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Chazot A, Zimberger C, Feracci M, Moussa A, Good S, Sommadossi JP, Alvarez K, Ferron F, Canard B. The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution. PLoS Biol 2024; 22:e3002743. [PMID: 39190717 DOI: 10.1371/journal.pbio.3002743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Bemnifosbuvir (AT-527) and AT-752 are guanosine analogues currently in clinical trials against several RNA viruses. Here, we show that these drugs require a minimal set of 5 cellular enzymes for activation to their common 5'-triphosphate AT-9010, with an obligate order of reactions. AT-9010 selectively inhibits essential viral enzymes, accounting for antiviral potency. Functional and structural data at atomic resolution decipher N6-purine deamination compatible with its metabolic activation. Crystal structures of human histidine triad nucleotide binding protein 1, adenosine deaminase-like protein 1, guanylate kinase 1, and nucleoside diphosphate kinase at 2.09, 2.44, 1.76, and 1.9 Å resolution, respectively, with cognate precursors of AT-9010 illuminate the activation pathway from the orally available bemnifosbuvir to AT-9010, pointing to key drug-protein contacts along the activation pathway. Our work provides a framework to integrate the design of antiviral nucleotide analogues, confronting requirements and constraints associated with activation enzymes along the 5'-triphosphate assembly line.
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Affiliation(s)
- Aurélie Chazot
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - Claire Zimberger
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - Mikael Feracci
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - Adel Moussa
- ATEA Pharmaceuticals, Inc., Boston, Massachusetts, United States of America
| | - Steven Good
- ATEA Pharmaceuticals, Inc., Boston, Massachusetts, United States of America
| | | | - Karine Alvarez
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - François Ferron
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
- European Virus Bioinformatics Center, Jena, Germany
| | - Bruno Canard
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
- European Virus Bioinformatics Center, Jena, Germany
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2
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Chen S, Lai W, Li Y, Liu Y, Jiang J, Li X, Jiang G, Wang H. Aberrant DNA N 6 -methyladenine incorporation via adenylate kinase 1 is suppressed by ADAL deaminase-dependent 2'-deoxynucleotide pool sanitation. EMBO J 2023; 42:e113684. [PMID: 37366109 PMCID: PMC10390868 DOI: 10.15252/embj.2023113684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Intracellular decay of N6 -methyladenine (m6A)-containing RNA potentially induces aberrant N6 -methyl-2'-adenine (6mdA) misincorporation into DNA. Biophysically, misincorporated 6mdA may destabilize the DNA duplex in a manner similar to bona fide methylated 6mdA DNA, thereby affecting DNA replication and transcription. Utilizing heavy stable isotope labeling and ultrasensitive UHPLC-MS/MS assay, we demonstrate that intracellular m6A-RNA decay does not generate free 6mdA species, nor lead to any misincorporated DNA 6mdA in most mammalian cell lines tested, unveiling the existence of a sanitation mechanism that prevents 6mdA misincorporation. Depletion of deaminase ADAL increases the levels of free 6mdA species, concomitant with the presence of DNA-misincorporated 6mdA resulting from intracellular RNA m6A decay, suggesting that ADAL catabolizes 6mdAMP in vivo. Furthermore, we show that the overexpression of adenylate kinase 1 (AK1) promotes 6mdA misincorporation, while AK1 knockdown diminishes 6mdA incorporation, in ADAL-deficient cells. We conclude that ADAL together with other factors (such as MTH1) contributes to 2'-deoxynucleotide pool sanitation in most cells but compromised sanitation (e.g., in NIH3T3 cells) and increased AK1 expression may facilitate aberrant 6mdA incorporation. This sanitation mechanism may provide a framework for the maintenance of the epigenetic 6mdA landscape.
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Affiliation(s)
- Shaokun Chen
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Weiyi Lai
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Yanan Li
- Institute of Environment and Health, Institute for Advanced StudyUCASHangzhouChina
| | - Yan Liu
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Jie Jiang
- Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Xiangjun Li
- School of Chemical SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Guibin Jiang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Institute of Environment and Health, Institute for Advanced StudyUCASHangzhouChina
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- Institute of Environment and Health, Institute for Advanced StudyUCASHangzhouChina
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3
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Shannon A, Canard B. Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2. Antiviral Res 2023; 210:105501. [PMID: 36567022 PMCID: PMC9773703 DOI: 10.1016/j.antiviral.2022.105501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase for incorporation into the viral RNA genome. Incorporated analogues can either 'kill' (terminate) synthesis, or 'corrupt' (genetically or chemically) the RNA. Against coronaviruses, the use of NAs has been further complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities. Here, we describe the mechanism of action of four promising anti-COVID-19 NAs; remdesivir, molnupiravir, favipiravir and bemnifosbuvir. Their distinct mechanisms of action best exemplify the concept of 'killers' and 'corruptors'. We review available data regarding their ability to be incorporated and excised, and discuss the specific structural features that dictate their overall potency, toxicity, and mutagenic potential. This should guide the synthesis of novel analogues, lend insight into the potential for resistance mutations, and provide a rational basis for upcoming combinations therapies.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.
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4
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Jia Q, Zhang J, Zeng H, Tang J, Xiao N, Gao S, Li H, Xie W. Substrate Specificity of GSDA Revealed by Cocrystal Structures and Binding Studies. Int J Mol Sci 2022; 23:ijms232314976. [PMID: 36499303 PMCID: PMC9739398 DOI: 10.3390/ijms232314976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
In plants, guanosine deaminase (GSDA) catalyzes the deamination of guanosine for nitrogen recycling and re-utilization. We previously solved crystal structures of GSDA from Arabidopsis thaliana (AtGSDA) and identified several novel substrates for this enzyme, but the structural basis of the enzyme activation/inhibition is poorly understood. Here, we continued to solve 8 medium-to-high resolution (1.85-2.60 Å) cocrystal structures, which involved AtGSDA and its variants bound by a few ligands, and investigated their binding modes through structural studies and thermal shift analysis. Besides the lack of a 2-amino group of these guanosine derivatives, we discovered that AtGSDA's inactivity was due to the its inability to seclude its active site. Furthermore, the C-termini of the enzyme displayed conformational diversities under certain circumstances. The lack of functional amino groups or poor interactions/geometries of the ligands at the active sites to meet the precise binding and activation requirements for deamination both contributed to AtGSDA's inactivity toward the ligands. Altogether, our combined structural and biochemical studies provide insight into GSDA.
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Xia R, Chen LS, Liu LJ, Xia C, Sun LP. Diversity-Oriented Synthesis of 2-Substituted Purine Nucleosides from Available Nucleosides via the Late-Stage Nitration/Derivatization. HETEROCYCLES 2022. [DOI: 10.3987/com-22-14689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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6
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Jiang Z, Wang C, Wu Z, Chen K, Yang W, Deng H, Song H, Zhou X. Enzymatic deamination of the epigenetic nucleoside N6-methyladenosine regulates gene expression. Nucleic Acids Res 2021; 49:12048-12068. [PMID: 34850126 PMCID: PMC8643624 DOI: 10.1093/nar/gkab1124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most extensively studied epigenetic modification due to its crucial role in regulating an array of biological processes. Herein, Bsu06560, formerly annotated as an adenine deaminase derived from Bacillus subtilis 168, was recognized as the first enzyme capable of metabolizing the epigenetic nucleoside N6-methyladenosine. A model of Bsu06560 was constructed, and several critical residues were putatively identified via mutational screening. Two mutants, F91L and Q150W, provided a superiorly enhanced conversion ratio of adenosine and N6-methyladenosine. The CRISPR-Cas9 system generated Bsu06560-knockout, F91L, and Q150W mutations from the B. subtilis 168 genome. Transcriptional profiling revealed a higher global gene expression level in BS-F91L and BS-Q150W strains with enhanced N6-methyladenosine deaminase activity. The differentially expressed genes were categorized using GO, COG, KEGG and verified through RT-qPCR. This study assessed the crucial roles of Bsu06560 in regulating adenosine and N6-methyladenosine metabolism, which influence a myriad of biological processes. This is the first systematic research to identify and functionally annotate an enzyme capable of metabolizing N6-methyladenosine and highlight its significant roles in regulation of bacterial metabolism. Besides, this study provides a novel method for controlling gene expression through the mutations of critical residues.
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Affiliation(s)
- Zhuoran Jiang
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Chao Wang
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Zixin Wu
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Kun Chen
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Wei Yang
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Hexiang Deng
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Heng Song
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Xiang Zhou
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
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7
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Marchetti M, Faggiano S, Mozzarelli A. Enzyme Replacement Therapy for Genetic Disorders Associated with Enzyme Deficiency. Curr Med Chem 2021; 29:489-525. [PMID: 34042028 DOI: 10.2174/0929867328666210526144654] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/23/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
Mutations in human genes might lead to loss of functional proteins, causing diseases. Among these genetic disorders, a large class is associated with the deficiency in metabolic enzymes, resulting in both an increase in the concentration of substrates and a loss in the metabolites produced by the catalyzed reactions. The identification of therapeutic actions based on small molecules represents a challenge to medicinal chemists because the target is missing. Alternative approaches are biology-based, ranging from gene and stem cell therapy, CRISPR/Cas9 technology, distinct types of RNAs, and enzyme replacement therapy (ERT). This review will focus on the latter approach that since the 1990s has been successfully applied to cure many rare diseases, most of them being lysosomal storage diseases or metabolic diseases. So far, a dozen enzymes have been approved by FDA/EMA for lysosome storage disorders and only a few for metabolic diseases. Enzymes for replacement therapy are mainly produced in mammalian cells and some in plant cells and yeasts and are further processed to obtain active, highly bioavailable, less degradable products. Issues still under investigation for the increase in ERT efficacy are the optimization of enzymes interaction with cell membrane and internalization, the reduction in immunogenicity, and the overcoming of blood-brain barrier limitations when neuronal cells need to be targeted. Overall, ERT has demonstrated its efficacy and safety in the treatment of many genetic rare diseases, both saving newborn lives and improving patients' life quality, and represents a very successful example of targeted biologics.
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Affiliation(s)
- Marialaura Marchetti
- Biopharmanet-TEC Interdepartmental Center, University of Parma, Parco Area delle Scienze, Bldg 33., 43124, Parma, Italy
| | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23/A, 43124, Parma, Italy
| | - Andrea Mozzarelli
- Institute of Biophysics, National Research Council, Via Moruzzi 1, 56124, Pisa, Italy
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8
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Hagen NR, Nguyen ML, Williams JD, Bowlin TL, Gentry BG. Pentostatin antagonizes the antiviral activity of MBX-2168 by inhibiting the biosynthesis of the active compound. Antiviral Res 2021; 187:105018. [PMID: 33476709 DOI: 10.1016/j.antiviral.2021.105018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
MBX-2168 has a mechanism of action similar to that of acyclovir (ACV) and ganciclovir (GCV), but two unique steps differentiate this drug from ACV/GCV. First, MBX-2168 is, at least partially, phosphorylated by the endogenous cellular kinase TAOK3 to a monophosphate. The second involves the removal of a moiety at the 6-position of MBX-2168-MP by adenosine deaminase like protein-1 (ADAL-1). It has been previously demonstrated that co-incubation with pentostatin (dCF), an ADAL-1 inhibitor, antagonizes the anti-viral activity of MBX-2168. We therefore hypothesize that inhibiting ADAL-1 results in a reduction of active compound produced in virus-infected cells. To test this, we examined the effect dCF has on the conversion of MBX-2168 to a triphosphate in HSV-1 and HCMV-infected cells. Our results demonstrate incubation of MBX-2168 alone or with dCF in HCMV-infected cells resulted in 53.1 ± 0.7 and 39.4 ± 1.5 pmol triphosphate/106 cells at 120 h, respectively. Incubation of MBX-2168 alone or with dCF in Vero cells resulted in 12.8 ± 0.1 and 6.7 ± 0.7 pmol triphosphate/106 cells at 24 h, respectively. HSV-1-infected Vero cells demonstrated no statistical difference in triphosphate accumulation at 24 h (13.1 ± 0.3 pmol triphosphate/106 cells). As expected, incubation with dCF resulted in the accumulation of MBX-2168-MP in both HFF (9.8 ± 0.9 pmol MBX-2168-MP/106 cells at 120 h) and Vero cells (4.7 ± 0.3 pmol MBX-2168-MP/106 cells at 24 h) while no detectable levels of monophosphate were observed in cultures not incubated with dCF. We conclude that dCF antagonizes the anti-viral effect of MBX-2168 by inhibiting the production of triphosphate, the active compound.
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Affiliation(s)
- Natalie R Hagen
- Department of Pharmaceutical and Administrative Sciences, College of Pharmacy and Health Sciences, Drake University, Des Moines, IA, 50311, USA
| | - Marie L Nguyen
- Department of Microbiology and Immunology, College of Osteopathic Medicine, Des Moines University, Des Moines, IA, 50312, USA
| | | | | | - Brian G Gentry
- Department of Pharmaceutical and Administrative Sciences, College of Pharmacy and Health Sciences, Drake University, Des Moines, IA, 50311, USA.
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9
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Wang G, Dyatkina N, Prhavc M, Williams C, Serebryany V, Hu Y, Huang Y, Wu X, Chen T, Huang W, Rajwanshi VK, Deval J, Fung A, Jin Z, Stoycheva A, Shaw K, Gupta K, Tam Y, Jekle A, Smith DB, Beigelman L. Synthesis and Anti-HCV Activity of Sugar-Modified Guanosine Analogues: Discovery of AL-611 as an HCV NS5B Polymerase Inhibitor for the Treatment of Chronic Hepatitis C. J Med Chem 2020; 63:10380-10395. [PMID: 32816483 DOI: 10.1021/acs.jmedchem.0c00935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chronic hepatitis C (CHC) is a major liver disease caused by the hepatitis C virus. The current standard of care for CHC can achieve cure rates above 95%; however, the drugs in current use are administered for a period of 8-16 weeks. A combination of safe and effective drugs with a shorter treatment period is highly desirable. We report synthesis and biological evaluation of a series of 2',3'- and 2',4'-substituted guanosine nucleotide analogues. Their triphosphates exhibited potent inhibition of the HCV NS5B polymerase with IC50 as low as 0.13 μM. In the HCV replicon assay, the phosphoramidate prodrugs of these analogues demonstrated excellent activity with EC50 values as low as 5 nM. A lead compound AL-611 showed high levels of the nucleoside 5'-triphosphate in vitro in primary human hepatocytes and in vivo in dog liver following oral administration.
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Affiliation(s)
- Guangyi Wang
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Natalia Dyatkina
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Marija Prhavc
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Caroline Williams
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Vladimir Serebryany
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Yujian Hu
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P. R. China
| | - Yongfei Huang
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P. R. China
| | - Xiangyang Wu
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, P. R. China
| | - Tongqian Chen
- Pharmaron Beijing, Co. Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, P. R. China
| | - Wensheng Huang
- Pharmaron Beijing, Co. Ltd., No. 6, TaiHe Road, BDA, Beijing 100176, P. R. China
| | - Vivek K Rajwanshi
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Jerome Deval
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Amy Fung
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Zhinan Jin
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Antitsa Stoycheva
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Kenneth Shaw
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Kusum Gupta
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Yuen Tam
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Andreas Jekle
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - David B Smith
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
| | - Leonid Beigelman
- Janssen BioPharma, Inc., 260 E. Grand Avenue, South San Francisco, California 94080, United States
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10
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Scaletti ER, Vallin KS, Bräutigam L, Sarno A, Warpman Berglund U, Helleday T, Stenmark P, Jemth AS. MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool. J Biol Chem 2020; 295:4761-4772. [PMID: 32144205 PMCID: PMC7152754 DOI: 10.1074/jbc.ra120.012636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/02/2020] [Indexed: 12/17/2022] Open
Abstract
MutT homologue 1 (MTH1) removes oxidized nucleotides from the nucleotide pool and thereby prevents their incorporation into the genome and thereby reduces genotoxicity. We previously reported that MTH1 is an efficient catalyst of O6-methyl-dGTP hydrolysis suggesting that MTH1 may also sanitize the nucleotide pool from other methylated nucleotides. We here show that MTH1 efficiently catalyzes the hydrolysis of N6-methyl-dATP to N6-methyl-dAMP and further report that N6-methylation of dATP drastically increases the MTH1 activity. We also observed MTH1 activity with N6-methyl-ATP, albeit at a lower level. We show that N6-methyl-dATP is incorporated into DNA in vivo, as indicated by increased N6-methyl-dA DNA levels in embryos developed from MTH1 knock-out zebrafish eggs microinjected with N6-methyl-dATP compared with noninjected embryos. N6-methyl-dATP activity is present in MTH1 homologues from distantly related vertebrates, suggesting evolutionary conservation and indicating that this activity is important. Of note, N6-methyl-dATP activity is unique to MTH1 among related NUDIX hydrolases. Moreover, we present the structure of N6-methyl-dAMP-bound human MTH1, revealing that the N6-methyl group is accommodated within a hydrophobic active-site subpocket explaining why N6-methyl-dATP is a good MTH1 substrate. N6-methylation of DNA and RNA has been reported to have epigenetic roles and to affect mRNA metabolism. We propose that MTH1 acts in concert with adenosine deaminase-like protein isoform 1 (ADAL1) to prevent incorporation of N6-methyl-(d)ATP into DNA and RNA. This would hinder potential dysregulation of epigenetic control and RNA metabolism via conversion of N6-methyl-(d)ATP to N6-methyl-(d)AMP, followed by ADAL1-catalyzed deamination producing (d)IMP that can enter the nucleotide salvage pathway.
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Affiliation(s)
- Emma Rose Scaletti
- Department of Biochemistry and Biophysics, Stockholm University S-106 91, Stockholm, Sweden
- Department of Experimental Medical Science, Lund University, Lund 221 00, Sweden
| | - Karl S Vallin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Lars Bräutigam
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Pathology, St. Olavs Hospital, 7006 Trondheim, Norway
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, United Kingdom
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University S-106 91, Stockholm, Sweden
- Department of Experimental Medical Science, Lund University, Lund 221 00, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
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11
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Good SS, Moussa A, Zhou XJ, Pietropaolo K, Sommadossi JP. Preclinical evaluation of AT-527, a novel guanosine nucleotide prodrug with potent, pan-genotypic activity against hepatitis C virus. PLoS One 2020; 15:e0227104. [PMID: 31914458 PMCID: PMC6949113 DOI: 10.1371/journal.pone.0227104] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023] Open
Abstract
Despite the availability of highly effective direct-acting antiviral (DAA) regimens for the treatment of hepatitis C virus (HCV) infections, sustained viral response (SVR) rates remain suboptimal for difficult-to-treat patient populations such as those with HCV genotype 3, cirrhosis or prior treatment experience, warranting development of more potent HCV replication antivirals. AT-527 is the hemi-sulfate salt of AT-511, a novel phosphoramidate prodrug of 2’-fluoro-2’-C-methylguanosine-5'-monophosphate that has potent in vitro activity against HCV. The EC50 of AT-511, determined using HCV laboratory strains and clinical isolates with genotypes 1–5, ranged from 5–28 nM. The active 5'-triphosphate metabolite, AT-9010, specifically inhibited the HCV RNA-dependent RNA polymerase. AT-511 did not inhibit the replication of other selected RNA or DNA viruses in vitro. AT-511 was approximately 10-fold more active than sofosbuvir (SOF) against a panel of laboratory strains and clinical isolates of HCV genotypes 1–5 and remained fully active against S282T resistance-associated variants, with up to 58-fold more potency than SOF. In vitro, AT-511 did not inhibit human DNA polymerases or elicit cytotoxicity or mitochondrial toxicity at concentrations up to 100 μM. Unlike the other potent guanosine analogs PSI-938 and PSI-661, no mutagenic O6-alkylguanine bases were formed when incubated with cytochrome P450 (CYP) 3A4, and AT-511 had IC50 values ≥25 μM against a panel of CYP enzymes. In hepatocytes from multiple species, the active triphosphate was the predominant metabolite produced from the prodrug, with a half-life of 10 h in human hepatocytes. When given orally to rats and monkeys, AT-527 preferentially delivered high levels of AT-9010 in the liver in vivo. These favorable preclinical attributes support the ongoing clinical development of AT-527 and suggest that, when used in combination with an HCV DAA from a different class, AT-527 may increase SVR rates, especially for difficult-to-treat patient populations, and could potentially shorten treatment duration for all patients.
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Affiliation(s)
- Steven S. Good
- Atea Pharmaceuticals, Inc., Boston, Massachusetts, United States of America
- * E-mail:
| | - Adel Moussa
- Atea Pharmaceuticals, Inc., Boston, Massachusetts, United States of America
| | - Xiao-Jian Zhou
- Atea Pharmaceuticals, Inc., Boston, Massachusetts, United States of America
| | - Keith Pietropaolo
- Atea Pharmaceuticals, Inc., Boston, Massachusetts, United States of America
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12
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Jia Q, Xie W. Alternative conformation induced by substrate binding for Arabidopsis thalianaN6-methyl-AMP deaminase. Nucleic Acids Res 2019; 47:3233-3243. [PMID: 30721978 PMCID: PMC6451127 DOI: 10.1093/nar/gkz070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/03/2022] Open
Abstract
Adenosine deaminase is involved in adenosine degradation and salvage pathway, and plays important physiological roles in purine metabolism. Recently, a novel type of adenosine deaminase-like protein has been identified, which displays deamination activity toward N6-methyl-adenosine monophosphate but not adenosine or AMP, and was consequently named N6-methyl-AMP deaminase (MAPDA). The underlying structural basis of MAPDA recognition and catalysis is poorly understood. Here, we present the crystal structures of MAPDA from Arabidopsis thaliana in the free and in the ligand-bound forms. The protein contains a conserved (β/α)8 Tim-barrel domain and a typical zinc-binding site, but it also exhibits idiosyncratic local differences for two flexible helices important for substrate binding. The extensive interactions between the N6-methyl-AMP substrate or the inosine monophosphate product and the enzyme were identified, and subsequently evaluated by the deamination activity assays. Importantly, each structure reported here represents a different stage of the catalytic pathway and their structural differences suggested that the enzyme can exist in two distinct conformational states. The open state switches to the closed one upon the binding of ligands, brought about by the two critical helices. Our structural studies provide the first look of this important metabolic enzyme and shed lights on its catalytic pathway, which holds promise for the structure-based drug design for MAPDA-related diseases.
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Affiliation(s)
- Qian Jia
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, People's Republic of China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, 510006, People's Republic of China
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13
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Safety, pharmacokinetics and antiviral activity of AT-527, a novel purine nucleotide prodrug, in HCV-infected subjects with and without cirrhosis. Antimicrob Agents Chemother 2019:AAC.01201-19. [PMID: 31570394 PMCID: PMC6879261 DOI: 10.1128/aac.01201-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AT-527 is a novel modified guanosine nucleotide prodrug inhibitor of the hepatitis C virus (HCV) NS5B polymerase, with increased in vitro antiviral activity compared to sofosbuvir and a highly differentiated favorable preclinical profile compared to other anti-HCV nucleoside/nucleotide analogs. AT-527 is a novel modified guanosine nucleotide prodrug inhibitor of the hepatitis C virus (HCV) NS5B polymerase, with increased in vitro antiviral activity compared to sofosbuvir and a highly differentiated favorable preclinical profile compared to other anti-HCV nucleoside/nucleotide analogs. This was a multiple-part clinical study where multiple ascending doses of AT-527 up to 600 mg (expressed as AT-527 salt form; equivalent to 553 mg free base) once daily for 7 days were evaluated in a randomized, double-blind, placebo-controlled study of treatment-naive, noncirrhotic, genotype 1b, HCV-infected subjects. The highest dose of AT-527 for the same duration was then evaluated in two open-label cohorts of (i) noncirrhotic, genotype 3, HCV-infected subjects and (ii) HCV-infected subjects of any genotype with compensated (Child-Pugh A) cirrhosis. AT-527 was well tolerated for 7 days in all cohorts. At the highest dose tested, mean HCV RNA reductions of up to 2.4 log10 IU/ml occurred within the first 24 h of dosing. Mean maximum reductions observed with 7 days of dosing were 4.4, 4.5, and 4.6 log10 IU/ml in noncirrhotic subjects with HCV genotype 1b, noncirrhotic subjects with HCV genotype 3, and subjects with compensated cirrhosis, respectively. The systemic half-life of AT-273, the nucleoside metabolite considered a surrogate of intracellular phosphates including the active triphosphate, exceeded 20 h, supporting once-daily dosing. In summary, AT-527 demonstrated rapid, potent, dose/exposure-related, and pangenotypic antiviral activity with similar responses between subjects with and without cirrhosis. Exposure-antiviral response analysis identified 550 mg (free base equivalent) as the optimal dose of AT-527. Safety and antiviral activity data from this study warrant continued clinical development of AT-527 dosed once daily. (This study has been registered in the European Union Drug Regulating Authorities Clinical Trials Database [EudraCT] under number 2017-002148-34 and at ClinicalTrials.gov under identifier NCT03219957.)
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14
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Activation of 6-Alkoxy-Substituted Methylenecyclopropane Nucleoside Analogs Requires Enzymatic Modification by Adenosine Deaminase-Like Protein 1. Antimicrob Agents Chemother 2019; 63:AAC.01301-19. [PMID: 31332074 DOI: 10.1128/aac.01301-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 07/19/2019] [Indexed: 01/09/2023] Open
Abstract
To determine the mechanism of action of third-generation methylenecyclopropane nucleoside analogs (MCPNAs), DNA sequencing of herpes simplex virus 1 (HSV-1) isolates resistant to third-generation MCPNAs resulted in the discovery of G841S and N815S mutations in HSV-1 UL30. Purified HSV-1 UL30 or human cytomegalovirus (HCMV) UL54 was then subjected to increasing concentrations of MBX-2168-triphosphate (TP), with results demonstrating a 50% inhibitory concentration (IC50) of ∼200 μM, indicating that MBX-2168-TP does not inhibit the viral DNA polymerase. Further metabolic studies showed the removal of a moiety on the guanine ring of MBX-2168. Therefore, we hypothesized that enzymatic removal of a moiety at the 6-position of the guanine ring of third-generation MCPNAs is an essential step in activation. To test this hypothesis, pentostatin (deoxycoformycin [dCF]), an adenosine deaminase-like protein 1 (ADAL-1) inhibitor, was coincubated with MBX-2168. The results showed that dCF antagonized the effect of MBX-2168, with a >40-fold increase in the 50% effective concentration (EC50) at 50 μM dCF (EC50 of 63.1 ± 8.7 μM), compared with MBX-2168 alone (EC50 of 0.2 ± 0.1 μM). Purified ADAL-1 demonstrated time-dependent removal of the moiety on the guanine ring of MBX-2168-monophosphate (MP), with a Km of 17.5 ± 2.4 μM and a V max of 0.12 ± 0.04 nmol min-1 Finally, synguanol-TP demonstrated concentration-dependent inhibition of HSV-1 UL30 and HCMV UL54, with IC50s of 0.33 ± 0.16 and 0.38 ± 0.11 μM, respectively. We conclude that ADAL-1 is the enzyme responsible for removing the moiety from the guanine ring of MBX-2168-MP prior to conversion to a TP, the active compound that inhibits the viral DNA polymerase.
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Wu B, Zhang D, Nie H, Shen S, Li Y, Li S. Structure of Arabidopsis thaliana N6-methyl-AMP deaminase ADAL with bound GMP and IMP and implications for N6-methyl-AMP recognition and processing. RNA Biol 2019; 16:1504-1512. [PMID: 31318636 DOI: 10.1080/15476286.2019.1642712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Arabidopsis thaliana aminohydrolase (AtADAL) has been shown to be involved in the metabolism of N6-methyl-AMP, a proposed intermediate during m6A-modified RNA metabolism, which can be subsequently incorporated into newly synthesized RNA by Pol II. It has been proposed that AtADAL will prevent N6-methyl-AMP reuse and catabolize it to inosine monophosphate (IMP). Here, we have solved the crystal structures of AtADAL in the apo form and in complex with GMP and IMP in the presence of Zn2+. We have identified the substrate-binding pocket of AtADAL and compared it with that for adenosine deaminase (ADA), adenine deaminase (ADE) and AMP deaminase (AMPD) from multiple species. The comparisons reveal that plant ADAL1 may have the potential ability to catalyze different alkyl-group substituted substrates.
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Affiliation(s)
- Baixing Wu
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Dong Zhang
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Hongbo Nie
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Senlin Shen
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Yan Li
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
| | - Sisi Li
- Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China
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16
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Zhou L, Zhang H, Tao S, Ehteshami M, Cho JH, McBrayer TR, Tharnish P, Whitaker T, Amblard F, Coats SJ, Schinazi RF. Synthesis and Evaluation of 2,6-Modified Purine 2'-C-Methyl Ribonucleosides as Inhibitors of HCV Replication. ACS Med Chem Lett 2016; 7:17-22. [PMID: 26819659 DOI: 10.1021/acsmedchemlett.5b00402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 11/23/2015] [Indexed: 01/22/2023] Open
Abstract
A variety of 2,6-modified purine 2'-C-methylribonucleosides and their phosphoramidate prodrugs were synthesized and evaluated for inhibition of HCV RNA replication in Huh-7 cells and for cytotoxicity in various cell lines. Cellular pharmacology and HCV polymerase incorporation studies on the most potent and selective compound are reported.
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Affiliation(s)
- Longhu Zhou
- Center for AIDS Research, Laboratory of
Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | - Hongwang Zhang
- Center for AIDS Research, Laboratory of
Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | - Sijia Tao
- Center for AIDS Research, Laboratory of
Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | - Maryam Ehteshami
- Center for AIDS Research, Laboratory of
Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | - Jong Hyun Cho
- Center for AIDS Research, Laboratory of
Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | | | - Philip Tharnish
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Tony Whitaker
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of
Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | - Steven J. Coats
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of
Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
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17
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Zhou L, Zhang HW, Tao S, Bassit L, Whitaker T, McBrayer TR, Ehteshami M, Amiralaei S, Pradere U, Cho JH, Amblard F, Bobeck D, Detorio M, Coats SJ, Schinazi RF. β-D-2'-C-Methyl-2,6-diaminopurine Ribonucleoside Phosphoramidates are Potent and Selective Inhibitors of Hepatitis C Virus (HCV) and Are Bioconverted Intracellularly to Bioactive 2,6-Diaminopurine and Guanosine 5'-Triphosphate Forms. J Med Chem 2015; 58:3445-58. [PMID: 25849312 PMCID: PMC7714489 DOI: 10.1021/jm501874e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The conversion of selected β-D-2,6-diaminopurine nucleosides (DAPNs) to their phosphoramidate prodrug (PD) substantially blocks the conversion to the G-analog allowing for the generation of two bioactive nucleoside triphosphates (NTPs) in human hepatocytes. A variety of 2'-C-methyl DAPN-PDs were prepared and evaluated for inhibition of HCV viral replication in Huh-7 cells, cytotoxicity in various cell lines, and cellular pharmacology in both Huh-7 and primary human liver cells. The DAPN-PDs were pan-genotypic, effective against various HCV resistant mutants, and resistant variants could not be selected. 2'-C-Me-DAPN-TP and 2'-C-Me-GTP were chain terminators for genotype 1b HCV-pol, and single nucleotide incorporation assays revealed that 2'-C-Me-DAPN-TP was incorporated opposite U. No cytotoxicity was observed with our DAPN-PD when tested up to 50 μM. A novel, DAPN-PD, 15c, has been selected for further evaluation because of its good virologic and toxicologic profile and its ability to deliver two active metabolites, potentially simplifying HCV treatment.
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Affiliation(s)
- Longhu Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Hong-wang Zhang
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Sijia Tao
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
| | - Tony Whitaker
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Tamara R. McBrayer
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Maryam Ehteshami
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Sheida Amiralaei
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Ugo Pradere
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Jong Hyun Cho
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
| | - Drew Bobeck
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Mervi Detorio
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
| | - Steven J. Coats
- CoCrystal Pharma, Inc., Tucker, Georgia 30084, United States
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Veterans Affairs Medical Center, Decatur, Georgia 30033, United States
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18
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Iglesias LE, Lewkowicz ES, Medici R, Bianchi P, Iribarren AM. Biocatalytic approaches applied to the synthesis of nucleoside prodrugs. Biotechnol Adv 2015; 33:412-34. [PMID: 25795057 DOI: 10.1016/j.biotechadv.2015.03.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 03/01/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Nucleosides are valuable bioactive molecules, which display antiviral and antitumour activities. Diverse types of prodrugs are designed to enhance their therapeutic efficacy, however this strategy faces the troublesome selectivity issues of nucleoside chemistry. In this context, the aim of this review is to give an overview of the opportunities provided by biocatalytic procedures in the preparation of nucleoside prodrugs. The potential of biocatalysis in this research area will be presented through examples covering the different types of nucleoside prodrugs: nucleoside analogues as prodrugs, nucleoside lipophilic prodrugs and nucleoside hydrophilic prodrugs.
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Affiliation(s)
- Luis E Iglesias
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Elizabeth S Lewkowicz
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Rosario Medici
- Biocatalysis Group, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Paola Bianchi
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Adolfo M Iribarren
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina; Laboratorio de Química de Ácidos Nucleicos, INGEBI-CONICET, Vuelta de Obligado 2490, 1428 Ciudad Autónoma de Buenos Aires, Argentina.
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Cortés A, Gracia E, Moreno E, Mallol J, Lluís C, Canela EI, Casadó V. Moonlighting Adenosine Deaminase: A Target Protein for Drug Development. Med Res Rev 2014; 35:85-125. [DOI: 10.1002/med.21324] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Antoni Cortés
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Eduard Gracia
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Estefania Moreno
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Josefa Mallol
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Carme Lluís
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Enric I. Canela
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
| | - Vicent Casadó
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED); Institute of Biomedicine of the University of Barcelona (IBUB); Department of Biochemistry and Molecular Biology; Faculty of Biology; University of Barcelona; Barcelona Spain
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20
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Fu XZ, Jiang FJ, Ou Y, Fu S, Cha YF, Zhang S, Liu ZY, Zhou W, Wang AM, Wang YL. Synthesis and anti-HBV evaluation of mono l-amino acid ester, mono non-steroid anti-inflammation drug carboxylic ester derivatives of acyclonucleoside phosphonates. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2013.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1. PLoS One 2013; 8:e80755. [PMID: 24260472 PMCID: PMC3834327 DOI: 10.1371/journal.pone.0080755] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 10/15/2013] [Indexed: 11/19/2022] Open
Abstract
The gene dnph1 (or rcl) encodes a hydrolase that cleaves the 2’-deoxyribonucleoside 5’-monophosphate (dNMP) N-glycosidic bond to yield a free nucleobase and 2-deoxyribose 5-phosphate. Recently, the crystal structure of rat DNPH1, a potential target for anti-cancer therapies, suggested that various analogs of AMP may inhibit this enzyme. From this result, we asked whether N6-substituted AMPs, and among them, cytotoxic cytokinin riboside 5’-monophosphates, may inhibit DNPH1. Here, we characterized the structural and thermodynamic aspects of the interactions of these various analogs with DNPH1. Our results indicate that DNPH1 is inhibited by cytotoxic cytokinins at concentrations that inhibit cell growth.
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22
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Meneghesso S, Vanderlinden E, Brancale A, Balzarini J, Naesens L, McGuigan C. Synthesis and Biological Evaluation of Purine 2′-Fluoro-2′-deoxyriboside ProTides as Anti-influenza Virus Agents. ChemMedChem 2013; 8:415-25. [DOI: 10.1002/cmdc.201200562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/08/2013] [Indexed: 11/10/2022]
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23
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Bourdin C, McGuigan C, Brancale A, Chamberlain S, Vernachio J, Hutchins J, Gorovits E, Kolykhalov A, Muhammad J, Patti J, Henson G, Bleiman B, Bryant KD, Ganguly B, Hunley D, Obikhod A, Walters CR, Wang J, Ramamurty CVS, Battina SK, Srivinas Rao C. Synthesis and evaluation against hepatitis C virus of 7-deaza analogues of 2'-C-methyl-6-O-methyl guanosine nucleoside and L-Alanine ester phosphoramidates. Bioorg Med Chem Lett 2012; 23:2260-4. [PMID: 23453067 DOI: 10.1016/j.bmcl.2012.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/03/2012] [Accepted: 12/04/2012] [Indexed: 11/24/2022]
Abstract
7-Deazapurines are known to possess broad antiviral activity, however the 2'-C-methylguanosine analogue displays poor cell permeation and limited phosphorylation, thus is not an efficient inhibitor of hepatitis C virus (HCV) replication. We previously reported the 6-O-methyl entity as a prodrug moiety to increase liphophilicity of guanine nucleosides and the ProTide approach applied to 2'-C-methyl-6-O-methylguanosine has lead to potent HCV inhibitors now in clinical trials. In this Letter, we report the synthesis and biological evaluation of 2'-C-methyl-6-O-methyl-7-deaza guanosine and ProTide derivatives. In contrast to prior studies, removal of the N-7 of the nucleobase entirely negates anti-HCV activity compared to the 2'-C-methyl-6-O-methylguanosine analogues. To understand better this significant loss of activity, enzymatic assays and molecular modeling were carried out and suggested 2'-C-methyl-6-O-methyl-7-deaza guanosine and related ProTides do not act as efficient prodrugs of the free nucleotide, in marked contrast to the case of the parent guanine analogue.
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Affiliation(s)
- Claire Bourdin
- School of Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
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24
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Du J, Bao D, Chun BK, Jiang Y, Reddy PG, Zhang HR, Ross BS, Bansal S, Bao H, Espiritu C, Lam AM, Murakami E, Niu C, Micolochick Steuer HM, Furman PA, Otto MJ, Sofia MJ. β-D-2'-α-F-2'-β-C-Methyl-6-O-substituted 3',5'-cyclic phosphate nucleotide prodrugs as inhibitors of hepatitis C virus replication: a structure-activity relationship study. Bioorg Med Chem Lett 2012; 22:5924-9. [PMID: 22892115 DOI: 10.1016/j.bmcl.2012.07.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 11/26/2022]
Abstract
The 3',5'-cyclic phosphate prodrug 9-[β-d-2'-deoxy-2'-α-fluoro-2'-β-C-methylribofuranosyl]-2-amino-6-ethoxypurine, PSI-352938 1, has demonstrated promising anti-HCV efficacy in vitro and in human clinical trials. A structure-activity relationship study of the nucleoside 3',5'-cyclic phosphate series of β-d-2'-deoxy-2'-α-fluoro-2'-β-C-methylribofuranosyl nucleoside prodrugs was undertaken and the anti-HCV activity and in vitro safety profile were assessed. Cycloalkyl 3',5'-cyclic phosphate prodrugs were shown to be significantly more potent as inhibitors of HCV replication than branched and straight chain alkyl 3',5'-cyclic phosphate prodrugs. No cytotoxicity and mitochondrial toxicity for prodrugs 12, 13 and 19 were observed at concentrations up to 100 μm in vitro. Cycloalkyl esters of 3',5'-cyclic phosphate nucleotide prodrugs demonstrated the ability to produce high levels of active triphosphate in clone-A cells and primary human hepatocytes. Compounds 12, 13 and 19 also demonstrated the ability to effectively deliver in vivo high levels of active nucleoside phosphates to rat liver.
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Affiliation(s)
- Jinfa Du
- Pharmasset, Inc., Princeton 303A College Road East, Princeton, NJ 08540, USA.
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Metabolic activation of the anti-hepatitis C virus nucleotide prodrug PSI-352938. Antimicrob Agents Chemother 2012; 56:3767-75. [PMID: 22526308 DOI: 10.1128/aac.00530-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PSI-352938 is a novel cyclic phosphate prodrug of β-D-2'-deoxy-2'-α-fluoro-2'-β-C-methylguanosine-5'-monophosphate with potent anti-HCV activity. In order to inhibit the NS5B RNA-dependent RNA polymerase, PSI-352938 must be metabolized to the active triphosphate form, PSI-352666. During in vitro incubations with PSI-352938, significantly larger amounts of PSI-352666 were formed in primary hepatocytes than in clone A hepatitis C virus (HCV) replicon cells. Metabolism and biochemical assays were performed to define the molecular mechanism of PSI-352938 activation. The first step, removal of the isopropyl group on the 3',5'-cyclic phosphate moiety, was found to be cytochrome P450 (CYP) 3A4 dependent, with other CYP isoforms unable to catalyze the reaction. The second step, opening of the cyclic phosphate ring, was catalyzed by phosphodiesterases (PDEs) 2A1, 5A, 9A, and 11A4, all known to be expressed in the liver. The role of these enzymes in the activation of PSI-352938 was confirmed in primary human hepatocytes, where prodrug activation was reduced by inhibitors of CYP3A4 and PDEs. The third step, removal of the O(6)-ethyl group on the nucleobase, was shown to be catalyzed by adenosine deaminase-like protein 1. The resulting monophosphate was consecutively phosphorylated to the diphosphate and to the triphosphate PSI-352666 by guanylate kinase 1 and nucleoside diphosphate kinase, respectively. In addition, formation of nucleoside metabolites was observed in primary hepatocytes, and ecto-5'-nucleotidase was able to dephosphorylate the monophosphate metabolites. Since CYP3A4 is highly expressed in the liver, the CYP3A4-dependent metabolism of PSI-352938 makes it an effective liver-targeted prodrug, in part accounting for the potent antiviral activity observed clinically.
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