1
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Yoon J, Lee J, Kim J, Lee SM, Kim S, Park HG. A novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension reaction. Biosens Bioelectron 2024; 253:116174. [PMID: 38432074 DOI: 10.1016/j.bios.2024.116174] [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: 01/03/2024] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
We herein present a novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction. The detection probe employed as a key component in this technique serves as a substrate for RNase H and triggers the PS-THSP reaction upon the RNase H-mediated degradation of the probe. As a consequence, a large number of long concatemeric amplification products could be produced and used to identify the RNase H activity through the fluorescence signals produced by the nucleic acid-specific fluorescent dye, SYTO 9. Importantly, the use of the gp32 protein allowed the PS-THSP reaction to be performed at 37 °C, ultimately enabling an isothermal one-step RNase H assay. Based on this sophisticated design principle, the RNase H activity was very sensitively detected, down to 0.000237 U mL-1 with high specificity. We further verified its practical applicability through its successful application to the screening of RNase H inhibitors. With its operational convenience and excellent analytical performance, this technique could serve as a new platform for RNase H assay in a wide range of biological applications.
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Affiliation(s)
- Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jinhwan Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jaemin Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Mo Lee
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soohyun Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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2
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Ding WW, Zhou Y, Song S, Han ZY. Palladium-Catalyzed and Photoinduced Benzylic C-H Carbonylation/Annulation under Mild Conditions. Org Lett 2022; 24:7350-7354. [PMID: 36197837 DOI: 10.1021/acs.orglett.2c02877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A Pd-catalyzed and photoinduced benzylic cascade benzylic C-H carbonylation/annulation reaction is realized under mild conditions (35 °C, 2 bar CO). The use of a catalytic amount of base is crucial for the reaction to achieve high yields. The reaction consists of a Pd-catalyzed generation of amidyl radical from O-benzyl hydroxylamide substrates and 1,5-HAT to give a benzylic radical, followed by carbonylation and annulation. Various homophthalimides, which could be readily converted to a number of bioactive compounds, could be obtained with up to 96% yield.
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Affiliation(s)
- Wei-Wei Ding
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yu Zhou
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Shun Song
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Zhi-Yong Han
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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3
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Mahboubi-Rabbani M, Abbasi M, Hajimahdi Z, Zarghi A. HIV-1 Reverse Transcriptase/Integrase Dual Inhibitors: A Review of Recent Advances and Structure-activity Relationship Studies. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:333-369. [PMID: 34567166 PMCID: PMC8457747 DOI: 10.22037/ijpr.2021.115446.15370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The significant threat to humanity is HIV infection, and it is uncertain whether a definitive treatment or a safe HIV vaccine is. HIV-1 is continually evolving and resistant to commonly used HIV-resistant medications, presenting significant obstacles to HIV infection management. The drug resistance adds to the need for new anti-HIV drugs; it chooses ingenious approaches to fight the emerging virus. Highly Active Antiretroviral Therapy (HAART), a multi-target approach for specific therapies, has proved effective in AIDS treatment. Therefore, it is a dynamic system with high prescription tension, increased risk of medication reactions, and adverse effects, leading to poor compliance with patients. In the HIV-1 lifecycle, two critical enzymes with high structural and functional analogies are reverse transcriptase (RT) and integrase (IN), which can be interpreted as druggable targets for modern dual-purpose inhibitors. Designed multifunctional ligand (DML) is a new technique that recruited many targets to be achieved by one chemical individual. A single chemical entity that acts for multiple purposes can be much more successful than a complex multidrug program. The production of these multifunctional ligands as antiretroviral drugs is valued with the advantage that the viral-replication process may end in two or more phases. This analysis will discuss the RT-IN dual-inhibitory scaffolds' developments documented so far.
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Affiliation(s)
- Mohammad Mahboubi-Rabbani
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abbasi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zahra Hajimahdi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Zarghi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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4
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Development of Human Immunodeficiency Virus Type 1 Resistance to 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (EFdA) Starting with Wild-Type or Nucleoside Reverse Transcriptase Inhibitor Resistant-Strains. Antimicrob Agents Chemother 2021; 65:e0116721. [PMID: 34516245 DOI: 10.1128/aac.01167-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA, MK-8591, islatravir) is a nucleoside reverse transcriptase translocation inhibitor (NRTTI) with exceptional potency against WT and drug-resistant HIV-1, in Phase III clinical trials. EFdA resistance is not well characterized. To study EFdA-resistance patterns as it may emerge in naïve or tenofovir- (TFV), emtricitabine/lamivudine- (FTC/3TC), or zidovudine- (AZT) treated patients we performed viral passaging experiments starting with wild-type, K65R, M184V, or D67N/K70R/T215F/K219Q HIV-1. Regardless the starting viral sequence, all selected EFdA-resistant variants included the M184V RT mutation. Using recombinant viruses, we validated the role for M184V as the primary determinant of EFdA resistance; none of the observed connection subdomain (R358K and E399K) or RNase H domain (A502V) mutations significantly contributed to EFdA resistance. A novel EFdA resistance mutational pattern that included A114S was identified in the background of M184V. A114S/M184V exhibited higher EFdA resistance (∼24-fold) than M184V (∼8-fold) or A114S alone (∼2-fold). Remarkably, A114S/M184V and A114S/M184V/A502V resistance mutations were up to 50-fold more sensitive to tenofovir than WT HIV-1. These mutants also had significantly lower specific infectivity than WT. Biochemical experiments confirmed decreases in the enzymatic efficiency (kcat/Km) of WT vs. A114S (2.1-fold) and A114S/M184V/A502V (6.5-fold) RTs, with no effect of A502V on enzymatic efficiency or specific infectivity. The rather modest EFdA resistance of M184V or A114S/M184V (8- and 24-fold), their hypersusceptibility to tenofovir, and strong published in vitro and in vivo data, suggest that EFdA is an excellent therapeutic candidate for naïve, AZT-, FTC/3TC, and especially tenofovir-treated patients.
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5
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Liu D, Ndongwe TP, Puray-Chavez M, Casey MC, Izumi T, Pathak VK, Tedbury PR, Sarafianos SG. Effect of P-body component Mov10 on HCV virus production and infectivity. FASEB J 2020; 34:9433-9449. [PMID: 32496609 DOI: 10.1096/fj.201800641r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 03/28/2020] [Accepted: 05/04/2020] [Indexed: 12/11/2022]
Abstract
Mov10 is a processing body (P-body) protein and an interferon-stimulated gene that can affect replication of retroviruses, hepatitis B virus, and hepatitis C virus (HCV). The mechanism of HCV inhibition by Mov10 is unknown. Here, we investigate the effect of Mov10 on HCV infection and determine the virus life cycle steps affected by changes in Mov10 overexpression. Mov10 overexpression suppresses HCV RNA in both infectious virus and subgenomic replicon systems. Additionally, Mov10 overexpression decreases the infectivity of released virus, unlike control P-body protein DCP1a that has no effect on HCV RNA production or infectivity of progeny virus. Confocal imaging of uninfected cells shows endogenous Mov10 localized at P-bodies. However, in HCV-infected cells, Mov10 localizes in circular structures surrounding cytoplasmic lipid droplets with NS5A and core protein. Mutagenesis experiments show that the RNA binding activity of Mov10 is required for HCV inhibition, while its P-body localization, helicase, and ATP-binding functions are not required. Unexpectedly, endogenous Mov10 promotes HCV replication, as CRISPR-Cas9-based Mov10 depletion decreases HCV replication and infection levels. Our data reveal an important and complex role for Mov10 in HCV replication, which can be perturbed by excess or insufficient Mov10.
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Affiliation(s)
- Dandan Liu
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Tanyaradzwa P Ndongwe
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Maritza Puray-Chavez
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Mary C Casey
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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6
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Xi Z, Wang Z, Sarafianos SG, Myshakina NS, Ishima R. Determinants of Active-Site Inhibitor Interaction with HIV-1 RNase H. ACS Infect Dis 2019; 5:1963-1974. [PMID: 31577424 DOI: 10.1021/acsinfecdis.9b00300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ribonuclease H (RNH) activity of HIV-1 reverse transcriptase (RT) is essential for viral replication and can be a target for drug development. Yet, no RNH inhibitor to date has substantial antiviral activity to allow advancement into clinical development. Herein, we describe our characterization of the detailed binding mechanisms of RNH active-site inhibitors, YLC2-155 and ZW566, that bind to the RNH domain through divalent metal ions, using NMR, molecular docking, and quantum mechanical calculations. In the presence of Mg2+, NMR spectra of RNH exhibited split (two) resonances for some residues upon inhibitor binding, suggesting two binding modes, an observation consistent with the docking results. The relative populations of the two binding conformers were independent of inhibitor or Mg2+ concentration, with one conformation consistently more favored. In our docking study, one distinctive pose of ZW566 showed more interactions with surrounding residues of RNH compared to the analogous binding pose of YLC2-155. Inhibitor titration experiments revealed a lower dissociation constant for ZW566 compared to YLC2-155, in agreement with its higher inhibitory activity. Mg2+ titration data also indicated a stronger dependence on Mg2+ for the RNH interaction with ZW566 compared to YLC2-155. Combined docking and quantum mechanical calculation results suggest that stronger metal coordination as well as more protein-inhibitor interactions may account for the higher binding affinity of ZW566. These findings support the idea that strategies for the development of potent competitive active site RNH inhibitors should take into account not only metal-inhibitor coordination but also protein-inhibitor interaction and conformational selectivity.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, 516 Delaware Street SE, PWB 7-215,
MMC 204, Minneapolis, Minnesota 55455, United States
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Nataliya S. Myshakina
- Department of Natural Science, Chatham University, Woodland Road, Pittsburgh, Pennsylvania 15232, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
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7
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Biological evaluation of molecules of the azaBINOL class as antiviral agents: Inhibition of HIV-1 RNase H activity by 7-isopropoxy-8-(naphth-1-yl)quinoline. Bioorg Med Chem 2019; 27:3595-3604. [DOI: 10.1016/j.bmc.2019.06.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/22/2019] [Accepted: 06/27/2019] [Indexed: 12/13/2022]
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8
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Poongavanam V, Corona A, Steinmann C, Scipione L, Grandi N, Pandolfi F, Di Santo R, Costi R, Esposito F, Tramontano E, Kongsted J. Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies. MEDCHEMCOMM 2018; 9:562-575. [PMID: 30108947 PMCID: PMC6072344 DOI: 10.1039/c7md00600d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/29/2018] [Indexed: 11/21/2022]
Abstract
Persistent HIV infection requires lifelong treatment and among the 2.1 million new HIV infections that occur every year there is an increased rate of transmitted drug-resistant mutations. This fact requires a constant and timely effort in order to identify and develop new HIV inhibitors with innovative mechanisms. The HIV-1 reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only viral encoded enzyme that still lacks an efficient inhibitor despite the fact that it is a well-validated target whose functional abrogation compromises viral infectivity. Identification of new drugs is a long and expensive process that can be speeded up by in silico methods. In the present study, a structure-guided screening is coupled with a similarity-based search on the Specs database to identify a new class of HIV-1 RNase H inhibitors. Out of the 45 compounds selected for experimental testing, 15 inhibited the RNase H function below 100 μM with three hits exhibiting IC50 values <10 μM. The most active compound, AA, inhibits HIV-1 RNase H with an IC50 of 5.1 μM and exhibits a Mg-independent mode of inhibition. Site-directed mutagenesis studies provide valuable insight into the binding mode of newly identified compounds; for instance, compound AA involves extensive interactions with a lipophilic pocket formed by Ala502, Lys503, and Trp (406, 426 and 535) and polar interactions with Arg557 and the highly conserved RNase H primer-grip residue Asn474. The structural insights obtained from this work provide the bases for further lead optimization.
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Affiliation(s)
- Vasanthanathan Poongavanam
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
| | - Angela Corona
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Casper Steinmann
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Fabiana Pandolfi
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Enzo Tramontano
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
- Istituto di Ricerca Genetica e Biomedica , Consiglio Nazionale delle Ricerche (CNR) , Monserrato(CA) , Italy
| | - Jacob Kongsted
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
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9
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Kankanala J, Kirby KA, Huber AD, Casey MC, Wilson DJ, Sarafianos SG, Wang Z. Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H. Eur J Med Chem 2017; 141:149-161. [PMID: 29031062 DOI: 10.1016/j.ejmech.2017.09.054] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/13/2017] [Accepted: 09/25/2017] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only HIV enzymatic function not targeted by current antiviral drugs. Although various chemotypes have been reported to inhibit HIV RNase H, few have shown significant antiviral activities. We report herein the design, synthesis and biological evaluation of a novel N-hydroxy thienopyrimidine-2,3-dione chemotype (11) which potently and selectively inhibited RNase H with considerable potency against HIV-1 in cell culture. Current structure-activity-relationship (SAR) identified analogue 11d as a nanomolar inhibitor of RNase H (IC50 = 0.04 μM) with decent antiviral potency (EC50 = 7.4 μM) and no cytotoxicity (CC50 > 100 μM). In extended biochemical assays compound 11d did not inhibit RT polymerase (pol) while inhibiting integrase strand transfer (INST) with 53 fold lower potency (IC50 = 2.1 μM) than RNase H inhibition. Crystallographic and molecular modeling studies confirmed the RNase H active site binding mode.
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Affiliation(s)
- Jayakanth Kankanala
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Karen A Kirby
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Andrew D Huber
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Mary C Casey
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA; Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
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10
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A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase. Antimicrob Agents Chemother 2017; 61:AAC.01351-17. [PMID: 28760905 DOI: 10.1128/aac.01351-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 11/20/2022] Open
Abstract
The RNase H (RNH) function of HIV-1 reverse transcriptase (RT) plays an essential part in the viral life cycle. We report the characterization of YLC2-155, a 2-hydroxyisoquinoline-1,3-dione (HID)-based active-site RNH inhibitor. YLC2-155 inhibits both polymerase (50% inhibitory concentration [IC50] = 2.6 μM) and RNH functions (IC50 = 0.65 μM) of RT but is more effective against RNH. X-ray crystallography, nuclear magnetic resonance (NMR) analysis, and molecular modeling were used to show that YLC2-155 binds at the RNH-active site in multiple conformations.
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11
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3-Hydroxypyrimidine-2,4-Diones as Novel Hepatitis B Virus Antivirals Targeting the Viral Ribonuclease H. Antimicrob Agents Chemother 2017; 61:AAC.00245-17. [PMID: 28320718 DOI: 10.1128/aac.00245-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/13/2017] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) RNase H (RNH) is an appealing therapeutic target due to its essential role in viral replication. RNH inhibitors (RNHIs) could help to more effectively control HBV infections. Here, we report 3-hydroxypyrimidine-2,4-diones as novel HBV RNHIs with antiviral activity. We synthesized and tested 52 analogs and found 4 that inhibit HBV RNH activity in infected cells. Importantly, 2 of these compounds inhibited HBV replication in the low micromolar range.
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12
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Tang J, Kirby KA, Huber AD, Casey MC, Ji J, Wilson DJ, Sarafianos SG, Wang Z. 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione as an inhibitor scaffold of HIV reverase transcriptase: Impacts of the 3-OH on inhibiting RNase H and polymerase. Eur J Med Chem 2017; 128:168-179. [PMID: 28182989 DOI: 10.1016/j.ejmech.2017.01.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 01/24/2023]
Abstract
3-Hydroxypyrimidine-2,4-dione (HPD) represents a versatile chemical core in the design of inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H and integrase strand transfer (INST). We report herein the design, synthesis and biological evaluation of an HPD subtype (4) featuring a cyclohexylmethyl group at the C-6 position. Antiviral testing showed that most analogues of 4 inhibited HIV-1 in the low nanomolar to submicromolar range, without cytotoxicity at concentrations up to 100 μM. Biochemically, these analogues dually inhibited both the polymerase (pol) and the RNase H functions of RT, but not INST. Co-crystal structure of 4a with RT revealed a nonnucleoside RT inhibitor (NNRTI) binding mode. Interestingly, chemotype 11, the synthetic precursor of 4 lacking the 3-OH group, did not inhibit RNase H while potently inhibiting pol. By virtue of the potent antiviral activity and biochemical RNase H inhibition, HPD subtype 4 could provide a viable platform for eventually achieving potent and selective RNase H inhibition through further medicinal chemistry.
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Affiliation(s)
- Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Karen A Kirby
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Andrew D Huber
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Juan Ji
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
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13
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Tang X, Zhu Y, Baker SL, Bowler MW, Chen BJ, Chen C, Hogg JR, Goff SP, Song H. Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus. Nat Commun 2016; 7:12070. [PMID: 27329342 PMCID: PMC4917968 DOI: 10.1038/ncomms12070] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/25/2016] [Indexed: 01/24/2023] Open
Abstract
Retroviral reverse transcriptase (RT) of Moloney murine leukemia virus (MoMLV) is expressed in the form of a large Gag–Pol precursor protein by suppression of translational termination in which the maximal efficiency of stop codon read-through depends on the interaction between MoMLV RT and peptidyl release factor 1 (eRF1). Here, we report the crystal structure of MoMLV RT in complex with eRF1. The MoMLV RT interacts with the C-terminal domain of eRF1 via its RNase H domain to sterically occlude the binding of peptidyl release factor 3 (eRF3) to eRF1. Promotion of read-through by MoMLV RNase H prevents nonsense-mediated mRNA decay (NMD) of mRNAs. Comparison of our structure with that of HIV RT explains why HIV RT cannot interact with eRF1. Our results provide a mechanistic view of how MoMLV manipulates the host translation termination machinery for the synthesis of its own proteins. Retroviral reverse transcriptase from Moloney Murine Leukemia Virus (MoMLV) requires interaction with peptidyl release factor 1. Here, the authors report the crystal structure of this complex, and provide insights into how MoMLV uses the host translation machinery to synthesize its own proteins.
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Affiliation(s)
- Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yiping Zhu
- Department of Biochemistry and Molecular Biophysics, Columbia University, HHSC 1310C, 701 West 168th Street, New York, New York 10032, USA.,Howard Hughes Medical Institute, Columbia University, HHSC 1310C, 701 West 168th Street, New York, NY 10032, USA
| | - Stacey L Baker
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, Maryland 20892, USA
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble F-38042, France.,Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, Grenoble F-38042, France
| | - Benjamin Jieming Chen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Chen Chen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, Maryland 20892, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University, HHSC 1310C, 701 West 168th Street, New York, New York 10032, USA.,Howard Hughes Medical Institute, Columbia University, HHSC 1310C, 701 West 168th Street, New York, NY 10032, USA
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.,Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China.,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore
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14
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Kankanala J, Kirby KA, Liu F, Miller L, Nagy E, Wilson DJ, Parniak MA, Sarafianos SG, Wang Z. Design, Synthesis, and Biological Evaluations of Hydroxypyridonecarboxylic Acids as Inhibitors of HIV Reverse Transcriptase Associated RNase H. J Med Chem 2016; 59:5051-62. [PMID: 27094954 DOI: 10.1021/acs.jmedchem.6b00465] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Targeting the clinically unvalidated reverse transcriptase (RT) associated ribonuclease H (RNase H) for human immunodeficiency virus (HIV) drug discovery generally entails chemotypes capable of chelating two divalent metal ions in the RNase H active site. The hydroxypyridonecarboxylic acid scaffold has been implicated in inhibiting homologous HIV integrase (IN) and influenza endonuclease via metal chelation. We report herein the design, synthesis, and biological evaluations of a novel variant of the hydroxypyridonecarboxylic acid scaffold featuring a crucial N-1 benzyl or biarylmethyl moiety. Biochemical studies show that most analogues consistently inhibited HIV RT-associated RNase H in the low micromolar range in the absence of significant inhibition of RT polymerase or IN. One compound showed reasonable cell-based antiviral activity (EC50 = 10 μM). Docking and crystallographic studies corroborate favorable binding to the active site of HIV RNase H, providing a basis for the design of more potent analogues.
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Affiliation(s)
- Jayakanth Kankanala
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Karen A Kirby
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center , Columbia, Missouri 65211, United States
| | - Feng Liu
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Lena Miller
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15219, United States
| | - Eva Nagy
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15219, United States
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Michael A Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15219, United States
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology and Department of Biochemistry, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center , Columbia, Missouri 65211, United States
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
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15
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A versatile salicyl hydrazonic ligand and its metal complexes as antiviral agents. J Inorg Biochem 2015; 150:9-17. [PMID: 26047528 DOI: 10.1016/j.jinorgbio.2015.05.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/21/2015] [Accepted: 05/24/2015] [Indexed: 11/20/2022]
Abstract
Acylhydrazones are very versatile ligands and their coordination properties can be easily tuned, giving rise to metal complexes with different nuclearities. In the last few years, we have been looking for new pharmacophores able to coordinate simultaneously two metal ions, because many enzymes have two metal ions in the active site and their coordination can be a successful strategy to inhibit the activity of the metalloenzyme. As a part of this ongoing research, we synthesized the acylhydrazone H2L and its complexes with Mg(II), Mn(II), Co(II), Ni(II), Cu(II) and Zn(II). Their characterization, both in solution--also by means of potentiometric studies--and in the solid state, evidenced the ability of the o-vanillin hydrazone scaffold to give rise to different types of metal complexes, depending on the metal and the reaction conditions. Furthermore, we evaluated both the free ligand and its metal complexes in in vitro studies against a panel of diverse DNA- and RNA-viruses. In particular, the Mg(II), Mn(II), Ni(II) and Zn(II) complexes had EC50 values in the low micromolar range, with a pronounced activity against vaccinia virus.
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16
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A hybrid chimeric system for versatile and ultra-sensitive RNase detection. Sci Rep 2015; 5:9558. [PMID: 25828752 PMCID: PMC4381352 DOI: 10.1038/srep09558] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/11/2015] [Indexed: 12/21/2022] Open
Abstract
We developed a new versatile strategy that allows the detection of several classes of RNases (i.e., targeting ss- or ds-RNA, DNA/RNA hetero-hybrid or junctions) with higher sensitivity than existing assays. Our two-step approach consists of a DNA-RNA-DNA chimeric Hairpin Probe (cHP) conjugated to magnetic microparticles and containing a DNAzyme sequence in its terminal region, and molecular beacons for fluorescence signal generation. In the first step, the digestion of the RNA portion of the cHP sequences in presence of RNases leads to the release of multiple copies of the DNAzyme in solution. Then, after magnetic washing, each DNAzyme molecule elicits the catalytic cleavage of numerous molecular beacons, providing a strong amplification of the overall sensitivity of the assay. We successfully applied our approach to detect very low concentrations of RNase A, E. coli RNase I, and RNase H. Furthermore, we analyzed the effect of two antibiotics (penicillin and streptomycin) on RNase H activity, demonstrating the applicability of our strategy for the screening of inhibitors. Finally, we exploited our system to detect RNase activity directly in crude biological samples (i.e., blood and saliva) and in cell culture medium, highlighting its suitability as cheap and sensitive tool for the detection of RNase levels.
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17
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Vernekar SKV, Liu Z, Nagy E, Miller L, Kirby KA, Wilson DJ, Kankanala J, Sarafianos SG, Parniak MA, Wang Z. Design, synthesis, biochemical, and antiviral evaluations of C6 benzyl and C6 biarylmethyl substituted 2-hydroxylisoquinoline-1,3-diones: dual inhibition against HIV reverse transcriptase-associated RNase H and polymerase with antiviral activities. J Med Chem 2014; 58:651-64. [PMID: 25522204 PMCID: PMC4306517 DOI: 10.1021/jm501132s] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Reverse transcriptase (RT) associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function not targeted by current chemotherapy against human immunodeficiency virus (HIV). Although numerous chemotypes have been reported to inhibit HIV RNase H biochemically, few show significant antiviral activity against HIV. We report herein the design, synthesis, and biological evaluations of a novel variant of 2-hydroxyisoquinoline-1,3-dione (HID) scaffold featuring a crucial C-6 benzyl or biarylmethyl moiety. The synthesis involved a recently reported metal-free direct benzylation between tosylhydrazone and boronic acid, which allowed the generation of structural diversity for the hydrophobic aromatic region. Biochemical studies showed that the C-6 benzyl and biarylmethyl HID analogues, previously unknown chemotypes, consistently inhibited HIV RT-associated RNase H and polymerase with IC50s in low to submicromolar range. The observed dual inhibitory activity remained uncompromised against RT mutants resistant to non-nucleoside RT inhibitors (NNRTIs), suggesting the involvement of binding site(s) other than the NNRTI binding pocket. Intriguingly, these same compounds inhibited the polymerase, but not the RNase H function of Moloney Murine Leukemia Virus (MoMLV) RT and also inhibited Escherichia coli RNase H. Additional biochemical testing revealed a substantially reduced level of inhibition against HIV integrase. Molecular docking corroborates favorable binding of these analogues to the active site of HIV RNase H. Finally, a number of these analogues also demonstrated antiviral activity at low micromolar concentrations.
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Affiliation(s)
- Sanjeev Kumar V Vernekar
- Center for Drug Design, Academic Health Center, University of Minnesota , 516 Delaware Street SE, PWB 7-224, MMC 204 Minneapolis, Minnesota 55455, United States
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18
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Hirsch DR, Cox G, D'Erasmo MP, Shakya T, Meck C, Mohd N, Wright GD, Murelli RP. Inhibition of the ANT(2")-Ia resistance enzyme and rescue of aminoglycoside antibiotic activity by synthetic α-hydroxytropolones. Bioorg Med Chem Lett 2014; 24:4943-7. [PMID: 25283553 PMCID: PMC4798002 DOI: 10.1016/j.bmcl.2014.09.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 11/17/2022]
Abstract
Aminoglycoside-2"-O-nucleotidyltransferase ANT(2")-Ia is an aminoglycoside resistance enzyme prevalent among Gram-negative bacteria, and is one of the most common determinants of enzyme-dependant aminoglycoside-resistance. The following report outlines the use of our recently described oxidopyrylium cycloaddition/ring-opening strategy in the synthesis and profiling of a library of synthetic α-hydroxytropolones against ANT(2")-Ia. In addition, we show that two of these synthetic constructs are capable of rescuing gentamicin activity against ANT-(2")-Ia-expressing bacteria.
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Affiliation(s)
- Danielle R Hirsch
- Department of Chemistry, Brooklyn College, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, United States; Department of Chemistry, The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States
| | - Georgina Cox
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8N 4K1, Canada
| | - Michael P D'Erasmo
- Department of Chemistry, Brooklyn College, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, United States; Department of Chemistry, The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States
| | - Tushar Shakya
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8N 4K1, Canada
| | - Christine Meck
- Department of Chemistry, Brooklyn College, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, United States; Department of Chemistry, The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States
| | - Noushad Mohd
- Department of Chemistry, Brooklyn College, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, United States
| | - Gerard D Wright
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8N 4K1, Canada
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, United States; Department of Chemistry, The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States.
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19
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Meck C, D'Erasmo MP, Hirsch DR, Murelli RP. The biology and synthesis of α-hydroxytropolones. MEDCHEMCOMM 2014; 5:842-852. [PMID: 25089179 PMCID: PMC4114738 DOI: 10.1039/c4md00055b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
α-Hydroxytropolones are a subclass of the troponoid family of natural products that are of high interest due to their broad biological activity and potential as treatment options for several diseases. Despite this promise, there have been scarce synthetic chemistry-driven optimization studies on the molecules. The following review highlights key developments in the biological studies conducted on α-hydroxytropolones to date, including the few synthetic chemistry-driven optimization studies. In addition, we provide an overview of the methods currently available to access these molecules. This review is intended to serve as a resource for those interested in biological activity of α-hydroxytropolones, and inspire the development of new synthetic methods and strategies that could aid in this pursuit.
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Affiliation(s)
- Christine Meck
- Brooklyn College, City University of New York, Department of Chemistry, 2900 Bedford 4 Avenue, Brooklyn, New York, USA
| | - Michael P D'Erasmo
- Brooklyn College, City University of New York, Department of Chemistry, 2900 Bedford 4 Avenue, Brooklyn, New York, USA
| | - Danielle R Hirsch
- Brooklyn College, City University of New York, Department of Chemistry, 2900 Bedford 4 Avenue, Brooklyn, New York, USA
| | - Ryan P Murelli
- Brooklyn College, City University of New York, Department of Chemistry, 2900 Bedford 4 Avenue, Brooklyn, New York, USA
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20
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Michailidis E, Huber AD, Ryan EM, Ong YT, Leslie MD, Matzek KB, Singh K, Marchand B, Hagedorn AN, Kirby KA, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos SG. 4'-Ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) inhibits HIV-1 reverse transcriptase with multiple mechanisms. J Biol Chem 2014; 289:24533-48. [PMID: 24970894 DOI: 10.1074/jbc.m114.562694] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
4'-Ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) is a nucleoside analog that, unlike approved anti-human immunodeficiency virus type 1 (HIV-1) nucleoside reverse transcriptase inhibitors, has a 3'-OH and exhibits remarkable potency against wild-type and drug-resistant HIVs. EFdA triphosphate (EFdA-TP) is unique among nucleoside reverse transcriptase inhibitors because it inhibits HIV-1 reverse transcriptase (RT) with multiple mechanisms. (a) EFdA-TP can block RT as a translocation-defective RT inhibitor that dramatically slows DNA synthesis, acting as a de facto immediate chain terminator. Although non-translocated EFdA-MP-terminated primers can be unblocked, they can be efficiently converted back to the EFdA-MP-terminated form. (b) EFdA-TP can function as a delayed chain terminator, allowing incorporation of an additional dNTP before blocking DNA synthesis. In such cases, EFdA-MP-terminated primers are protected from excision. (c) EFdA-MP can be efficiently misincorporated by RT, leading to mismatched primers that are extremely hard to extend and are also protected from excision. The context of template sequence defines the relative contribution of each mechanism and affects the affinity of EFdA-MP for potential incorporation sites, explaining in part the lack of antagonism between EFdA and tenofovir. Changes in the type of nucleotide before EFdA-MP incorporation can alter its mechanism of inhibition from delayed chain terminator to immediate chain terminator. The versatility of EFdA in inhibiting HIV replication by multiple mechanisms may explain why resistance to EFdA is more difficult to emerge.
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Affiliation(s)
- Eleftherios Michailidis
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Andrew D Huber
- From the Christopher Bond Life Sciences Center and Departments of Veterinary Pathobiology and
| | - Emily M Ryan
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Yee T Ong
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Maxwell D Leslie
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Kayla B Matzek
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Kamalendra Singh
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Bruno Marchand
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Ariel N Hagedorn
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Karen A Kirby
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211
| | - Lisa C Rohan
- Magee-Womens Research Institute and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Eiichi N Kodama
- Division of Emerging Infectious Diseases, Tohoku University, Sendai 980-8575, Japan
| | - Hiroaki Mitsuya
- Department of Internal Medicine, Kumamoto University, Kumamoto 860-8556, Japan, Experimental Retrovirology Section, HIV/AIDS Malignancy Branch, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Michael A Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Stefan G Sarafianos
- From the Christopher Bond Life Sciences Center and Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65211, Biochemistry, University of Missouri, Columbia, Missouri 65211,
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21
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Kang D, Song Y, Chen W, Zhan P, Liu X. “Old Dogs with New Tricks”: exploiting alternative mechanisms of action and new drug design strategies for clinically validated HIV targets. MOLECULAR BIOSYSTEMS 2014; 10:1998-2022. [DOI: 10.1039/c4mb00147h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Stafford KA, Palmer Iii AG. Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site. F1000Res 2014; 3:67. [PMID: 25075292 PMCID: PMC4032109 DOI: 10.12688/f1000research.3605.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/07/2014] [Indexed: 11/26/2022] Open
Abstract
Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially of the E. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. In this work, we describe molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states. Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion. Notably, representatives of bacterial, eukaryotic, and retroviral RNases H all exhibit similar active-site rigidity, suggesting that this dynamic feature is only subtly modulated by amino acid sequence and is primarily imposed by the distinctive RNase H protein fold.
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Affiliation(s)
- Kate A Stafford
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Arthur G Palmer Iii
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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23
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Schneider A, Peter D, Schmitt J, Leo B, Richter F, Rösch P, Wöhrl BM, Hartl MJ. Structural requirements for enzymatic activities of foamy virus protease-reverse transcriptase. Proteins 2013; 82:375-85. [DOI: 10.1002/prot.24394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/30/2013] [Accepted: 08/09/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Anna Schneider
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr. 30; D-95447 Bayreuth Germany
| | - Daniel Peter
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr. 30; D-95447 Bayreuth Germany
| | - Jessica Schmitt
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr. 30; D-95447 Bayreuth Germany
| | - Berit Leo
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr. 30; D-95447 Bayreuth Germany
| | - Franziska Richter
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr. 30; D-95447 Bayreuth Germany
| | - Paul Rösch
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr. 30; D-95447 Bayreuth Germany
| | - Birgitta M. Wöhrl
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr. 30; D-95447 Bayreuth Germany
| | - Maximilian J. Hartl
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr. 30; D-95447 Bayreuth Germany
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24
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Michailidis E, Ryan EM, Hachiya A, Kirby KA, Marchand B, Leslie MD, Huber AD, Ong YT, Jackson JC, Singh K, Kodama EN, Mitsuya H, Parniak MA, Sarafianos SG. Hypersusceptibility mechanism of Tenofovir-resistant HIV to EFdA. Retrovirology 2013; 10:65. [PMID: 23800377 PMCID: PMC3695782 DOI: 10.1186/1742-4690-10-65] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/13/2013] [Indexed: 11/28/2022] Open
Abstract
Background The K65R substitution in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is the major resistance mutation selected in patients treated with first-line antiretroviral tenofovir disoproxil fumarate (TDF). 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA), is the most potent nucleoside analog RT inhibitor (NRTI) that unlike all approved NRTIs retains a 3'-hydroxyl group and has remarkable potency against wild-type (WT) and drug-resistant HIVs. EFdA acts primarily as a chain terminator by blocking translocation following its incorporation into the nascent DNA chain. EFdA is in preclinical development and its effect on clinically relevant drug resistant HIV strains is critically important for the design of optimal regimens prior to initiation of clinical trials. Results Here we report that the K65R RT mutation causes hypersusceptibility to EFdA. Specifically, in single replication cycle experiments we found that EFdA blocks WT HIV ten times more efficiently than TDF. Under the same conditions K65R HIV was inhibited over 70 times more efficiently by EFdA than TDF. We determined the molecular mechanism of this hypersensitivity using enzymatic studies with WT and K65R RT. This substitution causes minor changes in the efficiency of EFdA incorporation with respect to the natural dATP substrate and also in the efficiency of RT translocation following incorporation of the inhibitor into the nascent DNA. However, a significant decrease in the excision efficiency of EFdA-MP from the 3’ primer terminus appears to be the primary cause of increased susceptibility to the inhibitor. Notably, the effects of the mutation are DNA-sequence dependent. Conclusion We have elucidated the mechanism of K65R HIV hypersusceptibility to EFdA. Our findings highlight the potential of EFdA to improve combination strategies against TDF-resistant HIV-1 strains.
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Affiliation(s)
- Eleftherios Michailidis
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65211, USA
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25
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Evaluation of Combinations of 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine with Clinically Used Antiretroviral Drugs. Antimicrob Agents Chemother 2013; 57:4554-4558. [PMID: 23796932 DOI: 10.1128/aac.00283-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 06/15/2013] [Indexed: 11/20/2022] Open
Abstract
Drug combination studies of 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) with FDA-approved drugs were evaluated by two different methods, MacSynergy II and CalcuSyn. Most of the combinations, including the combination of the two adenosine analogs EFdA and tenofovir, were essentially additive, without substantial antagonism or synergism. The combination of EFdA and rilpivirine showed apparent synergism. These studies provide information that may be useful for the design of EFdA combination regimens for initial and salvage therapy assessment.
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26
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Abstract
RNase H (retroviral ribonuclease H) cleaves the phosphate backbone of the RNA template within an RNA/DNA hybrid to complete the synthesis of double-stranded viral DNA. In the present study we have determined the complete structure of the RNase H domain from XMRV (xenotropic murine leukaemia virus-related virus) RT (reverse transcriptase). The basic protrusion motif of the XMRV RNase H domain is folded as a short helix and an adjacent highly bent loop. Structural superposition and subsequent mutagenesis experiments suggest that the basic protrusion motif plays a role in direct binding to the major groove in RNA/DNA hybrid, as well as in establishing the co-ordination among modules in RT necessary for proper function.
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27
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Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SFJ, Nowotny M. Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 2013; 41:3874-87. [PMID: 23382176 PMCID: PMC3616737 DOI: 10.1093/nar/gkt053] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/11/2013] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
A key step in proliferation of retroviruses is the conversion of their RNA genome to double-stranded DNA, a process catalysed by multifunctional reverse transcriptases (RTs). Dimeric and monomeric RTs have been described, the latter exemplified by the enzyme of Moloney murine leukaemia virus. However, structural information is lacking that describes the substrate binding mechanism for a monomeric RT. We report here the first crystal structure of a complex between an RNA/DNA hybrid substrate and polymerase-connection fragment of the single-subunit RT from xenotropic murine leukaemia virus-related virus, a close relative of Moloney murine leukaemia virus. A comparison with p66/p51 human immunodeficiency virus-1 RT shows that substrate binding around the polymerase active site is conserved but differs in the thumb and connection subdomains. Small-angle X-ray scattering was used to model full-length xenotropic murine leukaemia virus-related virus RT, demonstrating that its mobile RNase H domain becomes ordered in the presence of a substrate-a key difference between monomeric and dimeric RTs.
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Affiliation(s)
- Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Wojciech Potrzebowski
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Petr V. Konarev
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Jason W. Rausch
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marion K. Bona
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Dmitri I. Svergun
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Janusz M. Bujnicki
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Stuart F. J. Le Grice
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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Leo B, Schweimer K, Rösch P, Hartl MJ, Wöhrl BM. The solution structure of the prototype foamy virus RNase H domain indicates an important role of the basic loop in substrate binding. Retrovirology 2012; 9:73. [PMID: 22962864 PMCID: PMC3443672 DOI: 10.1186/1742-4690-9-73] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/10/2012] [Indexed: 11/13/2022] Open
Abstract
Background The ribonuclease H (RNase H) domains of retroviral reverse transcriptases play an essential role in the replication cycle of retroviruses. During reverse transcription of the viral genomic RNA, an RNA/DNA hybrid is created whose RNA strand needs to be hydrolyzed by the RNase H to enable synthesis of the second DNA strand by the DNA polymerase function of the reverse transcriptase. Here, we report the solution structure of the separately purified RNase H domain from prototype foamy virus (PFV) revealing the so-called C-helix and the adjacent basic loop, which both were suggested to be important in substrate binding and activity. Results The solution structure of PFV RNase H shows that it contains a mixed five-stranded β-sheet, which is sandwiched by four α-helices (A-D), including the C-helix, on one side and one α-helix (helix E) on the opposite side. NMR titration experiments demonstrate that upon substrate addition signal changes can be detected predominantly in the basic loop as well as in the C-helix. All these regions are oriented towards the bound substrate. In addition, signal intensities corresponding to residues in the B-helix and the active site decrease, while only minor or no changes of the overall structure of the RNase H are detectable upon substrate binding. Dynamic studies confirm the monomeric state of the RNase H domain. Structure comparisons with HIV-1 RNase H, which lacks the basic protrusion, indicate that the basic loop is relevant for substrate interaction, while the C-helix appears to fulfill mainly structural functions, i.e. positioning the basic loop in the correct orientation for substrate binding. Conclusions The structural data of PFV RNase H demonstrate the importance of the basic loop, which contains four positively charged lysines, in substrate binding and the function of the C-helix in positioning of the loop. In the dimeric full length HIV-1 RT, the function of the basic loop is carried out by a different loop, which also harbors basic residues, derived from the connection domain of the p66 subunit. Our results suggest that RNases H which are also active as separate domains might need a functional basic loop for proper substrate binding.
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Affiliation(s)
- Berit Leo
- Universität Bayreuth, Lehrstuhl Biopolymere, Universitätsstr, 30, D-95447 Bayreuth, Germany
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Zhou D, Chung S, Miller M, Grice SFJL, Wlodawer A. Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus. J Struct Biol 2012; 177:638-45. [PMID: 22366278 DOI: 10.1016/j.jsb.2012.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 10/28/2022]
Abstract
The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site α-hydroxytropolone inhibitor. Enzymatic assays showed that the intact RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with β-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.
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Affiliation(s)
- Dongwen Zhou
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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