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Kothapalli Y, Jones RA, Chu CK, Singh US. Synthesis of Fluorinated Nucleosides/Nucleotides and Their Antiviral Properties. Molecules 2024; 29:2390. [PMID: 38792251 PMCID: PMC11124531 DOI: 10.3390/molecules29102390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The FDA has approved several drugs based on the fluorinated nucleoside pharmacophore, and numerous drugs are currently in clinical trials. Fluorine-containing nucleos(t)ides offer significant antiviral and anticancer activity. The insertion of a fluorine atom, either in the base or sugar of nucleos(t)ides, alters its electronic and steric parameters and transforms the lipophilicity, pharmacodynamic, and pharmacokinetic properties of these moieties. The fluorine atom restricts the oxidative metabolism of drugs and provides enzymatic metabolic stability towards the glycosidic bond of the nucleos(t)ide. The incorporation of fluorine also demonstrates additional hydrogen bonding interactions in receptors with enhanced biological profiles. The present article discusses the synthetic methodology and antiviral activities of FDA-approved drugs and ongoing fluoro-containing nucleos(t)ide drug candidates in clinical trials.
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Affiliation(s)
| | | | - Chung K. Chu
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (Y.K.); (R.A.J.)
| | - Uma S. Singh
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (Y.K.); (R.A.J.)
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2
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Sun M, Manson ML, Guo T, de Lange ECM. CNS Viral Infections-What to Consider for Improving Drug Treatment: A Plea for Using Mathematical Modeling Approaches. CNS Drugs 2024; 38:349-373. [PMID: 38580795 PMCID: PMC11026214 DOI: 10.1007/s40263-024-01082-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Neurotropic viruses may cause meningitis, myelitis, encephalitis, or meningoencephalitis. These inflammatory conditions of the central nervous system (CNS) may have serious and devastating consequences if not treated adequately. In this review, we first summarize how neurotropic viruses can enter the CNS by (1) crossing the blood-brain barrier or blood-cerebrospinal fluid barrier; (2) invading the nose via the olfactory route; or (3) invading the peripheral nervous system. Neurotropic viruses may then enter the intracellular space of brain cells via endocytosis and/or membrane fusion. Antiviral drugs are currently used for different viral CNS infections, even though their use and dosing regimens within the CNS, with the exception of acyclovir, are minimally supported by clinical evidence. We therefore provide considerations to optimize drug treatment(s) for these neurotropic viruses. Antiviral drugs should cross the blood-brain barrier/blood cerebrospinal fluid barrier and pass the brain cellular membrane to inhibit these viruses inside the brain cells. Some antiviral drugs may also require intracellular conversion into their active metabolite(s). This illustrates the need to better understand these mechanisms because these processes dictate drug exposure within the CNS that ultimately determine the success of antiviral drugs for CNS infections. Finally, we discuss mathematical model-based approaches for optimizing antiviral treatments. Thereby emphasizing the potential of CNS physiologically based pharmacokinetic models because direct measurement of brain intracellular exposure in living humans faces ethical restrictions. Existing physiologically based pharmacokinetic models combined with in vitro pharmacokinetic/pharmacodynamic information can be used to predict drug exposure and evaluate efficacy of antiviral drugs within the CNS, to ultimately optimize the treatments of CNS viral infections.
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Affiliation(s)
- Ming Sun
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Martijn L Manson
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Tingjie Guo
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Elizabeth C M de Lange
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Center for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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3
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Gniech T, Humboldt A, Keith KA, James SH, Richert C. A ProTide of AZT Shows Activity Against Human Papillomaviruses. ChemMedChem 2024; 19:e202300661. [PMID: 38241205 DOI: 10.1002/cmdc.202300661] [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: 11/26/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 01/21/2024]
Abstract
Infection by human papillomaviruses (HPV) can cause warts and tumors. So far, no small molecule antiviral has been approved for the treatment of infections with this DNA virus, although preclinical studies show activity for nucleosidic compounds, such as 9-(2-phosphonylmethoxy)ethylguanine (PMEG) or cidofovir. This prompted us to test new prodrug versions of the nucleoside analog 3'-azido-2',3'-dideoxythymidine (AZT), known to be active against reverse transcriptases and approved for the treatment of HIV. Here we report the synthesis of an ethylbutyl alaninyl ester phosphosphoramidate prodrug of AZT, dubbed AZAEB, and its activity against HPV, a target not known to be sensitive to AZT. A methyl ester derivative was found to be inactive against this and three other DNA viruses, while the phosphoramidate prodrug AZAEB showed a modest inhibitory effect against HPV types 6, 11, 18 and 31. Our results open up new avenues of study for the treatment of diseases caused by members of the papillomaviridae family.
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Affiliation(s)
- Tim Gniech
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Adrian Humboldt
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Kathy A Keith
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Scott H James
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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4
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Humboldt A, Rami F, Topp FM, Arnold D, Göhringer D, Pallan PS, Egli M, Richert C. Prolinyl Phosphoramidates of Nucleotides with Increased Reactivity. Angew Chem Int Ed Engl 2024; 63:e202319958. [PMID: 38300702 DOI: 10.1002/anie.202319958] [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: 12/23/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Nucleoside monophosphates (NMPs) are the subunits of RNA. They are incorporated into growing complementary strands when sequences are copied in enzyme-free reactions using organic leaving groups at the phosphates. Amino acids are rarely considered as leaving groups, but proline can act as a leaving group when N-linked to NMPs, so that prolinyl NMPs hydrolyze in aqueous buffer at 37 °C, with half-life times as short as 2.4 h, and they act as monomers in enzyme-free primer extension. Still, their level of reactivity is insufficient for practical purposes, requiring months for some extensions. Herein we report the synthesis of eight substituted prolinyl AMPs together with seven related compounds and the results of a study of their reactivity. A δ-carboxy prolinyl NMP was found to be converted with a half-life time of just 11 min in magnesium-free buffer, and a δ-isopropyl prolinyl NMP was shown to react sevenfold faster than its prolinyl counterpart in enzyme-free genetic copying of RNA. Our results indicate that both anchimeric and steric effects can be employed to increase the reactivity of aminoacidyl nucleotides, i.e. compounds that combine two fundamental classes of biomolecules in one functional entity.
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Affiliation(s)
- Adrian Humboldt
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Fabian Rami
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Franka M Topp
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Dejana Arnold
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Daniela Göhringer
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee, 37232, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee, 37232, USA
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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5
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Jia X, Kullik GA, Bufano M, Brancale A, Schols D, Meier C. Membrane-permeable tenofovir-di- and monophosphate analogues. Eur J Med Chem 2024; 264:116020. [PMID: 38086193 DOI: 10.1016/j.ejmech.2023.116020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
The development of new antiviral agents such as nucleoside analogues or acyclic nucleotide analogues (ANPs) and prodrugs thereof is an ongoing task. We report on the synthesis of three types of lipophilic triphosphate analogues of (R)-PMPA and dialkylated diphosphate analogues of (R)-PMPA. A highly selective release of the different nucleotide analogues ((R)-PMPA-DP, (R)-PMPA-MP, and (R)-PMPA) from these compounds was achieved. All dialkylated (R)-PMPA-prodrugs proved to be very stable in PBS as well as in CEM/0 cell extracts and human plasma. In primer extension assays, both the monoalkylated and the dialkylated (R)-PMPA-DP derivatives acted as (R)-PMPA-DP as a substrate for HIV-RT. In contrast, no incorporation events were observed using human polymerase γ. The dialkylated (R)-PMPA-compounds exhibited significant anti-HIV efficacy in HIV-1/2 infected cells (CEM/0 and CEM/TK-). Remarkably, the dialkylated (R)-PMPA-MP derivative 9a showed a 326-fold improved activity as compared to (R)-PMPA in HIV-2 infected CEM/TK- cells as well as a very high SI of 14,000. We are convinced that this study may significantly contribute to advancing antiviral agents developed based on nucleotide analogues in the future.
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Affiliation(s)
- Xiao Jia
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Giuliano A Kullik
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Marianna Bufano
- Dipartimento Chimica e Tecnologie del Farmaco, Facoltà di Farmacia e Medicina, University of Rome "La Sapienza", Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Andrea Brancale
- Department of Organic Chemistry, Vysoká Škola Chemicko-Technologická v Praze, Technická 5, 16628, Prague, Czech Republic
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Chris Meier
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany; Centre for Structural Systems Biology (CSSB), Hamburg, DESY Campus, Notkestrasse 85, D-22607, Hamburg, Germany.
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6
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Krishna Rao MV, Kareem S, Vali SR, Subba Reddy BV. Recent advances in metal directed C-H amidation/amination using sulfonyl azides and phosphoryl azides. Org Biomol Chem 2023; 21:8426-8462. [PMID: 37831479 DOI: 10.1039/d3ob01160g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Transition metal-catalyzed C-N bond formation reactions have gained popularity as a method for selectively transforming common C-H bonds into N-functionalized molecules. This approach is particularly useful for synthesizing aminated molecules, which require aminating reagents and amidated building blocks. Over the past two decades, significant advancements have been achieved in transition-metal-catalyzed C-H functionalization, with organic azides emerging as promising amino sources and internal oxidants. This review focuses on recent developments in utilizing sulfonyl and phosphoryl azides as building blocks for directed intra- and intermolecular C-H functionalization reactions. Specifically, it discusses methods for synthesizing sulfonamidates and phosphoramidates using sulfonyl and phosphoryl azides, respectively. The article highlights the potential of C-H functionalization reactions with organic azides for efficiently and sustainably synthesizing N-functionalized molecules, providing valuable insights into the latest advancements in this field.
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Affiliation(s)
- M V Krishna Rao
- Department of Fluoro & Agrochemicals, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007, India.
| | - Shaik Kareem
- Department of Fluoro & Agrochemicals, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007, India.
| | - Shaik Ramjan Vali
- Department of Fluoro & Agrochemicals, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007, India.
| | - B V Subba Reddy
- Department of Fluoro & Agrochemicals, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007, India.
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7
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Ojeda-Porras AC, Roy V, Bourzikat O, Favetta P, Agrofoglio LA. Cobalt-assisted route to rare carbocyclic C-ribonucleosides. RSC Adv 2023; 13:30777-30786. [PMID: 37869399 PMCID: PMC10587889 DOI: 10.1039/d3ra04937j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023] Open
Abstract
(Re)emerging RNA viruses have been major threats to public health in the past years, and from the few drugs available, nucleoside analogues are still at the cornerstone of the antiviral therapy. Among them, the synthesis of carbocyclic C-nucleosides is suffering from long syntheses and poor yields. Herein we report a concise stereoselective synthesis of rare carbocyclic C-nucleosides (11a-l) bearing non-canonical nucleobases through a cobalt-assisted-route as key step starting from the optically pure (-)-cyclopentenone 1. This approach paves the route for novel carbocyclic C-nucleoside discovery.
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Affiliation(s)
- A C Ojeda-Porras
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
| | - V Roy
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
| | - O Bourzikat
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
| | - P Favetta
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
| | - L A Agrofoglio
- Université d'Orléans et CNRS, ICOA, UMR 7311 F-45067 Orléans France
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8
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Gao LJ, Lin Y, De Jonghe S, Waer M, Herdewijn P. Synthesis of mizoribine prodrugs and their in vivo evaluation as immunosuppressive agents. Bioorg Med Chem Lett 2023; 95:129490. [PMID: 37770001 DOI: 10.1016/j.bmcl.2023.129490] [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: 08/07/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Mizoribine is a well-known immunosuppressive drug, based on a nucleoside scaffold, that targets inosine-monophosphate dehydrogenase (IMPDH). In an effort to increase its in vivo efficacy, three different types of prodrugs (a phosphoramidate prodrug, a lipophilic ester derivative and an amino acid conjugate) were prepared. Screening of these prodrugs in a rapid whole blood assay revealed that the two ester-based mizoribine prodrugs potently inhibited interleukin 2 secretion. Moreover, these prodrugs were able to prolong graft survival, when evaluated in a mouse model of cardiac allograft transplantation. Strikingly, a combination therapy of these mizoribine prodrugs with tacrolimus had a synergistic in vivo effect.
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Affiliation(s)
- Ling-Jie Gao
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, Box 1030, 3000 Leuven, Belgium
| | - Yuan Lin
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Immunology, Herestraat 49, Box 1042, 3000 Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Mark Waer
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Immunology, Herestraat 49, Box 1042, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, Box 1030, 3000 Leuven, Belgium.
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9
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To EE. Cell and Tissue Specific Metabolism of Nucleoside and Nucleotide Drugs: Case Studies and Implications for Precision Medicine. Drug Metab Dispos 2023; 51:360-368. [PMID: 36446610 DOI: 10.1124/dmd.122.000856] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 10/31/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
Many clinically used antiviral drugs are nucleoside or nucleotide analog drugs, which have a unique mechanism of action that requires intracellular phosphorylation. This dependence on intracellular activation presents novel challenges for the discovery and development of nucleoside/nucleotide analog drugs. Contrary to many small molecule drug development programs that rely on plasma pharmacokinetics and systemic exposures, the precise mechanisms that result in efficacious intracellular nucleoside triphosphate concentrations must be understood in the process of nucleoside/nucleotide drug development. The importance is highlighted here, using the following as case studies: the herpes treatment acyclovir, the cytomegalovirus therapy ganciclovir, and human immunodeficiency virus (HIV) treatments based on tenofovir, which are also in use for HIV prophylaxis. For each drug, the specificity of metabolism that results in its activation in different cells or tissues is discussed, and the implications explored. Acyclovir's dependence on a viral enzyme for activation provides selective pressure for resistance mutations. Ganciclovir is also dependent on a viral enzyme for activation, and suicide gene therapy capitalizes on that for a novel oncology treatment. The tissue of most relevance for tenofovir activation depends on its use as treatment or as prophylaxis, and the pharmacogenomics and drug-drug interactions in those tissues must be considered. Finally, differential metabolism of different tenofovir prodrugs and its effects on toxicity risk are explored. Taken together, these examples highlight the importance of understanding tissue specific metabolism for optimal use of nucleoside/nucleotide drugs in the clinic. SIGNIFICANCE STATEMENT: Nucleoside and nucleotide analogue drugs are cornerstones in current antiviral therapy and prevention efforts that require intracellular phosphorylation for activity. Understanding their cell and tissue specific metabolism enables their rational, precision use for maximum efficacy.
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Affiliation(s)
- Elaine E To
- Gilead Sciences, Inc., Foster City, California, USA
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10
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Souza TML, Pinho VD, Setim CF, Sacramento CQ, Marcon R, Fintelman-Rodrigues N, Chaves OA, Heller M, Temerozo JR, Ferreira AC, Mattos M, Momo PB, Dias SSG, Gesto JSM, Pereira-Dutra F, Viola JPB, Queiroz-Junior CM, Guimarães LC, Chaves IM, Guimarães PPG, Costa VV, Teixeira MM, Bou-Habib DC, Bozza PT, Aguillón AR, Siqueira-Junior J, Macedo-Junior S, Andrade EL, Fadanni GP, Tolouei SEL, Potrich FB, Santos AA, Marques NF, Calixto JB, Rabi JA. Preclinical development of kinetin as a safe error-prone SARS-CoV-2 antiviral able to attenuate virus-induced inflammation. Nat Commun 2023; 14:199. [PMID: 36639383 PMCID: PMC9837764 DOI: 10.1038/s41467-023-35928-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Orally available antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are necessary because of the continuous circulation of new variants that challenge immunized individuals. Because severe COVID-19 is a virus-triggered immune and inflammatory dysfunction, molecules endowed with both antiviral and anti-inflammatory activity are highly desirable. We identified here that kinetin (MB-905) inhibits the in vitro replication of SARS-CoV-2 in human hepatic and pulmonary cell lines. On infected monocytes, MB-905 reduced virus replication, IL-6 and TNFα levels. MB-905 is converted into its triphosphate nucleotide to inhibit viral RNA synthesis and induce error-prone virus replication. Coinhibition of SARS-CoV-2 exonuclease, a proofreading enzyme that corrects erroneously incorporated nucleotides during viral RNA replication, potentiated the inhibitory effect of MB-905. MB-905 shows good oral absorption, its metabolites are stable, achieving long-lasting plasma and lung concentrations, and this drug is not mutagenic nor cardiotoxic in acute and chronic treatments. SARS-CoV-2-infected hACE-mice and hamsters treated with MB-905 show decreased viral replication, lung necrosis, hemorrhage and inflammation. Because kinetin is clinically investigated for a rare genetic disease at regimens beyond the predicted concentrations of antiviral/anti-inflammatory inhibition, our investigation suggests the opportunity for the rapid clinical development of a new antiviral substance for the treatment of COVID-19.
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Affiliation(s)
- Thiago Moreno L Souza
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil. .,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil.
| | - Vagner D Pinho
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Cristina F Setim
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Carolina Q Sacramento
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Marcon
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Otavio A Chaves
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Melina Heller
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Jairo R Temerozo
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil.,Laboratório de Pesquisa sobre o Timo, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - André C Ferreira
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil.,Universidade Iguaçu, Nova Iguaçu, RJ, Brazil
| | - Mayara Mattos
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia B Momo
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Suelen S G Dias
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - João S M Gesto
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Filipe Pereira-Dutra
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - João P B Viola
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rua André Cavalcanti 37, 5th floor, Centro, Rio de Janeiro, Brazil
| | - Celso Martins Queiroz-Junior
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Lays Cordeiro Guimarães
- Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ian Meira Chaves
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Pedro Pires Goulart Guimarães
- Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vivian Vasconcelos Costa
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Mauro Martins Teixeira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Instituto de Ciências Biológicas, (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Dumith Chequer Bou-Habib
- National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil.,Laboratório de Pesquisa sobre o Timo, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Anderson R Aguillón
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil
| | - Jarbas Siqueira-Junior
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Sergio Macedo-Junior
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Edineia L Andrade
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Guilherme P Fadanni
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Sara E L Tolouei
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Francine B Potrich
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Adara A Santos
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - Naiani F Marques
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil
| | - João B Calixto
- Centro de Inovação e Ensaios Pré-clínicos and National Institute for Science and Technology on Innovation in Medicines and Identification of New Therapeutics Targets (INCT-INOVAMED). Avenida Luiz Boiteux Piazza, 1302 Cachoeira do Bom Jesus, 88056-000, Florianópolis, SC, Brazil.
| | - Jaime A Rabi
- Microbiológica Química e Farmacêutica, Doutor Nicanor, 238 Inhaúma, Rio de Janeiro, RJ, Brazil.
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11
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Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa I, Passow K, Kennelly S, Moorthy R, Dulin D, Feng J, Harki D, Kirchdoerfer R, Cameron C, Arnold J. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. Nucleic Acids Res 2023; 51:315-336. [PMID: 36546762 PMCID: PMC9841423 DOI: 10.1093/nar/gkac1177] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/11/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022] Open
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Pankaj Srivastava
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas K Anderson
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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12
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Roy B, Navarro V, Peyrottes S. Prodrugs of Nucleoside 5'-Monophosphate Analogues: Overview of the Recent Literature Concerning their Synthesis and Applications. Curr Med Chem 2023; 30:1256-1303. [PMID: 36093825 DOI: 10.2174/0929867329666220909122820] [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: 04/20/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 11/22/2022]
Abstract
Nucleoside analogues are widely used as anti-infectious and antitumoral agents. However, their clinical use may face limitations associated with their physicochemical properties, pharmacokinetic parameters, and/or their peculiar mechanisms of action. Indeed, once inside the cells, nucleoside analogues require to be metabolized into their corresponding (poly-)phosphorylated derivatives, mediated by cellular and/or viral kinases, in order to interfere with nucleic acid biosynthesis. Within this activation process, the first-phosphorylation step is often the limiting one and to overcome this limitation, numerous prodrug approaches have been proposed. Herein, we will focus on recent literature data (from 2015 and onwards) related to new prodrug strategies, the development of original synthetic approaches and novel applications of nucleotide prodrugs (namely pronucleotides) leading to the intracellular delivery of 5'-monophosphate nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
| | - Valentin Navarro
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
| | - Suzanne Peyrottes
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
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13
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Serpi M, Ferrari V, McGuigan C, Ghazaly E, Pepper C. Synthesis and Characterization of NUC-7738, an Aryloxy Phosphoramidate of 3'-Deoxyadenosine, as a Potential Anticancer Agent. J Med Chem 2022; 65:15789-15804. [PMID: 36417756 PMCID: PMC9743095 DOI: 10.1021/acs.jmedchem.2c01348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Indexed: 11/24/2022]
Abstract
3'-Deoxyadenosine (3'-dA, Cordycepin, 1) is a nucleoside analogue with anticancer properties, but its clinical development has been hampered due to its deactivation by adenosine deaminase (ADA) and poor cellular uptake due to low expression of the human equilibrative transporter (hENT1). Here, we describe the synthesis and characterization of NUC-7738 (7a), a 5'-aryloxy phosphoramidate prodrug of 3'-dA. We show in vitro evidence that 7a is an effective anticancer drug in a panel of solid and hematological cancer cell lines, showing its preferential cytotoxic effects on leukemic stem cells. We found that unlike 3'-dA, the activity of 7a was independent of hENT1 and kinase activity. Furthermore, it was resistant to ADA metabolic deactivation. Consistent with these findings, 7a showed increased levels of intracellular 3'-deoxyadenosine triphosphate (3'-dATP), the active metabolite. Mechanistically, levels of intracellular 3'-dATP were strongly associated with in vitro potency. NUC-7738 is now in Phase II, dose-escalation study in patients with advanced solid tumors.
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Affiliation(s)
- Michaela Serpi
- School
of Chemistry, Cardiff University Main Building, Park Place, Cardiff CF10 3AT, Wales, U.K.
| | - Valentina Ferrari
- School
of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, U.K.
| | - Christopher McGuigan
- School
of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, U.K.
| | - Essam Ghazaly
- Centre
for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, U.K.
| | - Chris Pepper
- Brighton
and Sussex Medical School, University of
Sussex, Brighton BN1 9PX, U.K.
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14
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Poudel TN, Panda S, Orimoloye M, Hegde P, Aldrich CC. 1'-Cyano Intermediate Enables Rapid and Stereoretentive Access to 1'-Modified Remdesivir Nucleosides. J Org Chem 2022; 87:14452-14462. [PMID: 36223099 DOI: 10.1021/acs.joc.2c01897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
While biochemical, structural, and computational studies have shown the importance of remdesivir's C1'-substituent in its perturbation of SARS-CoV-2 RdRp action, we recognized the paucity of methods to stereoselectively install substituents at this position as an obstacle to rigorous explorations of SAR and mechanism. We report the utilization of an anomerically pure 1'-cyano intermediate as an entry point to a chemically diverse set of substitutions, allowing for 1'diversification while obviating the need for the tedious separation of anomeric mixtures.
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Affiliation(s)
- Tej Narayan Poudel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Moyosore Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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15
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Inhibition of Viral RNA-Dependent RNA Polymerases by Nucleoside Inhibitors: An Illustration of the Unity and Diversity of Mechanisms. Int J Mol Sci 2022; 23:ijms232012649. [PMID: 36293509 PMCID: PMC9604226 DOI: 10.3390/ijms232012649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
RNA-dependent RNA polymerase (RdRP) is essential for the replication and expression of RNA viral genomes. This class of viruses comprise a large number of highly pathogenic agents that infect essentially all species of plants and animals including humans. Infections often lead to epidemics and pandemics that have remained largely out of control due to the lack of specific and reliable preventive and therapeutic regimens. This unmet medical need has led to the exploration of new antiviral targets, of which RdRP is a major one, due to the fact of its obligatory need in virus growth. Recent studies have demonstrated the ability of several synthetic nucleoside analogs to serve as mimics of the corresponding natural nucleosides. These mimics cause stalling/termination of RdRP, or misincorporation, preventing virus replication or promoting large-scale lethal mutations. Several such analogs have received clinical approval and are being routinely used in therapy. In parallel, the molecular structural basis of their inhibitory interactions with RdRP is being elucidated, revealing both traditional and novel mechanisms including a delayed chain termination effect. This review offers a molecular commentary on these mechanisms along with their clinical implications based on analyses of recent results, which should facilitate the rational design of structure-based antiviral drugs.
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16
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The First 5′-Phosphorylated 1,2,3-Triazolyl Nucleoside Analogues with Uracil and Quinazoline-2,4-Dione Moieties: A Synthesis and Antiviral Evaluation. Molecules 2022; 27:molecules27196214. [PMID: 36234748 PMCID: PMC9573387 DOI: 10.3390/molecules27196214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
A series of 5′-phosphorylated (dialkyl phosphates, diaryl phosphates, phosphoramidates, H-phosphonates, phosphates) 1,2,3-triazolyl nucleoside analogues in which the 1,2,3-triazole-4-yl-β-D-ribofuranose fragment is attached via a methylene group or a butylene chain to the N-1 atom of the heterocycle moiety (uracil or quinazoline-2,4-dione) was synthesized. All compounds were evaluated for antiviral activity against influenza virus A/PR/8/34/(H1N1). Antiviral assays revealed three compounds, 13b, 14b, and 17a, which showed moderate activity against influenza virus A (H1N1) with IC50 values of 17.9 μM, 51 μM, and 25 μM, respectively. In the first two compounds, the quinazoline-2,4-dione moiety is attached via a methylene or a butylene linker, respectively, to the 1,2,3-triazole-4-yl-β-D-ribofuranosyl fragment possessing a 5′-diphenyl phosphate substituent. In compound 17a, the uracil moiety is attached via the methylene unit to the 1,2,3-triazole-4-yl-β-D-ribofuranosyl fragment possessing a 5′-(phenyl methoxy-L-alaninyl)phosphate substituent. The remaining compounds appeared to be inactive against influenza virus A/PR/8/34/(H1N1). The results of molecular docking simulations indirectly confirmed the literature data that the inhibition of viral replication is carried out not by nucleoside analogues themselves, but by their 5′-triphosphate derivatives.
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17
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Chinthapatla R, Sotoudegan M, Anderson T, Moustafa IM, Passow KT, Kennelly SA, Moorthy R, Dulin D, Feng JY, Harki DA, Kirchdoerfer R, Cameron CE, Arnold JJ. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.11.503614. [PMID: 35982684 PMCID: PMC9387131 DOI: 10.1101/2022.08.11.503614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas Anderson
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M. Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T. Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A. Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y. Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert Kirchdoerfer
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E. Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J. Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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18
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Forbes KC, Jacobsen EN. Enantioselective hydrogen-bond-donor catalysis to access diverse stereogenic-at-P(V) compounds. Science 2022; 376:1230-1236. [PMID: 35679409 PMCID: PMC9427129 DOI: 10.1126/science.abp8488] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The stereoselective synthesis of molecules bearing stereogenic phosphorus(V) centers represents an enduring challenge in organic chemistry. Although stereospecific nucleophilic substitution at P(V) provides a general strategy for elaborating optically active P(V) compounds, existing methods for accessing the requisite chiral building blocks rely almost entirely on diastereocontrol using chiral auxiliaries. Catalytic, enantioselective methods for the synthesis of synthetically versatile stereogenic P(V) building blocks offer an alternative approach to stereogenic-at-P(V) targets without requiring stoichiometric quantities of chiral control elements. Here, we report an enantioselective hydrogen-bond-donor-catalyzed synthesis of aryl chlorophosphonamidates and the development of these products as versatile chiral P(V) building blocks. We demonstrate that the two leaving groups on these chlorophosphonamidates can be displaced sequentially and stereospecifically to access a wide variety of stereogenic-at-P(V) compounds featuring diverse substitution patterns.
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Affiliation(s)
- Katherine C. Forbes
- Department of Chemistry and Chemical Biology, Harvard University; Cambridge, MA 02138, USA
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University; Cambridge, MA 02138, USA
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19
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Patel D, Cox BD, Kasthuri M, Mengshetti S, Bassit L, Verma K, Ollinger-Russell O, Amblard F, Schinazi RF. In silico design of a novel nucleotide antiviral agent by free energy perturbation. Chem Biol Drug Des 2022; 99:801-815. [PMID: 35313085 PMCID: PMC9175506 DOI: 10.1111/cbdd.14042] [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: 11/16/2021] [Revised: 02/03/2022] [Accepted: 03/05/2022] [Indexed: 11/30/2022]
Abstract
Nucleoside analogs are the backbone of antiviral therapies. Drugs from this class undergo processing by host or viral kinases to form the active nucleoside triphosphate species that selectively inhibits the viral polymerase. It is the central hypothesis that the nucleoside triphosphate analog must be a favorable substrate for the viral polymerase and the nucleoside precursor must be a satisfactory substrate for the host kinases to inhibit viral replication. Herein, free energy perturbation (FEP) was used to predict substrate affinity for both host and viral enzymes. Several uridine 5'-monophosphate prodrug analogs known to inhibit hepatitis C virus (HCV) were utilized in this study to validate the use of FEP. Binding free energies to the host monophosphate kinase and viral RNA-dependent RNA polymerase (RdRp) were calculated for methyl-substituted uridine analogs. The 2'-C-methyl-uridine and 4'-C-methyl-uridine scaffolds delivered favorable substrate binding to the host kinase and HCV RdRp that were consistent with results from cellular antiviral activity in support of our new approach. In a prospective evaluation, FEP results suggest that 2'-C-dimethyl-uridine scaffold delivered favorable monophosphate and triphosphate substrates for both host kinase and HCV RdRp, respectively. Novel 2'-C-dimethyl-uridine monophosphate prodrug was synthesized and exhibited sub-micromolar inhibition of HCV replication. Using this novel approach, we demonstrated for the first time that nucleoside analogs can be rationally designed that meet the multi-target requirements for antiviral activity.
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Affiliation(s)
- Dharmeshkumar Patel
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Bryan D. Cox
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Mahesh Kasthuri
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Seema Mengshetti
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Kiran Verma
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Olivia Ollinger-Russell
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
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20
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Yoshida Y, Ti Z, Tanabe W, Tomoike F, Hashiya F, Suzuki T, Hirota S, Saiki Y, Horii A, Hirayama A, Soga T, Kimura Y, Abe H. Development of Fluorophosphoramidate as a New Biocompatible Transformable Functional Group and its Application as a Phosphate Prodrug for Nucleoside Analogs. ChemMedChem 2022; 17:e202200188. [PMID: 35393747 DOI: 10.1002/cmdc.202200188] [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: 04/04/2022] [Indexed: 11/12/2022]
Abstract
Synthetic phosphate-derived functional groups are important for controlling the function of bioactive molecules in vivo . Herein we describe the development of a new type of biocompatible phosphate analog, a fluorophosphoramidate (FPA) functional group that has characteristic P-F and P-N bonds. We found that FPA with a primary amino group was relatively unstable in aqueous solution and was converted to a monophosphate, while FPA with a secondary amino group was stable. Furthermore, by improving the molecular design of FPA, we developed a reaction in which a secondary amino group is converted to a primary amino group in the intracellular environment, and clarified that the FPA group functions as a phosphate prodrug of nucleoside. Various FPA-gemcitabine derivatives were synthesized and their anticancer activities were evaluated. One of the FPA-gemcitabine derivatives showed superior anticancer activity compared with gemcitabine and its ProTide prodrug, which methodology is widely used in various nucleoside analogs, including anti-cancer and anti-virus drugs.
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Affiliation(s)
- Yuki Yoshida
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Zheng Ti
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Wataru Tanabe
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Fumiaki Tomoike
- Gakushuin University: Gakushuin Daigaku, Graduate School of Science, JAPAN
| | - Fumitaka Hashiya
- Nagoya University: Nagoya Daigaku, Research Center for Material Science, JAPAN
| | | | - Shuto Hirota
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Yuriko Saiki
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Akira Horii
- Tohoku University: Tohoku Daigaku, School of Medicine, JAPAN
| | - Akiyoshi Hirayama
- Keio University: Keio Gijuku Daigaku, Institute for Biosciences, JAPAN
| | - Tomoyoshi Soga
- Keio University: Keio Gijuku Daigaku, Institute for Advance Biosciences, JAPAN
| | - Yasuaki Kimura
- Nagoya University: Nagoya Daigaku, Graduate School of Science, JAPAN
| | - Hiroshi Abe
- Nagoya University, Department of Chemistry, Graduate School of Science, Furo, Chikusa, 464-8602, Nagoya, JAPAN
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21
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Mackman RL. Phosphoramidate Prodrugs Continue to Deliver, The Journey of Remdesivir (GS-5734) from RSV to SARS-CoV-2. ACS Med Chem Lett 2022; 13:338-347. [PMID: 35291757 PMCID: PMC8887656 DOI: 10.1021/acsmedchemlett.1c00624] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/03/2022] [Indexed: 12/24/2022] Open
Abstract
![]()
Remdesivir (GS-5734) is a monophenol,
2-ethylbutylalanine phosphoramidate
prodrug of a 1′-cyano-4-aza-7,9-dideazaadenosine C-nucleoside
(GS-441524) that is FDA approved for the treatment of hospitalized
patients with COVID-19. The prodrug, initially invented for respiratory
syncytial virus, was later found to have activity toward emerging
RNA viruses, including Ebola and coronaviruses. Remdesivir is among
the first examples of a phosphoramidate prodrug aimed at delivering
a nucleoside monophosphate into lung cells to efficiently generate
the nucleoside triphosphate inhibitor of viral RNA polymerases. With
remdesivir as the central case study, the present work describes the
antiviral potency and in vitro metabolism evidence for lung cell activation
of phosphoramidates, together with their in vivo pharmacokinetics,
lung distribution, and antiviral efficacy toward respiratory viruses.
The lung delivery of nucleoside monophosphate analogs using prodrugs
warrants further investigation toward the development of novel respiratory
antivirals.
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22
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The development of broad-spectrum antiviral medical countermeasures to treat viral hemorrhagic fevers caused by natural or weaponized virus infections. PLoS Negl Trop Dis 2022; 16:e0010220. [PMID: 35259154 PMCID: PMC8903284 DOI: 10.1371/journal.pntd.0010220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense (JPEO-CBRND) began development of a broad-spectrum antiviral countermeasure against deliberate use of high-consequence viral hemorrhagic fevers (VHFs) in 2016. The effort featured comprehensive preclinical research, including laboratory testing and rapid advancement of lead molecules into nonhuman primate (NHP) models of Ebola virus disease (EVD). Remdesivir (GS-5734, Veklury, Gilead Sciences) was the first small molecule therapeutic to successfully emerge from this effort. Remdesivir is an inhibitor of RNA-dependent RNA polymerase, a viral enzyme that is essential for viral replication. Its robust potency and broad-spectrum antiviral activity against certain RNA viruses including Ebola virus and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) led to its clinical evaluation in randomized, controlled trials (RCTs) in human patients during the 2018 EVD outbreak in the Democratic Republic of the Congo (DRC) and the ongoing Coronavirus Disease 2019 (COVID-19) pandemic today. Remdesivir was recently approved by the US Food and Drug Administration (FDA) for the treatment of COVID-19 requiring hospitalization. Substantial gaps remain in improving the outcomes of acute viral infections for patients afflicted with both EVD and COVID-19, including how to increase therapeutic breadth and strategies for the prevention and treatment of severe disease. Combination therapy that joins therapeutics with complimentary mechanisms of action appear promising, both preclinically and in RCTs. Importantly, significant programmatic challenges endure pertaining to a clear drug and biological product development pathway for therapeutics targeting biodefense and emerging pathogens when human efficacy studies are not ethical or feasible. For example, remdesivir's clinical development was facilitated by outbreaks of Ebola and SARS-CoV-2; as such, the development pathway employed for remdesivir is likely to be the exception rather than the rule. The current regulatory licensure pathway for therapeutics targeting rare, weaponizable VHF agents is likely to require use of FDA's established Animal Rule (21 CFR 314.600-650 for drugs; 21 CFR 601.90-95 for biologics). The FDA may grant marketing approval based on adequate and well-controlled animal efficacy studies when the results of those studies establish that the drug is safe and likely to produce clinical benefit in humans. In practical terms, this is anticipated to include a series of rigorous, well-documented, animal challenge studies, to include aerosol challenge, combined with human safety data. While small clinical studies against naturally occurring, high-consequence pathogens are typically performed where possible, approval for the therapeutics currently under development against biodefense pathogens will likely require the Animal Rule pathway utilizing studies in NHPs. We review the development of remdesivir as illustrative of the effort that will be needed to field future therapeutics against highly lethal, infectious agents.
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23
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Prodrug Therapies for Infectious and Neurodegenerative Diseases. Pharmaceutics 2022; 14:pharmaceutics14030518. [PMID: 35335894 PMCID: PMC8953076 DOI: 10.3390/pharmaceutics14030518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023] Open
Abstract
Prodrugs are bioreversible drug derivatives which are metabolized into a pharmacologically active drug following chemical or enzymatic modification. This approach is designed to overcome several obstacles that are faced by the parent drug in physiological conditions that include rapid drug metabolism, poor solubility, permeability, and suboptimal pharmacokinetic and pharmacodynamic profiles. These suboptimal physicochemical features can lead to rapid drug elimination, systemic toxicities, and limited drug-targeting to disease-affected tissue. Improving upon these properties can be accomplished by a prodrug design that includes the careful choosing of the promoiety, the linker, the prodrug synthesis, and targeting decorations. We now provide an overview of recent developments and applications of prodrugs for treating neurodegenerative, inflammatory, and infectious diseases. Disease interplay reflects that microbial infections and consequent inflammation affects neurodegenerative diseases and vice versa, independent of aging. Given the high prevalence, personal, social, and economic burden of both infectious and neurodegenerative disorders, therapeutic improvements are immediately needed. Prodrugs are an important, and might be said a critical tool, in providing an avenue for effective drug therapy.
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24
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Nucleosides and emerging viruses: a new story. Drug Discov Today 2022; 27:1945-1953. [PMID: 35189369 PMCID: PMC8856764 DOI: 10.1016/j.drudis.2022.02.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/13/2022] [Accepted: 02/16/2022] [Indexed: 12/24/2022]
Abstract
With several US Food and Drug Administration (FDA)-approved drugs and high barriers to resistance, nucleoside and nucleotide analogs remain the cornerstone of antiviral therapies for not only herpesviruses, but also HIV and hepatitis viruses (B and C); however, with the exception of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which vaccines have been developed at unprecedented speed, there are no vaccines or small antivirals yet available for (re)emerging viruses, which are primarily RNA viruses. Thus, herein, we present an overview of ribonucleoside analogs recently developed and acting as inhibitors of the viral RNA-dependent RNA polymerase (RdRp). They are new lead structures that will be exploited for the discovery of new antiviral nucleosides.
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25
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Česnek M, Šafránek M, Dračínský M, Tloušťová E, Mertlíková-Kaiserová H, Hayes MP, Watts VJ, Janeba Z. Halogen-Dance-Based Synthesis of Phosphonomethoxyethyl (PME) Substituted 2-Aminothiazoles as Potent Inhibitors of Bacterial Adenylate Cyclases. ChemMedChem 2022; 17:e202100568. [PMID: 34636150 PMCID: PMC8741643 DOI: 10.1002/cmdc.202100568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/11/2021] [Indexed: 01/07/2023]
Abstract
A series of acyclic nucleoside phosphonates (ANPs) was designed as inhibitors of bacterial adenylate cyclases (ACs), where adenine was replaced with 2-amino-4-arylthiazoles. The target compounds were prepared using the halogen dance reaction. Final AC inhibitors were evaluated in cell-based assays (prodrugs) and cell-free assays (phosphono diphosphates). Novel ANPs were potent inhibitors of adenylate cyclase toxin (ACT) from Bordetella pertussis and edema factor (EF) from Bacillus anthracis, with substantial selectivity over mammalian enzymes AC1, AC2, and AC5. Six of the new ANPs were more potent or equipotent ACT inhibitors (IC50 =9-18 nM), and one of them was more potent EF inhibitor (IC50 =12 nM), compared to adefovir diphosphate (PMEApp) with IC50 =18 nM for ACT and IC50 =36 nM for EF. Thus, these compounds represent the most potent ACT/EF inhibitors based on ANPs reported to date. The potency of the phosphonodiamidates to inhibit ACT activity in J774A.1 macrophage cells was somewhat weaker, where the most potent derivative had IC50 =490 nM compared to IC50 =150 nM of the analogous adefovir phosphonodiamidate. The results suggest that more efficient type of phosphonate prodrugs would be desirable to increase concentrations of the ANP-based active species in the cells in order to proceed with the development of ANPs as potential antitoxin therapeutics.
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Affiliation(s)
- Michal Česnek
- Institute of Organic Chemistry and Biochemistry of the
Czech Academy of Sciences, Flemingovo nám. 542/2, 16000, Prague 6 (Czech
Republic
| | - Michal Šafránek
- Institute of Organic Chemistry and Biochemistry of the
Czech Academy of Sciences, Flemingovo nám. 542/2, 16000, Prague 6 (Czech
Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the
Czech Academy of Sciences, Flemingovo nám. 542/2, 16000, Prague 6 (Czech
Republic
| | - Eva Tloušťová
- Institute of Organic Chemistry and Biochemistry of the
Czech Academy of Sciences, Flemingovo nám. 542/2, 16000, Prague 6 (Czech
Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry of the
Czech Academy of Sciences, Flemingovo nám. 542/2, 16000, Prague 6 (Czech
Republic
| | - Michael P. Hayes
- Department of Medicinal Chemistry and Molecular
Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West
Lafayette, IN – 47907 (USA)
| | - Val J. Watts
- Department of Medicinal Chemistry and Molecular
Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West
Lafayette, IN – 47907 (USA)
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry of the
Czech Academy of Sciences, Flemingovo nám. 542/2, 16000, Prague 6 (Czech
Republic
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26
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Fujita Y. [Remdesivir for COVID-19]. Nihon Yakurigaku Zasshi 2022; 157:31-37. [PMID: 34980809 DOI: 10.1254/fpj.21058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Remdesivir is a direct-acting antiviral agent that inhibits viral RNA synthesis developed by Gilead Sciences, Inc. in the United States. It has been shown to have antiviral activity against single-stranded RNA viruses, including coronaviruses, in cell culture systems and animal models, and has been developed as a therapeutic agent for Ebola virus infection since 2015. however, to date, it has not been approved in any country. A novel coronavirus infection (COVID-19) was identified in Wuhan, Hubei Province, China in Dec, 2019, and is a respiratory disease characterized by fever, cough, and dyspnea. In severe cases, it may cause serious pneumonia, multi-organ failure and death. Gilead Sciences, Inc. U.S. embarked on the development of COVID-19 as a therapeutic drug, using remdesivir, which has shown in vitro and in vivo antiviral activities against MERS-CoV and SARS-CoV, which are single-stranded RNA coronaviruses that cause Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS). The in vitro antiviral activity of remdesivir against SARS-CoV-2, which causes COVID-19, was confirmed and clinical studies were initiated in February 2020. Based on the results of clinical studies conducted by the National Institute of Allergy and Infectious Diseases (NIAID) and Gilead Sciences, Inc. and experience of administration from a compassionate use, an exceptional approval system based on the "Pharmaceuticals and Medical Devices Act" was also approved in Japan as of May 7, 2020 for the indication of "infections caused by SARS-CoV-2." In this article, the background of the development and clinical results of remdesivir are described.
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27
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Said MA, Albohy A, Abdelrahman MA, Ibarhim HS. Remdesivir analog as SARS-CoV-2 polymerase inhibitor: virtual screening of a database generated by scaffold replacement. RSC Adv 2022; 12:22448-22457. [PMID: 36105996 PMCID: PMC9366421 DOI: 10.1039/d2ra00486k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/22/2022] [Indexed: 01/18/2023] Open
Abstract
By the end of 2019, a novel strain of the corona viral family named SARS-CoV-2 emerged in Wuhan, China and started to spread worldwide causing one of the most dangerous lethal pandemics. Researchers utilized various reported inhibitors and drug databases for virtual screening analysis against this novel strain. Later on, they succeeded to fish and repurpose remdesivir, an antiviral nucleotide analogue that inhibits RNA polymerase of the Ebola virus, as a promising candidate against SARS-CoV-2. In this study, we used the interactions of the co-crystallized metabolite of remdesivir with SARS-CoV-2 RdRp isozyme (PDB 7BV2) to design an analog with potential extra activity. This design was based on a scaffold replacement of a pyrrolotriazine moiety. This design was guided by a generated structure-based pharmacophore. The database generated from scaffold replacement was subjected to molecular docking and molecular dynamics simulations within the active site of SARS-CoV-2 RdRp (PDB 7BV2) to suggest HA-130383 and HA-130384 as potential lead compounds. By the end of 2019, a novel strain of the corona viral family named SARS-CoV-2 emerged in Wuhan, China and started to spread worldwide causing one of the most dangerous lethal pandemics.![]()
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Affiliation(s)
- Mohamed A. Said
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt
| | - Amgad Albohy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt (BUE), Suez Desert Road, El-Sherouk City, Cairo 11837, Egypt
| | - Mohamed A. Abdelrahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt
| | - Hany S. Ibarhim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany
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28
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Moreno S, Brunner M, Delazer I, Rieder D, Lusser A, Micura R. Synthesis of 4-thiouridines with prodrug functionalization for RNA metabolic labeling. RSC Chem Biol 2022; 3:447-455. [PMID: 35441143 PMCID: PMC8985182 DOI: 10.1039/d2cb00001f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022] Open
Abstract
Metabolic labeling has emerged as a powerful tool to endow RNA with reactive handles allowing for subsequent chemical derivatization and processing. Recently, thiolated nucleosides, such as 4-thiouridine (4sU), have attracted great interest in metabolic labeling-based RNA sequencing approaches (TUC-seq, SLAM-seq, TimeLapse-seq) to study cellular RNA expression and decay dynamics. For these and other applications (e.g. PAR-CLIP), thus far only the naked nucleoside 4sU has been applied. Here we examined the concept of derivatizing 4sU into a 5′-monophosphate prodrug that would allow for cell permeation and potentially improve labeling efficiency by bypassing the rate-limiting first step of 5′ phosphorylation of the nucleoside into the ultimately bioactive 4sU triphosphate (4sUTP). To this end, we developed robust synthetic routes towards diverse 4sU monophosphate prodrugs. Using metabolic labeling assays, we found that most of the newly introduced 4sU prodrugs were well tolerated by the cells. One derivative, the bis(4-acetyloxybenzyl) 5′-monophosphate of 4sU, was also efficiently incorporated into nascent RNA. Synthetic access to 4-thiouridine (4sU) derivatives with monophosphate prodrug patterns creates additional possibilities for metabolic labeling of RNA for different applications.![]()
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Affiliation(s)
- Sarah Moreno
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Melanie Brunner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Isabel Delazer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 82, 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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Kapoor S, Dubey G, Khatun S, Bharatam PV. Remdesivir: Mechanism of Metabolic Conversion from Prodrug to Drug. Curr Drug Metab 2021; 23:73-81. [PMID: 34963432 DOI: 10.2174/1389200223666211228160314] [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: 09/29/2021] [Revised: 10/25/2021] [Accepted: 12/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Remdesivir (GS-5734) has emerged as a promising drug during the challenging times of COVID-19 pandemic. Being a prodrug, it undergoes several metabolic reactions before converting to its active triphosphate metabolite. It is important to establish the atomic level details and explore the energy profile of the prodrug to drug conversion process. METHODS In this work, Density Functional Theory (DFT) calculations were performed to explore the entire metabolic path. Further, the potential energy surface (PES) diagram for the conversion of prodrug remdesivir to its active metabolite was established. The role of catalytic triad of Hint1 phosphoramidase enzyme in P-N bond hydrolysis was also studied on a model system using combined molecular docking and quantum mechanics approach. RESULTS The overall energy of reaction is 11.47 kcal/mol exergonic and the reaction proceeds through many steps requiring high activation energies. In the absence of a catalyst, the P-N bond breaking step requires 41.78 kcal/mol, which is reduced to 14.26 kcal/mol in a catalytic environment. CONCLUSION The metabolic pathways of model system of remdesivir (MSR) were completely explored completely and potential energy surface diagrams at two levels of theory, B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d), were established and compared. The results highlight the importance of an additional water molecule in the metabolic reaction. The P-N bond cleavage step of the metabolic process requires the presence of an enzymatic environment.
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Affiliation(s)
- Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar (Mohali), 160062 Punjab, India
| | - Gurudutt Dubey
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar (Mohali), 160062 Punjab, India
| | - Samima Khatun
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar (Mohali), 160062 Punjab, India
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar (Mohali), 160062 Punjab, India
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30
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Yan L, Cao R, Zhang H, Li Y, Li W, Li X, Fan S, Li S, Zhong W. Design, synthesis and evaluation of 2'-acetylene-7-deaza-adenosine phosphoamidate derivatives as anti-EV71 and anti-EV-D68 agents. Eur J Med Chem 2021; 226:113852. [PMID: 34560428 DOI: 10.1016/j.ejmech.2021.113852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/29/2022]
Abstract
A series of phosphoamidate derivatives of nucleoside 2'-acetylene-7-deaza-adenosine (NITD008) were synthesized and evaluated for their in vitro antiviral activities against the enteroviruses EV71 and EV-D68. The phosphoamidate (15f) containing a hexyl ester of l-alanine exhibited the most promising activity against EV71 (IC50 = 0.13 ± 0.08 μM) and was 4-times more potent than NITD008. Meanwhile, the derivative containing a cyclohexyl ester of l-alanine (15l) exhibited the most potent activity with high selectivity index against both EV71 (IC50 = 0.19 ± 0.27 μM, SI = 117.00) and EV-D68 (IC50 = 0.17 ± 0.16 μM, SI = 130.76), which were both higher than that of NITD008. The results indicated that the phosphoamidate 15l was the most promising candidate for further development as antiviral agents for the treatment of both EV71 and EV-D68 infection.
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Affiliation(s)
- Linjie Yan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Ruiyuan Cao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Hongjie Zhang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Yuexiang Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Wei Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Xiaoyuan Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Shiyong Fan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Song Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China.
| | - Wu Zhong
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China.
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31
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Bouchareb F, Berredjem M. Recent progress in the synthesis of phosphoramidate and phosphonamide derivatives: A review. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2021.2012781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Fouzia Bouchareb
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar - Annaba University, Annaba, Algeria
- Faculty of Sciences and Technology, Department of Chemistry, Chadli Bendjedid - EL Tarf University, El Tarf, Algeria
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar - Annaba University, Annaba, Algeria
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32
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Sabourin A, Dufour J, Vors JP, Bernier D, Montchamp JL. Synthesis of P-Substituted 5- and 6-Membered Benzo-Phostams: 2,3-Dihydro-1 H-1,2-benzazaphosphole 2-Oxides and 2,3-Tetrahydro-1 H-1,2-benzazaphosphinine 2-Oxides. J Org Chem 2021; 86:14684-14694. [PMID: 34633805 DOI: 10.1021/acs.joc.1c01501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several approaches were developed for the preparation of phosphorus-substituted 5- and 6-membered benzophostams. Carbodiimide-promoted cyclization of zwitterionic aminophosphinates derived from a nitrobenzene precursor accomplished the cyclization in good yields. Alternatively, a novel copper-catalyzed cross-coupling between a phosphonamide and a bromobenzene precursor produced the heterocycles in moderate to good yields. Three different methods are compared for the synthesis of the P-ethoxy-substituted 5-membered benzophostam.
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Affiliation(s)
- Axel Sabourin
- Department of Chemistry and Biochemistry, TCU Box 298860, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Jeremy Dufour
- Bayer SAS, Centre de Recherche La Dargoire, 14-20 impasse Pierre Baizet, CEDEX, Lyon 69263, France
| | - Jean-Pierre Vors
- Bayer SAS, Centre de Recherche La Dargoire, 14-20 impasse Pierre Baizet, CEDEX, Lyon 69263, France
| | - David Bernier
- Bayer SAS, Centre de Recherche La Dargoire, 14-20 impasse Pierre Baizet, CEDEX, Lyon 69263, France
| | - Jean-Luc Montchamp
- Department of Chemistry and Biochemistry, TCU Box 298860, Texas Christian University, Fort Worth, Texas 76129, United States
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33
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Data S, Leung Wai J, Kumar S, Cameron AJ, Trehet M, Itumoh EJ, Feld J, Söhnel T, Leitao EM. The Step‐Wise Synthesis of Oligomeric Phosphoramidates. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shailja Data
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6140 Wellington New Zealand
| | - Jeffery Leung Wai
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
| | - Saawan Kumar
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
| | - Alan J. Cameron
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6140 Wellington New Zealand
- School of Biological Sciences University of Auckland 3b Symonds St 1142 Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery 1142 Auckland New Zealand
| | - Manon Trehet
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
| | - Emeka J. Itumoh
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6140 Wellington New Zealand
| | - Joey Feld
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
| | - Tilo Söhnel
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6140 Wellington New Zealand
| | - Erin M. Leitao
- School of Chemical Sciences University of Auckland Private Bag, 92019 1142 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6140 Wellington New Zealand
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Slusarczyk M, Serpi M, Ghazaly E, Kariuki BM, McGuigan C, Pepper C. Single Diastereomers of the Clinical Anticancer ProTide Agents NUC-1031 and NUC-3373 Preferentially Target Cancer Stem Cells In Vitro. J Med Chem 2021; 64:8179-8193. [PMID: 34085825 DOI: 10.1021/acs.jmedchem.0c02194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 3'-protected route toward the synthesis of the diastereomers of clinically active ProTides, NUC-1031 and NUC-3373, is described. The in vitro cytotoxic activities of the individual diastereomers were found to be similar to their diastereomeric mixtures. In the KG1a cell line, NUC-1031 and NUC-3373 have preferential cytotoxic effects on leukemic stem cells (LSCs). These effects were not diastereomer-specific and were not observed with the parental nucleoside analogues gemcitabine and FUDR, respectively. In addition, NUC-1031 preferentially targeted LSCs in primary AML samples and cancer stem cells in the prostate cancer cell line, LNCaP. Although the mechanism for this remains incompletely resolved, NUC-1031-treated cells showed increased levels of triphosphate in both LSC and bulk tumor fractions. As ProTides are not dependent on nucleoside transporters, it seems possible that the LSC targeting observed with ProTides may be caused, at least in part, by preferential accumulation of metabolized nucleos(t)ide analogues.
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Affiliation(s)
- Magdalena Slusarczyk
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Redwood Building, Cardiff CF10 3NB, U.K
| | - Michaela Serpi
- Cardiff University, School of Chemistry, Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Essam Ghazaly
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, U.K
| | - Benson M Kariuki
- Cardiff University, School of Chemistry, Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Christopher McGuigan
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Redwood Building, Cardiff CF10 3NB, U.K
| | - Chris Pepper
- Brighton and Sussex Medical School, University of Sussex, Medical Teaching Building, Brighton BN1 9PX, U.K
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Ambrosi A, Bringley DA, Calimsiz S, Garber JAO, Huynh H, Mohan S, Sarma K, Shen J, Curl J, Kwong B, Lapina O, Leung E, Lin L, Martins A, McGinitie T, Phull J, Roberts B, Rosario M, Shi B, Standley EA, Wang L, Wang X, Yu G. Synthesis of Rovafovir Etalafenamide (Part III): Evolution of the Synthetic Process to the Phosphonamidate Fragment. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.0c00428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andrea Ambrosi
- Process Chemistry, Gilead Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Dustin A. Bringley
- Process Chemistry, Gilead Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Selcuk Calimsiz
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Jeffrey A. O. Garber
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Huy Huynh
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Sankar Mohan
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Keshab Sarma
- Process Chemistry, Gilead Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Jinyu Shen
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Jonah Curl
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Bernard Kwong
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Olga Lapina
- Process Chemistry, Gilead Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Edmund Leung
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Lennie Lin
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Andrew Martins
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Teague McGinitie
- Analytical Chemistry, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Jaspal Phull
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Ben Roberts
- Process Chemistry, Gilead Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Mary Rosario
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Bing Shi
- Process Chemistry, Gilead Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Eric A. Standley
- Process Chemistry, Gilead Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Li Wang
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Xueqing Wang
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
| | - Guojun Yu
- Process Development, Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta T6S 1A1, Canada
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Chen KJ, Plaunt AJ, Leifer FG, Kang JY, Cipolla D. Recent advances in prodrug-based nanoparticle therapeutics. Eur J Pharm Biopharm 2021; 165:219-243. [PMID: 33979661 DOI: 10.1016/j.ejpb.2021.04.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/10/2021] [Accepted: 04/26/2021] [Indexed: 12/17/2022]
Abstract
Extensive research into prodrug modification of active pharmaceutical ingredients and nanoparticle drug delivery systems has led to unprecedented levels of control over the pharmacological properties of drugs and resulted in the approval of many prodrug or nanoparticle-based therapies. In recent years, the combination of these two strategies into prodrug-based nanoparticle drug delivery systems (PNDDS) has been explored as a way to further advance nanomedicine and identify novel therapies for difficult-to-treat indications. Many of the PNDDS currently in the clinical development pipeline are expected to enter the market in the coming years, making the rapidly evolving field of PNDDS highly relevant to pharmaceutical scientists. This review paper is intended to introduce PNDDS to the novice reader while also updating those working in the field with a comprehensive summary of recent efforts. To that end, first, an overview of FDA-approved prodrugs is provided to familiarize the reader with their advantages over traditional small molecule drugs and to describe the chemistries that can be used to create them. Because this article is part of a themed issue on nanoparticles, only a brief introduction to nanoparticle-based drug delivery systems is provided summarizing their successful application and unfulfilled opportunities. Finally, the review's centerpiece is a detailed discussion of rationally designed PNDDS formulations in development that successfully leverage the strengths of prodrug and nanoparticle approaches to yield highly effective therapeutic options for the treatment of many diseases.
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37
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Keough DT, Wun SJ, Baszczyňski O, Eng WS, Špaček P, Panjikar S, Naesens L, Pohl R, Rejman D, Hocková D, Ferrero RL, Guddat LW. Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase-A Putative Target for Drug Discovery against Gastrointestinal Tract Infections. J Med Chem 2021; 64:5710-5729. [PMID: 33891818 DOI: 10.1021/acs.jmedchem.0c02184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Helicobacter pylori (Hp) is a human pathogen that lives in the gastric mucosa of approximately 50% of the world's population causing gastritis, peptic ulcers, and gastric cancer. An increase in resistance to current drugs has sparked the search for new Hp drug targets and therapeutics. One target is the disruption of nucleic acid production, which can be achieved by impeding the synthesis of 6-oxopurine nucleoside monophosphates, the precursors of DNA and RNA. These metabolites are synthesized by Hp xanthine-guanine-hypoxanthine phosphoribosyltransferase (XGHPRT). Here, nucleoside phosphonates have been evaluated, which inhibit the activity of this enzyme with Ki values as low as 200 nM. The prodrugs of these compounds arrest the growth of Hp at a concentration of 50 μM in cell-based assays. The kinetic properties of HpXGHPRT have been determined together with its X-ray crystal structure in the absence and presence of 9-[(N-3-phosphonopropyl)-aminomethyl-9-deazahypoxanthine, providing a basis for new antibiotic development.
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Affiliation(s)
- Dianne T Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Shun Jie Wun
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Wai Soon Eng
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Petr Špaček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton 3168, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Lieve Naesens
- Katholieke Universiteit, Leuven, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Dana Hocková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Richard L Ferrero
- Hudson Institute of Medical Research, Clayton 3800, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton 3800, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Luke W Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
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38
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Mackman RL, Hui HC, Perron M, Murakami E, Palmiotti C, Lee G, Stray K, Zhang L, Goyal B, Chun K, Byun D, Siegel D, Simonovich S, Du Pont V, Pitts J, Babusis D, Vijjapurapu A, Lu X, Kim C, Zhao X, Chan J, Ma B, Lye D, Vandersteen A, Wortman S, Barrett KT, Toteva M, Jordan R, Subramanian R, Bilello JP, Cihlar T. Prodrugs of a 1'-CN-4-Aza-7,9-dideazaadenosine C-Nucleoside Leading to the Discovery of Remdesivir (GS-5734) as a Potent Inhibitor of Respiratory Syncytial Virus with Efficacy in the African Green Monkey Model of RSV. J Med Chem 2021; 64:5001-5017. [PMID: 33835812 DOI: 10.1021/acs.jmedchem.1c00071] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A discovery program targeting respiratory syncytial virus (RSV) identified C-nucleoside 4 (RSV A2 EC50 = 530 nM) as a phenotypic screening lead targeting the RSV RNA-dependent RNA polymerase (RdRp). Prodrug exploration resulted in the discovery of remdesivir (1, GS-5734) that is >30-fold more potent than 4 against RSV in HEp-2 and NHBE cells. Metabolism studies in vitro confirmed the rapid formation of the active triphosphate metabolite, 1-NTP, and in vivo studies in cynomolgus and African Green monkeys demonstrated a >10-fold higher lung tissue concentration of 1-NTP following molar normalized IV dosing of 1 compared to that of 4. A once daily 10 mg/kg IV administration of 1 in an African Green monkey RSV model demonstrated a >2-log10 reduction in the peak lung viral load. These early data following the discovery of 1 supported its potential as a novel treatment for RSV prior to its development for Ebola and approval for COVID-19 treatment.
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Affiliation(s)
- Richard L Mackman
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Hon C Hui
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Michel Perron
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Eisuke Murakami
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Christopher Palmiotti
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Gary Lee
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Kirsten Stray
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Lijun Zhang
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Bindu Goyal
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Kwon Chun
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Daniel Byun
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Dustin Siegel
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Scott Simonovich
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Venice Du Pont
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Jared Pitts
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Darius Babusis
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Arya Vijjapurapu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Xianghan Lu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Cynthia Kim
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Xiaofeng Zhao
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Julie Chan
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Bin Ma
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Diane Lye
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Adelle Vandersteen
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Sarah Wortman
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Kimberly T Barrett
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Maria Toteva
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Robert Jordan
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Raju Subramanian
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - John P Bilello
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Tomas Cihlar
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
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39
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Sorouri F, Emamgholipour Z, Keykhaee M, Najafi A, Firoozpour L, Sabzevari O, Sharifzadeh M, Foroumadi A, Khoobi M. The situation of small molecules targeting key proteins to combat SARS-CoV-2: Synthesis, metabolic pathway, mechanism of action, and potential therapeutic applications. Mini Rev Med Chem 2021; 22:273-311. [PMID: 33687881 DOI: 10.2174/1389557521666210308144302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/14/2020] [Accepted: 12/28/2020] [Indexed: 12/15/2022]
Abstract
Due to the global epidemic and high mortality of 2019 coronavirus disease (COVID-19), there is an immediate need to discover drugs that can help before a vaccine becomes available. Given that the process of producing new drugs is so long, the strategy of repurposing existing drugs is one of the promising options for the urgent treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19 disease. Although FDA has approved Remdesivir for the use in hospitalized adults and pediatric patients suffering from COVID-19, no fully effective and reliable drug has been yet identified worldwide to treat COVID-19 specifically. Thus, scientists are still trying to find antivirals specific to COVID-19. This work reviews the chemical structure, metabolic pathway, mechanism of action of existing drugs with potential therapeutic applications for COVID-19. Further, we summarized the molecular docking stimulation of the medications related to key protein targets. These already drugs could be developed for further clinical trials to supply suitable therapeutic options for patients suffering from COVID-19.
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Affiliation(s)
- Farzaneh Sorouri
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Zahra Emamgholipour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Maryam Keykhaee
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Alireza Najafi
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran. Iran
| | - Loghman Firoozpour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Omid Sabzevari
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran. Iran
| | - Mohammad Sharifzadeh
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Toxicology and Poisoning Research Centre, Tehran University of Medical Sciences, Tehran. Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
| | - Mehdi Khoobi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran. Iran
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40
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Vanden Avond MA, Meng H, Beatka MJ, Helbling DC, Prom MJ, Sutton JL, Slick RA, Dimmock DP, Pertusati F, Serpi M, Pileggi E, Crutcher P, Thomas S, Lawlor MW. The nucleotide prodrug CERC-913 improves mtDNA content in primary hepatocytes from DGUOK-deficient rats. J Inherit Metab Dis 2021; 44:492-501. [PMID: 33368311 DOI: 10.1002/jimd.12354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023]
Abstract
Loss-of-function mutations in the deoxyguanosine kinase (DGUOK) gene result in a mitochondrial DNA (mtDNA) depletion syndrome. DGUOK plays an important role in converting deoxyribonucleosides to deoxyribonucleoside monophosphates via the salvage pathway for mtDNA synthesis. DGUOK deficiency manifests predominantly in the liver; the most common cause of death is liver failure within the first year of life and no therapeutic options are currently available. in vitro supplementation with deoxyguanosine or deoxyguanosine monophosphate (dGMP) were reported to rescue mtDNA depletion in DGUOK-deficient, patient-derived fibroblasts and myoblasts. CERC-913, a novel ProTide prodrug of dGMP, was designed to bypass defective DGUOK while improving permeability and stability relative to nucleoside monophosphates. To evaluate CERC-913 for its ability to rescue mtDNA depletion, we developed a primary hepatocyte culture model using liver tissue from DGUOK-deficient rats. DGUOK knockout rat hepatocyte cultures exhibit severely reduced mtDNA copy number (~10%) relative to wild type by qPCR and mtDNA content remains stable for up to 8 days in culture. CERC-913 increased mtDNA content in DGUOK-deficient hepatocytes up to 2.4-fold after 4 days of treatment in a dose-dependent fashion, which was significantly more effective than dGMP at similar concentrations. These early results suggest primary hepatocyte culture is a useful model for the study of mtDNA depletion syndromes and that CERC-913 treatment can improve mtDNA content in this model.
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Affiliation(s)
- Mark A Vanden Avond
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Hui Meng
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Margaret J Beatka
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Daniel C Helbling
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mariah J Prom
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jessica L Sutton
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rebecca A Slick
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | - Elisa Pileggi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, UK
| | | | | | - Michael W Lawlor
- Department of Pathology and Laboratory Medicine and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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41
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Ghosh KG, Das D, Chandu P, Sureshkumar D. Visible-Light-Driven Organophotocatalyzed Mono-, Di-, and Tri-C(sp 3)-H Alkylation of Phosphoramides. J Org Chem 2021; 86:2644-2657. [PMID: 33440934 DOI: 10.1021/acs.joc.0c02695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A photocatalytic metal-free, visible-light-driven, highly atom-economic, direct multiple α-C(sp3)-H alkylation of phosphoramides and thiophosphoramides is demonstrated under environmentally benign conditions. Economically viable and commercially available Eosin-Y is used as an HAT photocatalyst for mono-α-C(sp3)-H alkylation of phosphoramide derivatives. Remarkably, di- and tri-C(sp3)-H alkylation of phosphoramides and thiophosphoramides using an acridinium photocatalyst is reported with good yield and selectivity. Mechanistic studies reveal that monoalkylation of phosphoramides by Eosin-Y follows the HAT mechanism, whereas di- and tri-C(sp3)-H alkylation by the acridinium photocatalyst follows the SET mechanism.
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Affiliation(s)
- Krishna Gopal Ghosh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata Mohanpur, Nadia, West Bengal741246, India
| | - Debabrata Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata Mohanpur, Nadia, West Bengal741246, India
| | - Palasetty Chandu
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata Mohanpur, Nadia, West Bengal741246, India
| | - Devarajulu Sureshkumar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata Mohanpur, Nadia, West Bengal741246, India
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42
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Zeng Z, Liu S, Luo W, Liang J, Peng A. Efficient Synthesis of Phosphorus/Nitrogen‐Containing Chrysin Derivatives via Classic Reactions. ChemistrySelect 2021. [DOI: 10.1002/slct.202004358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Ziyi Zeng
- School of Chemistry Sun Yat-sen University 135 Xingangxi Lu Guangzhou China
| | - Shuang Liu
- School of Chemistry Sun Yat-sen University 135 Xingangxi Lu Guangzhou China
| | - Wenjun Luo
- School of Chemistry Sun Yat-sen University 135 Xingangxi Lu Guangzhou China
| | - Jiaxin Liang
- School of Chemistry Sun Yat-sen University 135 Xingangxi Lu Guangzhou China
| | - Ai‐Yun Peng
- School of Chemistry Sun Yat-sen University 135 Xingangxi Lu Guangzhou China
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43
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Wohlgemuth R. Key advances in biocatalytic phosphorylations in the last two decades: Biocatalytic syntheses in vitro and biotransformations in vivo (in humans). Biotechnol J 2020; 16:e2000090. [PMID: 33283467 DOI: 10.1002/biot.202000090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Indexed: 01/05/2023]
Abstract
Biocatalytic phosphorylation reactions provide several benefits, such as more direct, milder, more selective, and shorter access routes to phosphorylated products. Favorable characteristics of biocatalytic methodologies represent advantages for in vitro as well as for in vivo phosphorylation reactions, leading to important advances in the science of synthesis towards bioactive phosphorylated compounds in various areas. The scope of this review covers key advances of biocatalytic phosphorylation reactions over the last two decades, for biocatalytic syntheses in vitro and for biotransformations in vivo (in humans). From the origins of probiotic life to in vitro synthetic applications and in vivo formation of bioactive pharmaceuticals, the common purpose is to outline the importance, relevance, and underlying connections of biocatalytic phosphorylations of small molecules. Asymmetric phosphorylations attracting increased attention are highlighted. Phosphohydrolases, phosphotransferases, phosphorylases, phosphomutases, and other enzymes involved in phosphorus chemistry provide powerful toolboxes for resource-efficient and selective in vitro biocatalytic syntheses of phosphorylated metabolites, chiral building blocks, pharmaceuticals as well as in vivo enzymatic formation of biologically active forms of pharmaceuticals. Nature's large diversity of phosphoryl-group-transferring enzymes, advanced enzyme and reaction engineering toolboxes make biocatalytic asymmetric phosphorylations using enzymes a powerful and privileged phosphorylation methodology.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland.,Swiss Coordination Committee Biotechnology, Zurich, Switzerland
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44
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Hucke FIL, Bugert JJ. Current and Promising Antivirals Against Chikungunya Virus. Front Public Health 2020; 8:618624. [PMID: 33384981 PMCID: PMC7769948 DOI: 10.3389/fpubh.2020.618624] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 12/21/2022] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of chikungunya fever (CHIKF) and is categorized as a(n) (re)emerging arbovirus. CHIKV has repeatedly been responsible for outbreaks that caused serious economic and public health problems in the affected countries. To date, no vaccine or specific antiviral therapies are available. This review gives a summary on current antivirals that have been investigated as potential therapeutics against CHIKF. The mode of action as well as possible compound targets (viral and host targets) are being addressed. This review hopes to provide critical information on the in vitro efficacies of various compounds and might help researchers in their considerations for future experiments.
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Han J, Funk C, Eyberg J, Bailer S, Richert C. An AZT Analog with Strongly Pairing Ethynylpyridone Nucleobase and Its Antiviral Activity against HSV1. Chem Biodivers 2020; 18:e2000937. [PMID: 33270983 DOI: 10.1002/cbdv.202000937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/03/2020] [Indexed: 12/23/2022]
Abstract
Challenges resulting from novel viruses or new strains of known viruses call for new antiviral agents. Nucleoside analogs that act as inhibitors of viral polymerases are an attractive class of antivirals. For nucleosides containing thymine, base pairing is weak, making it desirable to identify nucleobase analogs that pair more strongly with adenine, in order to compete successfully with the natural substrate. We have recently described a new class of strongly binding thymidine analogs that contain an ethynylmethylpyridone as base and a C-nucleosidic linkage to the deoxyribose. Here we report the synthesis of the 3'-azido-2',3'-deoxyribose derivative of this compound, dubbed AZW, both as free nucleoside and as ProTide phosphoramidate. As a proof of principle, we studied the activity against Herpes simplex virus type 1 (HSV1). Whereas the ProTide phosphoramidate suffered from low solubility, the free nucleoside showed a stronger inhibitory effect than that of AZT in a plaque reduction assay. This suggests that strongly pairing C-nucleoside analogs of pyrimidines have the potential to become active pharmaceutical ingredients with antiviral activity.
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Affiliation(s)
- Jianyang Han
- Institute of Organic Chemistry, University of Stuttgart, DE-70569, Stuttgart, Germany
| | - Christina Funk
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, DE-70569, Stuttgart, Germany
| | - Juri Eyberg
- Institute of Organic Chemistry, University of Stuttgart, DE-70569, Stuttgart, Germany
| | - Susanne Bailer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, DE-70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, DE-70569, Stuttgart, Germany
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Picarazzi F, Vicenti I, Saladini F, Zazzi M, Mori M. Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge. Molecules 2020; 25:E5695. [PMID: 33287144 PMCID: PMC7730706 DOI: 10.3390/molecules25235695] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) is an essential enzyme for the viral replication process, catalyzing the viral RNA synthesis using a metal ion-dependent mechanism. In recent years, RdRp has emerged as an optimal target for the development of antiviral drugs, as demonstrated by recent approvals of sofosbuvir and remdesivir against Hepatitis C virus (HCV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively. In this work, we overview the main sequence and structural features of the RdRp of emerging RNA viruses such as Coronaviruses, Flaviviruses, and HCV, as well as inhibition strategies implemented so far. While analyzing the structural information available on the RdRp of emerging RNA viruses, we provide examples of success stories such as for HCV and SARS-CoV-2. In contrast, Flaviviruses' story has raised attention about how the lack of structural details on catalytically-competent or ligand-bound RdRp strongly hampers the application of structure-based drug design, either in repurposing and conventional approaches.
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Affiliation(s)
- Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
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Jovanovic D, Tremmel P, Pallan PS, Egli M, Richert C. The Enzyme‐Free Release of Nucleotides from Phosphoramidates Depends Strongly on the Amino Acid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dejana Jovanovic
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| | - Peter Tremmel
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| | - Pradeep S. Pallan
- Department of Biochemistry Vanderbilt University School of Medicine Nashville TN 37232 USA
| | - Martin Egli
- Department of Biochemistry Vanderbilt University School of Medicine Nashville TN 37232 USA
| | - Clemens Richert
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
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Suzuki–Miyaura Reactions of (4-bromophenyl)-4,6-dichloropyrimidine through Commercially Available Palladium Catalyst: Synthesis, Optimization and Their Structural Aspects Identification through Computational Studies. Processes (Basel) 2020. [DOI: 10.3390/pr8111342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
5-(4-bromophenyl)-4,6-dichloropyrimidine was arylated with several aryl/heteroaryl boronic acids via the Suzuki cross-coupling reaction by using Pd(0) catalyst to yield novel pyrimidine analogs (3a-h). It was optimized so that good yields were obtained when 5 mol % Pd(PPh3)4 was used along with K3PO4 and 1,4-Dioxane. Electron-rich boronic acids were succeeded to produce good yields of products. Density functional theory (DFT) calculations were also applied on these new compounds to analyze their reactivity descriptors and electronic and structural relationship. According to DFT studies, compound 3f is the most reactive one, while 3g is the most stable one. As per DFT studies, the hyperpolarizability (β) values of these compounds do not show them as very good non-linear optical (NLO) materials. Compound 3f has the highest β value among all the compounds under study but still it is not high enough to render it a potent NLO material.
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Jia X, Weber S, Schols D, Meier C. Membrane Permeable, Bioreversibly Modified Prodrugs of Nucleoside Diphosphate-γ-Phosphonates. J Med Chem 2020; 63:11990-12007. [PMID: 32991174 DOI: 10.1021/acs.jmedchem.0c01294] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) are widely used as antiviral and anticancer agents, although they require intracellular phosphorylation into their antivirally active form, the triphosphorylated nucleoside analogue metabolites. We report on the synthesis and characterization of a new class of nucleoside triphosphate analogues comprising a C-alkyl-phosphonate moiety replacing the γ-phosphate. These compounds were converted into bioreversibly modified lipophilic prodrugs at the γ-phosphonate by the attachment of an acyloxybenzyl (ester) or an alkoxycarbonyloxybenzyl (carbonate) group. Such compounds formed γ-C-(alkyl)-nucleoside triphosphate analogues with high selectivity because of an enzyme-triggered delivery mechanism. The latter compounds were very stable in CD4+ T-lymphocyte (CEM cell) extracts, and they were substrates for HIV-reverse transcriptase without being substrates for DNA-polymerases α, β, and γ. In antiviral assays, the excellent antiviral activity of the prodrugs that was found in CEM/0 cells was completely kept in CEM/TK- cells. The activity was improved by 3 logs as compared to the parent nucleoside d4T.
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Affiliation(s)
- Xiao Jia
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
| | - Stefan Weber
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Chris Meier
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
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Novel Nucleoside Analogues as Effective Antiviral Agents for Zika Virus Infections. Molecules 2020; 25:molecules25204813. [PMID: 33092055 PMCID: PMC7594033 DOI: 10.3390/molecules25204813] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 01/17/2023] Open
Abstract
Previously considered a neglected flavivirus, Zika virus has recently emerged as a public health concern due to its ability to spread rapidly and cause severe neurological disorders, such as microcephaly in newborn babies from infected mothers, and Guillain-Barré syndrome in adults. Despite extensive efforts towards the identification of effective therapies, specific antivirals are still not available. As part of ongoing medicinal chemistry studies to identify new antiviral agents, we screened against Zika virus replication in vitro in a targeted internal library of small-molecule agents, comprising both nucleoside and non-nucleoside agents. Among the compounds evaluated, novel aryloxyphosphoramidate prodrugs of the nucleosides 2′-C-methyl-adenosine, 2-CMA, and 7-deaza-2′C-methyl-adenosine, 7-DMA, were found to significantly inhibit the virus-induced cytopathic effect in multiple relevant cell lines. In addition, one of these prodrugs exhibits a synergistic antiviral effect against Zika virus when applied in combination with an indirect antiviral agent, a l-dideoxy bicyclic pyrimidine nucleoside analogue, which potently inhibits vaccinia and measles viruses in vitro by targeting a host pathway. Our findings provide a solid basis for further development of an antiviral therapy for Zika virus infections, possibly exploiting a dual approach combining two different agents, one targeting the viral polymerase (direct-acting antiviral), the second targeting a host-directed autophagy mechanism.
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