothy M Chapman
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Claire Wallace
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Kevin J Gillen
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Preeti Bakrania
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Puneet Khurana
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Peter J Coombs
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Simon Fox
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Emilie A Bureau
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Janet Brownlees
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - David W Melton
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Barbara Saxty
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
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5
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Schreiner E, Braun S, Kwasnitschka C, Frank W, Müller TJJ. Consecutive Three-Component Synthesis of 2,6-Disubstituted Pyrimid-4(3H)-ones and 1,5-Disubstituted 3-Hydroxypyrazoles Initiated by Copper(I)-Catalyzed Carboxylation of Terminal Alkynes. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400411] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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6
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Wang M, Zhong M, Yan A, Li L, Yu C. Quantitative structure and bioactivity relationship study on HCV NS5B polymerase inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 25:1-15. [PMID: 24283437 DOI: 10.1080/1062936x.2013.820790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Several QSAR (quantitative structure-activity relationship) models for predicting the inhibitory activity of 333 hepatitis C virus (HCV) NS5B polymerase inhibitors were developed. All the inhibitors are HCV polymerase non-nucleoside analogue inhibitors (NNIs) fitting into the pocket of the NNI III binding site. For each molecule, global descriptors and 2D property autocorrelation descriptors were calculated from the program ADRIANA.Code. Pearson correlation analysis was used to select the significant descriptors for building models. The whole dataset was split into a training set and a test set randomly or using a Kohonen's self-organizing map (SOM). Then, the inhibitory activity of 333 HCV NS5B polymerase inhibitors was predicted using multilinear regression (MLR) analysis and support vector machine (SVM) method, respectively. For the test set of the best model (Model 2B), correlation coefficient of 0.91 was achieved. Some molecular descriptors, such as molecular complexity (Complexity), the number of hydrogen bonding donors (HDon) and the solubility of the molecule in water (log S) were found to be very important factors which determined the bioactivity of the HCV NS5B inhibitors. Some other molecular properties such as electrostatic and charge properties also played important roles in the interaction between the ligand and the protein. The selected molecular descriptors were further confirmed by analysing the interaction between two representative inhibitors and the polymerase in their crystal structures.
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Affiliation(s)
- M Wang
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , China
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7
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Weidlich IE, Filippov IV, Brown J, Kaushik-Basu N, Krishnan R, Nicklaus MC, Thorpe IF. Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods. Bioorg Med Chem 2013; 21:3127-37. [PMID: 23608107 PMCID: PMC3653294 DOI: 10.1016/j.bmc.2013.03.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/10/2013] [Accepted: 03/18/2013] [Indexed: 12/30/2022]
Abstract
Hepatitis C virus (HCV) is a global health challenge, affecting approximately 200 million people worldwide. In this study we developed SAR models with advanced machine learning classifiers Random Forest and k Nearest Neighbor Simulated Annealing for 679 small molecules with measured inhibition activity for NS5B genotype 1b. The activity was expressed as a binary value (active/inactive), where actives were considered molecules with IC50 ≤0.95 μM. We applied our SAR models to various drug-like databases and identified novel chemical scaffolds for NS5B inhibitors. Subsequent in vitro antiviral assays suggested a new activity for an existing prodrug, Candesartan cilexetil, which is currently used to treat hypertension and heart failure but has not been previously tested for anti-HCV activity. We also identified NS5B inhibitors with two novel non-nucleoside chemical motifs.
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Affiliation(s)
- Iwona E. Weidlich
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick National Laboratory for Cancer Research, 376 Boyles Street, Frederick, MD 21702
- Computational Drug Design Systems (CODDES) LLC, Rockville, MD
| | - Igor V. Filippov
- Chemical Biology Laboratory, Center for Cancer Research, SAIC-Frederick, Inc., 376 Boyles Street, Frederick, MD 21702
| | - Jodian Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Neerja Kaushik-Basu
- Department of Biochemistry and Molecular Biology, UMDNJ New Jersey Medical School, 185 South Orange Ave, Newark, NJ 07103
| | - Ramalingam Krishnan
- Department of Biochemistry and Molecular Biology, UMDNJ New Jersey Medical School, 185 South Orange Ave, Newark, NJ 07103
| | - Marc C. Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick National Laboratory for Cancer Research, 376 Boyles Street, Frederick, MD 21702
| | - Ian F. Thorpe
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
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8
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Viral enzymes containing magnesium: Metal binding as a successful strategy in drug design. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.07.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Finger-loop inhibitors of the HCV NS5b polymerase. Part 1: Discovery and optimization of novel 1,6- and 2,6-macrocyclic indole series. Bioorg Med Chem Lett 2012; 22:4431-6. [DOI: 10.1016/j.bmcl.2012.03.097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 03/27/2012] [Accepted: 03/28/2012] [Indexed: 12/26/2022]
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10
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Deore RR, Chen GS, Chang PT, Chern TR, Lai SY, Chuang MH, Lin JH, Kung FL, Chen CS, Chiou CT, Chern JW. Discovery of N-Arylalkyl-3-hydroxy-4-oxo-3,4-dihydroquinazolin-2-carboxamide Derivatives as HCV NS5B Polymerase Inhibitors. ChemMedChem 2012; 7:850-60. [DOI: 10.1002/cmdc.201200058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Indexed: 11/06/2022]
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11
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Sofia MJ, Chang W, Furman PA, Mosley RT, Ross BS. Nucleoside, nucleotide, and non-nucleoside inhibitors of hepatitis C virus NS5B RNA-dependent RNA-polymerase. J Med Chem 2012; 55:2481-531. [PMID: 22185586 DOI: 10.1021/jm201384j] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael J Sofia
- Pharmasset, Inc., 303A College Road East, Princeton, New Jersey 08540, United States.
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12
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Humphrey GR, Pye PJ, Zhong YL, Angelaud R, Askin D, Belyk KM, Maligres PE, Mancheno DE, Miller RA, Reamer RA, Weissman SA. Development of a Second-Generation, Highly Efficient Manufacturing Route for the HIV Integrase Inhibitor Raltegravir Potassium. Org Process Res Dev 2010. [DOI: 10.1021/op100257r] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guy R. Humphrey
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Philip J. Pye
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Yong-Li Zhong
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Remy Angelaud
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - David Askin
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Kevin M. Belyk
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Peter E. Maligres
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Danny E. Mancheno
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Ross A. Miller
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Robert A. Reamer
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Steven A. Weissman
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, United States
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13
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2-(3-Thienyl)-5,6-dihydroxypyrimidine-4-carboxylic acids as inhibitors of HCV NS5B RdRp. Bioorg Med Chem Lett 2009; 19:6245-9. [DOI: 10.1016/j.bmcl.2009.06.106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/10/2009] [Accepted: 06/10/2009] [Indexed: 11/23/2022]
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14
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Van der Jeught S, Stevens CV. Direct phosphonylation of aromatic azaheterocycles. Chem Rev 2009; 109:2672-702. [PMID: 19449857 DOI: 10.1021/cr800315j] [Citation(s) in RCA: 250] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah Van der Jeught
- Department of Organic Chemistry, Faculty of Bioscience Engineering, Gent University, Coupure Links 653, B-9000 Gent, Belgium.
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15
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Wang F, Liu H, Fu H, Jiang Y, Zhao Y. Highly Efficient Iron(II) Chloride/N-Bromosuccinimide-Mediated Synthesis of Imides and Acylsulfonamides. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200800668] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Zhong YL, Pipik B, Lee J, Kohmura Y, Okada S, Igawa K, Kadowaki C, Takezawa A, Kato S, Conlon DA, Zhou H, King AO, Reamer RA, Gauthier, Jr. DR, Askin D. Practical Synthesis of a HIV Integrase Inhibitor. Org Process Res Dev 2008. [DOI: 10.1021/op800153y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yong-Li Zhong
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Brenda Pipik
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Jaemoon Lee
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Yoshinori Kohmura
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Shigemitsu Okada
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Kazunobu Igawa
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Chie Kadowaki
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Akihiro Takezawa
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Shinji Kato
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - David A. Conlon
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Hua Zhou
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Anthony O. King
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Robert A. Reamer
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - Donald R. Gauthier, Jr.
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
| | - David Askin
- Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, U.S.A., and Department of PreClinical Development, Banyu Tsukuba Research Institute, 3 Okubo, Tsukuba-city, Ibaraki 3002611, Japan
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Pye P, Zhong YL, Jones G, Reamer R, Houk K, Askin D. A Polar Radical Pair Pathway To Assemble the Pyrimidinone Core of the HIV Integrase Inhibitor Raltegravir Potassium. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200703681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Pye P, Zhong YL, Jones G, Reamer R, Houk K, Askin D. A Polar Radical Pair Pathway To Assemble the Pyrimidinone Core of the HIV Integrase Inhibitor Raltegravir Potassium. Angew Chem Int Ed Engl 2008; 47:4134-6. [DOI: 10.1002/anie.200703681] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Chang JWW, Chan PWH. Highly efficient ruthenium(II) porphyrin catalyzed amidation of aldehydes. Angew Chem Int Ed Engl 2008; 47:1138-40. [PMID: 18163374 DOI: 10.1002/anie.200704695] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joyce Wei Wei Chang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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20
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Chang J, Chan P. Highly Efficient Ruthenium(II) Porphyrin Catalyzed Amidation of Aldehydes. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704695] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Gardelli C, Nizi E, Muraglia E, Crescenzi B, Ferrara M, Orvieto F, Pace P, Pescatore G, Poma M, Ferreira MDRR, Scarpelli R, Homnick CF, Ikemoto N, Alfieri A, Verdirame M, Bonelli F, Paz OG, Taliani M, Monteagudo E, Pesci S, Laufer R, Felock P, Stillmock KA, Hazuda D, Rowley M, Summa V. Discovery and Synthesis of HIV Integrase Inhibitors: Development of Potent and Orally Bioavailable N-Methyl Pyrimidones. J Med Chem 2007; 50:4953-75. [PMID: 17824681 DOI: 10.1021/jm0704705] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The human immunodeficiency virus type-1 (HIV-1) encodes three enzymes essential for viral replication: a reverse transcriptase, a protease, and an integrase. The latter is responsible for the integration of the viral genome into the human genome and, therefore, represents an attractive target for chemotherapeutic intervention against AIDS. A drug based on this mechanism has not yet been approved. Benzyl-dihydroxypyrimidine-carboxamides were discovered in our laboratories as a novel and metabolically stable class of agents that exhibits potent inhibition of the HIV integrase strand transfer step. Further efforts led to very potent compounds based on the structurally related N-Me pyrimidone scaffold. One of the more interesting compounds in this series is the 2-N-Me-morpholino derivative 27a, which shows a CIC95 of 65 nM in the cell in the presence of serum. The compound has favorable pharmacokinetic properties in three preclinical species and shows no liabilities in several counterscreening assays.
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Affiliation(s)
- Cristina Gardelli
- Department of Medicinal Chemistry - Istituto Di Ricerche Di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy.
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22
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Kinzel OD, Monteagudo E, Muraglia E, Orvieto F, Pescatore G, Ferreira MDRR, Rowley M, Summa V. The synthesis of tetrahydropyridopyrimidones as a new scaffold for HIV-1 integrase inhibitors. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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23
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Stansfield I, Pompei M, Conte I, Ercolani C, Migliaccio G, Jairaj M, Giuliano C, Rowley M, Narjes F. Development of carboxylic acid replacements in indole-N-acetamide inhibitors of hepatitis C virus NS5B polymerase. Bioorg Med Chem Lett 2007; 17:5143-9. [PMID: 17681757 DOI: 10.1016/j.bmcl.2007.06.093] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 06/28/2007] [Accepted: 06/29/2007] [Indexed: 12/16/2022]
Abstract
Allosteric inhibition of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase enzyme has recently emerged as a viable strategy toward blocking replication of viral RNA in cell-based systems. We report here 2 series of indole-N-acetamides, bearing physicochemically diverse carboxylic acid replacements, which show potent affinity for the NS5B enzyme with reduced potential for formation of glucuronide conjugates. Preliminary optimization of these series furnished compounds that are potent in the blockade of subgenomic HCV RNA replication in HUH-7 cells.
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Affiliation(s)
- Ian Stansfield
- IRBM (Merck Research Laboratories Rome), Via Pontina Km 30,600, 00040 Pomezia, Rome, Italy.
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24
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Chapter 18 Recent Progress on Novel HCV Inhibitors. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2007. [DOI: 10.1016/s0065-7743(07)42018-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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25
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Petrocchi A, Koch U, Matassa VG, Pacini B, Stillmock KA, Summa V. From dihydroxypyrimidine carboxylic acids to carboxamide HIV-1 integrase inhibitors: SAR around the amide moiety. Bioorg Med Chem Lett 2006; 17:350-3. [PMID: 17107799 DOI: 10.1016/j.bmcl.2006.10.054] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 10/20/2006] [Accepted: 10/20/2006] [Indexed: 11/18/2022]
Abstract
4,5-Dihyroxypyrimidine carboxamides, which evolved from a related series of HCV NS5b polymerase inhibitors, have been optimized to provide selective HIV integrase strand transfer inhibitors. Extensive SAR around the benzylamide moiety led to the identification of the p-fluorobenzylamide as optimal in the enzymatic assay.
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Affiliation(s)
- Alessia Petrocchi
- Department of Medicinal Chemistry and Drug Metabolism, IRBM-MRL Rome, Via Pontina, Km 30.600, 00040 Pomezia, Rome, Italy.
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26
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Koev G, Dekhtyar T, Han L, Yan P, Ng TI, Lin CT, Mo H, Molla A. Antiviral interactions of an HCV polymerase inhibitor with an HCV protease inhibitor or interferon in vitro. Antiviral Res 2006; 73:78-83. [PMID: 16945431 DOI: 10.1016/j.antiviral.2006.07.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Revised: 07/18/2006] [Accepted: 07/25/2006] [Indexed: 11/26/2022]
Abstract
The combinations of Abbott Hepatitis C virus (HCV) polymerase A-782759 with either Boehringer Ingelheim HCV NS3 protease inhibitor BILN-2061 or interferon (IFN) displayed additive to synergistic relationships over a range of concentrations of two-drug combination. Treatment of HCV replicon with A-782759, IFN or BILN-2061 for about 16 days resulted in dramatic reductions in HCV RNA (5.1, 3.0 and 3.9 log10 RNA copies, respectively). However, none of the compounds tested alone lead to replicon RNA reduction to undetectable levels. Ongoing replication in the presence of A-782759 or BILN-2061 was associated with the appearance of resistant mutations M414T in NS5B and D168V in NS3, respectively. In contrast, a combination of A-782759 with BILN-2061 resulted in greater than 7 logs RNA reduction leading to undetectable replicon RNA after 16 days of treatment. Our findings suggest that a monotherapy with either drug alone is likely to result in development of resistant mutants. However, a combination therapy with polymerase inhibitor has the potential to improve the efficacy of IFN or a protease inhibitor alone in vivo, due to the lower likelihood of resistance development.
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Affiliation(s)
- Gennadiy Koev
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
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27
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28
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Koch U, Attenni B, Malancona S, Colarusso S, Conte I, Di Filippo M, Harper S, Pacini B, Giomini C, Thomas S, Incitti I, Tomei L, De Francesco R, Altamura S, Matassa VG, Narjes F. 2-(2-Thienyl)-5,6-dihydroxy-4-carboxypyrimidines as inhibitors of the hepatitis C virus NS5B polymerase: discovery, SAR, modeling, and mutagenesis. J Med Chem 2006; 49:1693-705. [PMID: 16509585 DOI: 10.1021/jm051064t] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The polymerase of HCV is responsible for the replication of viral RNA. We recently disclosed dihydroxypyrimidine carboxylates 2 as novel, reversible inhibitors of the HCV NS5B polymerase. This series was further developed into 5,6-dihydroxy-2-(2-thienyl)pyrimidine-4-carboxylic acids such as 34 (EC50 9.3 microM), which now show activity in the cell-based HCV replication assay. The structure-activity relationship of these inhibitors is discussed in the context of their physicochemical properties and of the polymerase crystal structure. We also report the results of mutagenesis experiments which support the proposed binding model, which involves pyrophosphate-like chelation of the active site Mg ions.
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Affiliation(s)
- Uwe Koch
- Istituto Di Ricerche Di Biologia Molecolare, P. Angeletti S.p.A. (Merck Research Laboratories, Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy.
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29
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Zhong YL, Zhou H, Gauthier DR, Askin D. Efficient synthesis of functionalized pyrimidones via microwave-accelerated rearrangement reaction. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2005.12.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Mo H, Lu L, Pilot-Matias T, Pithawalla R, Mondal R, Masse S, Dekhtyar T, Ng T, Koev G, Stoll V, Stewart KD, Pratt J, Donner P, Rockway T, Maring C, Molla A. Mutations conferring resistance to a hepatitis C virus (HCV) RNA-dependent RNA polymerase inhibitor alone or in combination with an HCV serine protease inhibitor in vitro. Antimicrob Agents Chemother 2006; 49:4305-14. [PMID: 16189112 PMCID: PMC1251566 DOI: 10.1128/aac.49.10.4305-4314.2005] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Compounds A-782759 (an N-1-aza-4-hydroxyquinolone benzothiadiazine) and BILN-2061 are specific anti-hepatitis C virus (HCV) agents that inhibit the RNA-dependent RNA polymerase and the NS3 serine protease, respectively. Both compounds display potent activity against HCV replicons in tissue culture. In order to characterize the development of resistance to these anti-HCV agents, HCV subgenomic 1b-N replicon cells were cultured with A-782759 alone or in combination with BILN-2061 at concentrations 10 times above their corresponding 50% inhibitory concentrations in the presence of neomycin. Single substitutions in the NS5B polymerase gene (H95Q, N411S, M414L, M414T, or Y448H) resulted in substantial decreases in susceptibility to A-782759. Similarly, replicons containing mutations in the NS5B polymerase gene (M414L or M414T), together with single mutations in the NS3 protease gene (A156V or D168V), conferred high levels of resistance to both A-782759 and BILN-2061. However, the A-782759-resistant mutants remained susceptible to nucleoside and two other classes of nonnucleoside NS5B polymerase inhibitors, as well as interferon. In addition, we found that the frequency of replicons resistant to both compounds was significantly lower than the frequency of resistance to the single compound. Furthermore, the dually resistant mutants displayed significantly reduced replication capacities compared to the wild-type replicon. These findings provide strategic guidance for the future treatment of HCV infection.
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Affiliation(s)
- Hongmei Mo
- Antiviral Research, Abbott Laboratories Global Pharmaceutical Research and Development, Abbott Park, Illinois, USA.
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31
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Pfefferkorn JA, Greene ML, Nugent RA, Gross RJ, Mitchell MA, Finzel BC, Harris MS, Wells PA, Shelly JA, Anstadt RA, Kilkuskie RE, Kopta LA, Schwende FJ. Inhibitors of HCV NS5B polymerase. Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid. Bioorg Med Chem Lett 2005; 15:2481-6. [PMID: 15863301 DOI: 10.1016/j.bmcl.2005.03.066] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2005] [Revised: 03/16/2005] [Accepted: 03/17/2005] [Indexed: 12/09/2022]
Abstract
A novel series of nonnucleoside HCV NS5B polymerase inhibitors were prepared from (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid, a high throughput screening lead. SAR studies combined with structure based drug design focusing on the southern heterobiaryl region of the template led to the synthesis of several potent and orally bioavailable lead compounds. X-ray crystallography studies were also performed to understand the interaction of these inhibitors with HCV NS5B polymerase.
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Affiliation(s)
- Jeffrey A Pfefferkorn
- Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA.
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32
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Ding Y, Girardet JL, Smith KL, Larson G, Prigaro B, Lai VCH, Zhong W, Wu JZ. Parallel synthesis of pteridine derivatives as potent inhibitors for hepatitis C virus NS5B RNA-dependent RNA polymerase. Bioorg Med Chem Lett 2005; 15:675-8. [PMID: 15664835 DOI: 10.1016/j.bmcl.2004.11.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Revised: 11/08/2004] [Accepted: 11/12/2004] [Indexed: 12/13/2022]
Abstract
From compound library screening using an HCV NS5B RNA-dependent RNA polymerase enzymatic assay, we identified a pteridine hit compound with an IC(50) of 15 microM. Our SAR studies were focused on the different groups at the 6- and 7-positions, substitutions at the 4-position, and replacement of N(1) or N(3) with carbon in the pteridine ring. We found that NH or OH at 4-position is critical for the inhibitory activity. Furthermore, a hydrophobic substituent at the 4-position may help compounds permeate through the cell membrane.
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Affiliation(s)
- Yili Ding
- Valeant Pharmaceuticals International, 3300 Hyland Avenue Costa Mesa, CA 92626, USA.
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