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Diatlova EA, Mechetin GV, Yudkina AV, Zharkov VD, Torgasheva NA, Endutkin AV, Shulenina OV, Konevega AL, Gileva IP, Shchelkunov SN, Zharkov DO. Correlated Target Search by Vaccinia Virus Uracil-DNA Glycosylase, a DNA Repair Enzyme and a Processivity Factor of Viral Replication Machinery. Int J Mol Sci 2023; 24:ijms24119113. [PMID: 37298065 DOI: 10.3390/ijms24119113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/13/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
The protein encoded by the vaccinia virus D4R gene has base excision repair uracil-DNA N-glycosylase (vvUNG) activity and also acts as a processivity factor in the viral replication complex. The use of a protein unlike PolN/PCNA sliding clamps is a unique feature of orthopoxviral replication, providing an attractive target for drug design. However, the intrinsic processivity of vvUNG has never been estimated, leaving open the question whether it is sufficient to impart processivity to the viral polymerase. Here, we use the correlated cleavage assay to characterize the translocation of vvUNG along DNA between two uracil residues. The salt dependence of the correlated cleavage, together with the similar affinity of vvUNG for damaged and undamaged DNA, support the one-dimensional diffusion mechanism of lesion search. Unlike short gaps, covalent adducts partly block vvUNG translocation. Kinetic experiments show that once a lesion is found it is excised with a probability ~0.76. Varying the distance between two uracils, we use a random walk model to estimate the mean number of steps per association with DNA at ~4200, which is consistent with vvUNG playing a role as a processivity factor. Finally, we show that inhibitors carrying a tetrahydro-2,4,6-trioxopyrimidinylidene moiety can suppress the processivity of vvUNG.
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Affiliation(s)
- Evgeniia A Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Grigory V Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Vasily D Zharkov
- Biology Department, Tomsk State University, 634050 Tomsk, Russia
| | - Natalia A Torgasheva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Olga V Shulenina
- NRC "Kurchatov Institute"-B. P. Konstantinov Petersburg Nuclear Physics Institute, Leningrad Region, 188300 Gatchina, Russia
| | - Andrey L Konevega
- NRC "Kurchatov Institute"-B. P. Konstantinov Petersburg Nuclear Physics Institute, Leningrad Region, 188300 Gatchina, Russia
| | - Irina P Gileva
- State Research Center of Virology and Biotechnology Vector, Novosibirsk Region, 630559 Koltsovo, Russia
| | - Sergei N Shchelkunov
- State Research Center of Virology and Biotechnology Vector, Novosibirsk Region, 630559 Koltsovo, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
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Wang J, Shahed-Ai-Mahmud M, Chen A, Li K, Tan H, Joyce R. An Overview of Antivirals against Monkeypox Virus and Other Orthopoxviruses. J Med Chem 2023; 66:4468-4490. [PMID: 36961984 DOI: 10.1021/acs.jmedchem.3c00069] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The current monkeypox outbreaks during the COVID-19 pandemic have reignited interest in orthopoxvirus antivirals. Monkeypox belongs to the Orthopoxvirus genus of the Poxviridae family, which also includes the variola virus, vaccinia virus, and cowpox virus. Two orally bioavailable drugs, tecovirimat and brincidofovir, have been approved for treating smallpox infections. Given their human safety profiles and in vivo antiviral efficacy in animal models, both drugs have also been recommended to treat monkeypox infection. To facilitate the development of additional orthopoxvirus antivirals, we summarize the antiviral activity, mechanism of action, and mechanism of resistance of orthopoxvirus antivirals. This perspective covers both direct-acting and host-targeting antivirals with an emphasis on drug candidates showing in vivo antiviral efficacy in animal models. We hope to speed the orthopoxvirus antiviral drug discovery by providing medicinal chemists with insights into prioritizing proper drug targets and hits for further development.
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Affiliation(s)
- Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Md Shahed-Ai-Mahmud
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Angelo Chen
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Ryan Joyce
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
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3
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Abstract
Broadly effective antiviral therapies must be developed to be ready for clinical trials, which should begin soon after the emergence of new life-threatening viruses. Here, we pave the way towards this goal by reviewing conserved druggable virus-host interactions, mechanisms of action, immunomodulatory properties of available broad-spectrum antivirals (BSAs), routes of BSA delivery, and interactions of BSAs with other antivirals. Based on the review, we concluded that the range of indications of BSAs can be expanded, and new pan- and cross-viral mono- and combinational therapies can be developed. We have also developed a new scoring algorithm that can help identify the most promising few of the thousands of potential BSAs and BSA-containing drug cocktails (BCCs) to prioritize their development during the critical period between the identification of a new virus and the development of virus-specific vaccines, drugs, and therapeutic antibodies.
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A 3D structural SARS-CoV-2-human interactome to explore genetic and drug perturbations. Nat Methods 2021; 18:1477-1488. [PMID: 34845387 PMCID: PMC8665054 DOI: 10.1038/s41592-021-01318-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/05/2021] [Indexed: 01/08/2023]
Abstract
Emergence of new viral agents is driven by evolution of interactions between viral proteins and host targets. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV-1 arose in part through rapid evolution along the interface between the spike protein and its human receptor ACE2, leading to increased binding affinity. To facilitate broader exploration of how pathogen-host interactions might impact transmission and virulence in the ongoing COVID-19 pandemic, we performed state-of-the-art interface prediction followed by molecular docking to construct a three-dimensional structural interactome between SARS-CoV-2 and human. We additionally carried out downstream meta-analyses to investigate enrichment of sequence divergence between SARS-CoV-1 and SARS-CoV-2 or human population variants along viral-human protein-interaction interfaces, predict changes in binding affinity by these mutations/variants and further prioritize drug repurposing candidates predicted to competitively bind human targets. We believe this resource ( http://3D-SARS2.yulab.org ) will aid in development and testing of informed hypotheses for SARS-CoV-2 etiology and treatments.
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A New Class of Uracil-DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme. Molecules 2021; 26:molecules26216668. [PMID: 34771075 PMCID: PMC8587785 DOI: 10.3390/molecules26216668] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/24/2021] [Accepted: 10/30/2021] [Indexed: 11/17/2022] Open
Abstract
Uracil-DNA glycosylases are enzymes that excise uracil bases appearing in DNA as a result of cytosine deamination or accidental dUMP incorporation from the dUTP pool. The activity of Family 1 uracil-DNA glycosylase (UNG) activity limits the efficiency of antimetabolite drugs and is essential for virulence in some bacterial and viral infections. Thus, UNG is regarded as a promising target for antitumor, antiviral, antibacterial, and antiprotozoal drugs. Most UNG inhibitors presently developed are based on the uracil base linked to various substituents, yet new pharmacophores are wanted to target a wide range of UNGs. We have conducted virtual screening of a 1,027,767-ligand library and biochemically screened the best hits for the inhibitory activity against human and vaccinia virus UNG enzymes. Although even the best inhibitors had IC50 ≥ 100 μM, they were highly enriched in a common fragment, tetrahydro-2,4,6-trioxopyrimidinylidene (PyO3). In silico, PyO3 preferably docked into the enzyme's active site, and in kinetic experiments, the inhibition was better consistent with the competitive mechanism. The toxicity of two best inhibitors for human cells was independent of the presence of methotrexate, which is consistent with the hypothesis that dUMP in genomic DNA is less toxic for the cell than strand breaks arising from the massive removal of uracil. We conclude that PyO3 may be a novel pharmacophore with the potential for development into UNG-targeting agents.
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Mechetin GV, Endutkin AV, Diatlova EA, Zharkov DO. Inhibitors of DNA Glycosylases as Prospective Drugs. Int J Mol Sci 2020; 21:ijms21093118. [PMID: 32354123 PMCID: PMC7247160 DOI: 10.3390/ijms21093118] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
DNA glycosylases are enzymes that initiate the base excision repair pathway, a major biochemical process that protects the genomes of all living organisms from intrinsically and environmentally inflicted damage. Recently, base excision repair inhibition proved to be a viable strategy for the therapy of tumors that have lost alternative repair pathways, such as BRCA-deficient cancers sensitive to poly(ADP-ribose)polymerase inhibition. However, drugs targeting DNA glycosylases are still in development and so far have not advanced to clinical trials. In this review, we cover the attempts to validate DNA glycosylases as suitable targets for inhibition in the pharmacological treatment of cancer, neurodegenerative diseases, chronic inflammation, bacterial and viral infections. We discuss the glycosylase inhibitors described so far and survey the advances in the assays for DNA glycosylase reactions that may be used to screen pharmacological libraries for new active compounds.
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Affiliation(s)
- Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Evgeniia A. Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
- Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-383-363-5187
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Nuth M, Guan H, Xiao Y, Kulp JL, Parker MH, Strobel ED, Isaacs SN, Scott RW, Reitz AB, Ricciardi RP. Mutation and structure guided discovery of an antiviral small molecule that mimics an essential C-Terminal tripeptide of the vaccinia D4 processivity factor. Antiviral Res 2018; 162:178-185. [PMID: 30578797 PMCID: PMC10124107 DOI: 10.1016/j.antiviral.2018.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 12/31/2022]
Abstract
The smallpox virus (variola) remains a bioterrorism threat since a majority of the human population has never been vaccinated. In the event of an outbreak, at least two drugs against different targets of variola are critical to circumvent potential viral mutants that acquire resistance. Vaccinia virus (VACV) is the model virus used in the laboratory for studying smallpox. The VACV processivity factor D4 is an ideal therapeutic target since it is both essential and specific for poxvirus replication. Recently, we identified a tripeptide (Gly-Phe-Ile) motif at the C-terminus of D4 that is conserved among poxviruses and is necessary for maintaining protein function. In the current work, a virtual screening for small molecule mimics of the tripeptide identified a thiophene lead that effectively inhibited VACV, cowpox virus, and rabbitpox virus in cell culture (EC50 = 8.4-19.7 μM) and blocked in vitro processive DNA synthesis (IC50 = 13.4 μM). Compound-binding to D4 was demonstrated through various biophysical methods and a dose-dependent retardation of the proteolysis of D4 proteins. This study highlights an inhibitor design strategy that exploits a susceptible region of the protein and identifies a novel scaffold for a broad-spectrum poxvirus inhibitor.
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Affiliation(s)
- Manunya Nuth
- Department of Microbiology, School of Dental Medicine and the Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hancheng Guan
- Department of Microbiology, School of Dental Medicine and the Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuhong Xiao
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John L Kulp
- Conifer Point Pharmaceuticals, Doylestown, PA, USA
| | | | - Eric D Strobel
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, USA
| | - Stuart N Isaacs
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard W Scott
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, USA
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, USA
| | - Robert P Ricciardi
- Department of Microbiology, School of Dental Medicine and the Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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8
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Llano M, Peña-Hernandez MA. Defining Pharmacological Targets by Analysis of Virus-Host Protein Interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 111:223-242. [PMID: 29459033 PMCID: PMC6322211 DOI: 10.1016/bs.apcsb.2017.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Viruses are obligate parasites that depend on cellular factors for replication. Pharmacological inhibition of essential viral proteins, mostly enzymes, is an effective therapeutic alternative in the absence of effective vaccines. However, this strategy commonly encounters drug resistance mechanisms that allow these pathogens to evade control. Due to the dependency on host factors for viral replication, pharmacological disruption of the host-pathogen protein-protein interactions (PPIs) is an important therapeutic alternative to block viral replication. In this review we discuss salient aspects of PPIs implicated in viral replication and advances in the development of small molecules that inhibit viral replication through antagonism of these interactions.
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Affiliation(s)
- Manuel Llano
- University of Texas at El Paso, El Paso, TX, United States.
| | - Mario A Peña-Hernandez
- University of Texas at El Paso, El Paso, TX, United States; Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, Mexico
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9
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Delaune D, Iseni F, Ferrier-Rembert A, Peyrefitte CN, Ferraris O. The French Armed Forces Virology Unit: A Chronological Record of Ongoing Research on Orthopoxvirus. Viruses 2017; 10:E3. [PMID: 29295488 PMCID: PMC5795416 DOI: 10.3390/v10010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 01/04/2023] Open
Abstract
Since the official declaration of smallpox eradication in 1980, the general population vaccination has ceased worldwide. Therefore, people under 40 year old are generally not vaccinated against smallpox and have no cross protection against orthopoxvirus infections. This naïve population may be exposed to natural or intentional orthopoxvirus emergences. The virology unit of the Institut de Recherche Biomédicale des Armées (France) has developed research programs on orthopoxviruses since 2000. Its missions were conceived to improve the diagnosis capabilities, to foster vaccine development, and to develop antivirals targeting specific viral proteins. The role of the virology unit was asserted in 2012 when the responsibility of the National Reference Center for the Orthopoxviruses was given to the unit. This article presents the evolution of the unit activity since 2000, and the past and current research focusing on orthopoxviruses.
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Affiliation(s)
- Déborah Delaune
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
| | - Frédéric Iseni
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
| | - Audrey Ferrier-Rembert
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
| | - Christophe N Peyrefitte
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
| | - Olivier Ferraris
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
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10
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Kazmirchuk T, Dick K, Burnside DJ, Barnes B, Moteshareie H, Hajikarimlou M, Omidi K, Ahmed D, Low A, Lettl C, Hooshyar M, Schoenrock A, Pitre S, Babu M, Cassol E, Samanfar B, Wong A, Dehne F, Green JR, Golshani A. Designing anti-Zika virus peptides derived from predicted human-Zika virus protein-protein interactions. Comput Biol Chem 2017; 71:180-187. [DOI: 10.1016/j.compbiolchem.2017.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/03/2017] [Accepted: 10/27/2017] [Indexed: 01/22/2023]
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11
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Czarnecki MW, Traktman P. The vaccinia virus DNA polymerase and its processivity factor. Virus Res 2017; 234:193-206. [PMID: 28159613 DOI: 10.1016/j.virusres.2017.01.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/29/2017] [Indexed: 10/20/2022]
Abstract
Vaccinia virus is the prototypic poxvirus. The 192 kilobase double-stranded DNA viral genome encodes most if not all of the viral replication machinery. The vaccinia virus DNA polymerase is encoded by the E9L gene. Sequence analysis indicates that E9 is a member of the B family of replicative polymerases. The enzyme has both polymerase and 3'-5' exonuclease activities, both of which are essential to support viral replication. Genetic analysis of E9 has identified residues and motifs whose alteration can confer temperature-sensitivity, drug resistance (phosphonoacetic acid, aphidicolin, cytosine arabinsode, cidofovir) or altered fidelity. The polymerase is involved both in DNA replication and in recombination. Although inherently distributive, E9 gains processivity by interacting in a 1:1 stoichiometry with a heterodimer of the A20 and D4 proteins. A20 binds to both E9 and D4 and serves as a bridge within the holoenzyme. The A20/D4 heterodimer has been purified and can confer processivity on purified E9. The interaction of A20 with D4 is mediated by the N'-terminus of A20. The D4 protein is an enzymatically active uracil DNA glycosylase. The DNA-scanning activity of D4 is proposed to keep the holoenzyme tethered to the DNA template but allow polymerase translocation. The crystal structure of D4, alone and in complex with A201-50 and/or DNA has been solved. Screens for low molecular weight compounds that interrupt the A201-50/D4 interface have yielded hits that disrupt processive DNA synthesis in vitro and/or inhibit plaque formation. The observation that an active DNA repair enzyme is an integral part of the holoenzyme suggests that DNA replication and repair may be coupled.
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Affiliation(s)
- Maciej W Czarnecki
- Departments of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States; Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Paula Traktman
- Departments of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States; Departments of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, United States; Departments of the Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States; Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226, United States.
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12
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Schormann N, Zhukovskaya N, Bedwell G, Nuth M, Gillilan R, Prevelige PE, Ricciardi RP, Banerjee S, Chattopadhyay D. Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases. Protein Sci 2016; 25:2113-2131. [PMID: 27684934 DOI: 10.1002/pro.3058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 11/07/2022]
Abstract
Uracil-DNA glycosylases are ubiquitous enzymes, which play a key role repairing damages in DNA and in maintaining genomic integrity by catalyzing the first step in the base excision repair pathway. Within the superfamily of uracil-DNA glycosylases family I enzymes or UNGs are specific for recognizing and removing uracil from DNA. These enzymes feature conserved structural folds, active site residues and use common motifs for DNA binding, uracil recognition and catalysis. Within this family the enzymes of poxviruses are unique and most remarkable in terms of amino acid sequences, characteristic motifs and more importantly for their novel non-enzymatic function in DNA replication. UNG of vaccinia virus, also known as D4, is the most extensively characterized UNG of the poxvirus family. D4 forms an unusual heterodimeric processivity factor by attaching to a poxvirus-specific protein A20, which also binds to the DNA polymerase E9 and recruits other proteins necessary for replication. D4 is thus integrated in the DNA polymerase complex, and its DNA-binding and DNA scanning abilities couple DNA processivity and DNA base excision repair at the replication fork. The adaptations necessary for taking on the new function are reflected in the amino acid sequence and the three-dimensional structure of D4. An overview of the current state of the knowledge on the structure-function relationship of D4 is provided here.
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Affiliation(s)
- Norbert Schormann
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Natalia Zhukovskaya
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Gregory Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Manunya Nuth
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Richard Gillilan
- MacCHESS (Macromolecular Diffraction Facility at CHESS) Cornell University, Ithaca, New York, 14853
| | - Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Robert P Ricciardi
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104.,Abramson Cancer Center, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Surajit Banerjee
- Department of Chemistry and Chemical Biology, Cornell University, and NE-CAT, Argonne, Illinois, 60439
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13
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Contesto-Richefeu C, Tarbouriech N, Brazzolotto X, Burmeister WP, Peyrefitte CN, Iseni F. Structural analysis of point mutations at the Vaccinia virus A20/D4 interface. Acta Crystallogr F Struct Biol Commun 2016; 72:687-91. [PMID: 27599859 PMCID: PMC5012208 DOI: 10.1107/s2053230x16011778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/19/2016] [Indexed: 01/10/2023] Open
Abstract
The Vaccinia virus polymerase holoenzyme is composed of three subunits: E9, the catalytic DNA polymerase subunit; D4, a uracil-DNA glycosylase; and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase cofactor, the function of which is essential for processive DNA synthesis. The recent crystal structure of D4 bound to the first 50 amino acids of A20 (D4/A201-50) revealed the importance of three residues, forming a cation-π interaction at the dimerization interface, for complex formation. These are Arg167 and Pro173 of D4 and Trp43 of A20. Here, the crystal structures of the three mutants D4-R167A/A201-50, D4-P173G/A201-50 and D4/A201-50-W43A are presented. The D4/A20 interface of the three structures has been analysed for atomic solvation parameters and cation-π interactions. This study confirms previous biochemical data and also points out the importance for stability of the restrained conformational space of Pro173. Moreover, these new structures will be useful for the design and rational improvement of known molecules targeting the D4/A20 interface.
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Affiliation(s)
- Céline Contesto-Richefeu
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223 Brétigny-sur-Orge CEDEX, France
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Xavier Brazzolotto
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, BP 73, 91223 Brétigny-sur-Orge CEDEX, France
| | - Wim P. Burmeister
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes, 71 Avenue des Martyrs, 38042 Grenoble, France
| | | | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223 Brétigny-sur-Orge CEDEX, France
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Contesto-Richefeu C, Tarbouriech N, Brazzolotto X, Betzi S, Morelli X, Burmeister WP, Iseni F. Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20 N-terminal domain. PLoS Pathog 2014; 10:e1003978. [PMID: 24603707 PMCID: PMC3946371 DOI: 10.1371/journal.ppat.1003978] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/21/2014] [Indexed: 12/21/2022] Open
Abstract
Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for processive DNA synthesis. Genetic and biochemical data have established that residues located in the N-terminus of A20 are critical for binding to D4. However, no information regarding the residues of D4 involved in A20 binding is yet available. We expressed and purified the complex formed by D4 and the first 50 amino acids of A20 (D4/A20₁₋₅₀). We showed that whereas D4 forms homodimers in solution when expressed alone, D4/A20₁₋₅₀ clearly behaves as a heterodimer. The crystal structure of D4/A20₁₋₅₀ solved at 1.85 Å resolution reveals that the D4/A20 interface (including residues 167 to 180 and 191 to 206 of D4) partially overlaps the previously described D4/D4 dimer interface. A20₁₋₅₀ binding to D4 is mediated by an α-helical domain with important leucine residues located at the very N-terminal end of A20 and a second stretch of residues containing Trp43 involved in stacking interactions with Arg167 and Pro173 of D4. Point mutations of the latter residues disturb D4/A20₁₋₅₀ formation and reduce significantly thermal stability of the complex. Interestingly, small molecule docking with anti-poxvirus inhibitors selected to interfere with D4/A20 binding could reproduce several key features of the D4/A20₁₋₅₀ interaction. Finally, we propose a model of D4/A20₁₋₅₀ in complex with DNA and discuss a number of mutants described in the literature, which affect DNA synthesis. Overall, our data give new insights into the assembly of the poxvirus DNA polymerase cofactor and may be useful for the design and rational improvement of antivirals targeting the D4/A20 interface.
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Affiliation(s)
| | - Nicolas Tarbouriech
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host-Cell Interactions, UMI 3265, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Xavier Brazzolotto
- Département de Toxicologie et Risque Chimique, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Stéphane Betzi
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes & Aix-Marseille Universités, Marseille, France
| | - Xavier Morelli
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes & Aix-Marseille Universités, Marseille, France
| | - Wim P. Burmeister
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host-Cell Interactions, UMI 3265, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
- * E-mail:
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15
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Nuth M, Guan H, Zhukovskaya N, Saw YL, Ricciardi RP. Design of Potent Poxvirus Inhibitors of the Heterodimeric Processivity Factor Required for Viral Replication. J Med Chem 2013; 56:3235-46. [DOI: 10.1021/jm301735k] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manunya Nuth
- Department of Microbiology,
School of Dental Medicine, University of Pennsylvania, Pennsylvania
19104, United States
| | - Hancheng Guan
- Department of Microbiology,
School of Dental Medicine, University of Pennsylvania, Pennsylvania
19104, United States
| | - Natalia Zhukovskaya
- Department of Microbiology,
School of Dental Medicine, University of Pennsylvania, Pennsylvania
19104, United States
| | - Yih Ling Saw
- Department of Microbiology,
School of Dental Medicine, University of Pennsylvania, Pennsylvania
19104, United States
| | - Robert P. Ricciardi
- Department of Microbiology,
School of Dental Medicine, University of Pennsylvania, Pennsylvania
19104, United States
- Abramson
Cancer Center, School
of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
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16
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Flusin O, Saccucci L, Contesto-Richefeu C, Hamdi A, Bardou C, Poyot T, Peinnequin A, Crance JM, Colas P, Iseni F. A small molecule screen in yeast identifies inhibitors targeting protein-protein interactions within the vaccinia virus replication complex. Antiviral Res 2012; 96:187-95. [PMID: 22884885 DOI: 10.1016/j.antiviral.2012.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 07/23/2012] [Accepted: 07/24/2012] [Indexed: 12/20/2022]
Abstract
Genetic and biochemical data have identified at least four viral proteins essential for vaccinia virus (VACV) DNA synthesis: the DNA polymerase E9, its processivity factor (the heterodimer A20/D4) and the primase/helicase D5. These proteins are part of the VACV replication complex in which A20 is a central subunit interacting with E9, D4 and D5. We hypothesised that molecules able to modulate protein-protein interactions within the replication complex may represent a new class of compounds with anti-orthopoxvirus activities. In this study, we adapted a forward duplex yeast two-hybrid assay to screen more than 27,000 molecules in order to identify inhibitors of A20/D4 and/or A20/D5 interactions. We identified two molecules that specifically inhibited both interactions in yeast. Interestingly, we observed that these compounds displayed a similar antiviral activity to cidofovir (CDV) against VACV in cell culture. We further showed that these molecules were able to inhibit the replication of another orthopoxvirus (i.e. cowpox virus), but not the herpes simplex virus type 1 (HSV-1), an unrelated DNA virus. We also demonstrated that the antiviral activity of both compounds correlated with an inhibition of VACV DNA synthesis. Hence, these molecules may represent a starting point for the development of new anti-orthopoxvirus drugs.
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Affiliation(s)
- Olivier Flusin
- Unité de virologie, Institut de Recherche Biomédicale des Armées (IRBA), 24 avenue des Maquis du Grésivaudan, 38702 La Tronche, France
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17
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Prichard MN, Kern ER. Orthopoxvirus targets for the development of new antiviral agents. Antiviral Res 2012; 94:111-25. [PMID: 22406470 DOI: 10.1016/j.antiviral.2012.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/10/2012] [Accepted: 02/21/2012] [Indexed: 12/29/2022]
Abstract
Investments in the development of new drugs for orthopoxvirus infections have fostered new avenues of research, provided an improved understanding of orthopoxvirus biology and yielded new therapies that are currently progressing through clinical trials. These broad-based efforts have also resulted in the identification of new inhibitors of orthopoxvirus replication that target many different stages of viral replication cycle. This review will discuss progress in the development of new anti-poxvirus drugs and the identification of new molecular targets that can be exploited for the development of new inhibitors. The prototype of the orthopoxvirus group is vaccinia virus and its replication cycle will be discussed in detail noting specific viral functions and their associated gene products that have the potential to serve as new targets for drug development. Progress that has been achieved in recent years should yield new drugs for the treatment of these infections and might also reveal new approaches for antiviral drug development with other viruses.
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Affiliation(s)
- Mark N Prichard
- Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, AL 35233-1711, United States.
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