Design, Synthesis, and Biological Evaluations of Hydroxypyridonecarboxylic Acids as Inhibitors of HIV Reverse Transcriptase Associated RNase H

Kankanala, Jayakanth; Kirby, Karen A.; Liu, Feng; Miller, Lena; Nagy, Éva; Wilson, Daniel J.; Parniak, Michael A.; Sarafianos, Stefan G.; Wang, Zhengqiang

doi:10.1021/acs.jmedchem.6b00465

Cited by 59 publications

(62 citation statements)

References 44 publications

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“…A structure of RNase H in complex with the inhibitor shows that HPCAs bind at the active site, directly chelating the metal cations (21). In view of the structural similarity between the catalytic pocket of pUL89-C and RNase H, we hypothesize that these compounds would bind in a similar way to pUL89-C and inhibit its activity.…”

Section: Discussionmentioning

confidence: 95%

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Inhibition of Human Cytomegalovirus pUL89 Terminase Subunit Blocks Virus Replication and Genome Cleavage

Wang

Mao

Kankanala

et al. 2017

J Virol

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The human cytomegalovirus terminase complex cleaves concatemeric genomic DNA into unit lengths during genome packaging and particle assembly. This process is an attractive drug target because cleavage of concatemeric DNA is not required in mammalian cell DNA replication, indicating that drugs targeting the terminase complex could be safe and selective. One component of the human cytomegalovirus terminase complex, pUL89, provides the endonucleolytic activity for genome cleavage, and the domain responsible is reported to have an RNase H-like fold. We hypothesize that the pUL89 endonuclease activity is inhibited by known RNase H inhibitors. Using a novel enzyme-linked immunosorbent assay (ELISA) format as a screening assay, we found that a hydroxypyridonecarboxylic acid compound, previously reported to be an inhibitor of human immunodeficiency virus RNase H, inhibited pUL89 endonuclease activity at low-micromolar concentrations. Further characterization revealed that this pUL89 endonuclease inhibitor blocked human cytomegalovirus replication at a relatively late time point, similarly to other reported terminase complex inhibitors. Importantly, this inhibitor also prevented the cleavage of viral genomic DNA in infected cells. Taken together, these results substantiate our pharmacophore hypothesis and validate our ligand-based approach toward identifying novel inhibitors of pUL89 endonuclease.IMPORTANCE Human cytomegalovirus infection in individuals lacking a fully functioning immune system, such as newborns and transplant patients, can have severe and debilitating consequences. The U.S. Food and Drug Administration-approved anti-human cytomegalovirus drugs mainly target the viral polymerase, and resistance to these drugs has appeared. Therefore, anti-human cytomegalovirus drugs from novel targets are needed for use instead of, or in combination with, current polymerase inhibitors. pUL89 is a viral ATPase and endonuclease and is an attractive target for anti-human cytomegalovirus drug development. We identified and characterized an inhibitor of pUL89 endonuclease activity that also inhibits human cytomegalovirus replication in cell culture. pUL89 endonuclease, therefore, should be explored as a potential target for antiviral development against human cytomegalovirus.KEYWORDS human cytomegalovirus, terminase, pUL89 inhibitor, hydroxypyridonecarboxylic acid, metal chelation H uman cytomegalovirus (HCMV) infection is a significant cause of morbidity and mortality in immunocompromised patients, including transplant recipients and AIDS patients (reviewed in reference 1). In addition, HCMV infects 1% of all newborns and is a leading cause of brain damage and hearing loss (2). Currently, most of the U.S. Food and Drug Administration (FDA)-approved anti-HCMV drugs target the viral polymerase, including ganciclovir (GCV), valganciclovir, cidofovir, and foscarnet (reviewed in

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Section: Discussionmentioning

confidence: 95%

“…In our previous study, a series of hydroxypyridonecarboxylic acids (HPCAs) was designed to inhibit HIV RNase H via metal chelation (21). We hypothesize here that the chelating triad of the HPCAs could also interact with the two metal cations in the pUL89-C active site to inhibit endonuclease activity.…”

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confidence: 99%

Inhibition of Human Cytomegalovirus pUL89 Terminase Subunit Blocks Virus Replication and Genome Cleavage

Wang

Mao

Kankanala

et al. 2017

J Virol

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“…Several types of active site inhibitors of RT-associated RNase H have been reported in the literature (Figure 1A). These include diketoacids ( 1 ) [10], 2-hydroxyisoquinoline-1,3-diones (HID, 2 ) [11–13], hydroxylated tropolones ( 3 ) [14], pyrimidinol carboxylic acids ( 4 ) [3], hydroxypyridone carboxylic acids ( 5 ) [15], hydroxynaphthyridines ( 6 ) [16], and pyridopyrimidones ( 7 ) [17]. Notably, all these chemotypes feature a metal chelator and a peripheral hydrophobic moiety.…”

Section: Introductionmentioning

confidence: 99%

Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H

Kankanala

Kirby

Huber

et al. 2017

European Journal of Medicinal Chemistry

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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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“…2A). The crystal structure was solved by molecular replacement (25) using PDB accession number 5J1E as a starting model (16). Rigid-body studies, simulated annealing, atomic displacement parameter (ADP), real-space studies, and restrained refinement were carried out on the initial model (26), and several cycles of model building (27) and refinement (26) were performed (final statistics in Table S1 in the supplemental material).…”

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A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase

Kirby

Myshakina

Christen

et al. 2017

Antimicrob Agents Chemother

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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 [IC 50 ] ϭ 2.6 M) and RNH functions (IC 50 ϭ 0.65 M) 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.KEYWORDS RNase H, human immunodeficiency virus, inhibitor, reverse transcriptase H IV-1 reverse transcriptase (RT) plays a critical role in virus replication. It has multiple functions, including RNA-dependent DNA synthesis, RNase H (RNH) activity, and DNA-dependent DNA synthesis to convert the viral single-stranded RNA genome into double-stranded DNA for downstream incorporation into the host cell genome (1). At least one component of highly active antiretroviral therapy (HAART) administered to patients includes RT polymerase inhibitors, either a nucleoside RT inhibitor(s) or a nonnucleoside RT inhibitor, or both. Prolonged use of antivirals can lead to side effects or drug resistance (2, 3). Hence, new antivirals that act by novel mechanisms of action are needed. No currently approved therapeutics target the RNH function of HIV-1 RT. Hence, RNH is an attractive target for future antiviral therapies.RNH inhibitors of several different chemotypes have been identified and characterized for their effectiveness against HIV-1 (4). These include acylhydrazones (5-7), diketo acids (8, 9), ␣-hydroxytropolones (10), vinylogous ureas (11), naphthyridinones (12), pyridopyrimidinones (13,14), pyrimidinol carboxylic acids (15), hydroxypyridonecarboxylic acids (16), 3-hydroxypyrimidine-2,4-diones (17, 18), and 2-hydroxyisoquinoline-1,3-diones (HIDs) (19). Notably, many 2-hydroxyisoquinoline-1,3-diones inhibit both RT polymerase and RNH functions of RT (19). In order to further understand the mechanism of RT inhibition by HIDs, we further characterized YLC2-155, which is substituted at the C7 position of the 2-hydroxyisoquinoline-1,3-dione with a furan ring (Fig. 1).

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Design, Synthesis, and Biological Evaluations of Hydroxypyridonecarboxylic Acids as Inhibitors of HIV Reverse Transcriptase Associated RNase H

Cited by 59 publications

References 44 publications

Inhibition of Human Cytomegalovirus pUL89 Terminase Subunit Blocks Virus Replication and Genome Cleavage

Inhibition of Human Cytomegalovirus pUL89 Terminase Subunit Blocks Virus Replication and Genome Cleavage

Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H

A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase

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