New Anthraquinone Derivatives as Inhibitors of the HIV-1 Reverse Transcriptase-Associated Ribonuclease H Function

Esposito, Francesca; Corona, Angela; Zinzula, Luca; Kharlamova, Т. V.; Tramontano, Enzo

doi:10.1159/000343101

Cited by 27 publications

(27 citation statements)

References 49 publications

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“…Figure 1 shows the chemical structures of the inhibitors used in this study. When these HIV-1 RHIs were tested on PFV PR-RT in biochemical assays using the methods previously described for HIV-1 RT-associated RNase H and polymerase functions (34)(35)(36) and the reaction conditions previously optimized for PFV PR-RT (3), we observed that all selected RHIs inhibited the PFV PR-RT (Table 1 and Fig. 2).…”

Section: Resultsmentioning

confidence: 90%

Inhibition of Foamy Virus Reverse Transcriptase by Human Immunodeficiency Virus Type 1 RNase H Inhibitors

Corona

Schneider

Schweimer

et al. 2014

Antimicrob Agents Chemother

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bRNase H plays an essential role in the replication of human immunodeficiency virus type 1 (HIV-1). Therefore, it is a promising target for drug development. However, the identification of HIV-1 RNase H inhibitors (RHIs) has been hampered by the open morphology of its active site, the limited number of available RNase H crystal structures in complex with inhibitors, and the fact that, due to the high concentrations of Mg 2؉ needed for protein stability, HIV-1 RNase H is not suitable for nuclear magnetic resonance (NMR) inhibitor studies. We recently showed that the RNase H domains of HIV-1 and prototype foamy virus (PFV) reverse transcriptases (RTs) exhibit a high degree of structural similarity. Thus, we examined whether PFV RNase H can serve as an HIV-1 RNase H model for inhibitor interaction studies. Five HIV-1 RHIs inhibited PFV RNase H activity at low-micromolar concentrations similar to those of HIV-1 RNase H, suggesting pocket similarity of the RNase H domains. NMR titration experiments with the PFV RNase H domain and the RHI RDS1643 (6-[1-(4-fluorophenyl)methyl-1H-pyrrol-2-yl)]-2,4-dioxo-5-hexenoic acid ethyl ester) were performed to determine its binding site. Based on these results and previous data, in silico docking analysis showed a putative RDS1643 binding region that reaches into the PFV RNase H active site. Structural overlays were performed with HIV-1 and PFV RNase H to propose the RDS1643 binding site in HIV-1 RNase H. Our results suggest that this approach can be used to establish PFV RNase H as a model system for HIV-1 RNase H in order to identify putative inhibitor binding sites in HIV-1 RNase H.

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Section: Resultsmentioning

confidence: 90%

Inhibition of Foamy Virus Reverse Transcriptase by Human Immunodeficiency Virus Type 1 RNase H Inhibitors

Corona

Schneider

Schweimer

et al. 2014

Antimicrob Agents Chemother

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“…First, the compound prevents ABCA1 downregulation by Nef, and ABCA1 has been shown to inhibit HIV-1 replication by reducing lipid rafts abundance on the plasma membrane and affecting production and infectivity of nascent virions 3, 28, 35, 36 . Second, previous reports presented evidence that anthraquinone derivatives inhibit the ribonuclease H function of HIV-1 reverse transcriptase 43, 44 . Therefore, the action of compound NSC 13987 in HIV-1-infected cells may be a combination of inhibiting Nef-CNX interaction and a separate antiviral activity.…”

Section: Discussionmentioning

confidence: 99%

Interaction Between HIV-1 Nef and Calnexin

Hunegnaw

Vassylyeva

Dubrovsky

et al. 2016

ATVB

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Objective HIV-infected patients are at an increased risk of developing atherosclerosis, in part due to downmodulation and functional impairment of ATP-Binding Cassette A1 (ABCA1) cholesterol transporter by the HIV-1 protein Nef. The mechanism of this effect involves Nef interacting with an endoplasmic reticulum (ER) chaperone calnexin and disrupting calnexin binding to ABCA1, leading to ABCA1 retention in ER, its degradation and resulting suppression of cholesterol efflux. However, molecular details of Nef-calnexin interaction remained unknown, limiting translational impact of this finding. Approach and results Here, we used molecular modeling and mutagenesis to characterize Nef-calnexin interaction and to identify small molecule compounds that could block it. We demonstrated that interaction between Nef and calnexin is direct and can be reconstituted using recombinant proteins in vitro with a binding affinity of 89.1 nM measured by surface plasmon resonance. The cytoplasmic tail of calnexin is essential and sufficient for interaction with Nef, and binds Nef with affinity of 9.4 nM. Replacing lysine residues in positions 4 and 7 of Nef with alanines abrogates Nef-calnexin interaction, prevents ABCA1 downregulation by Nef, and preserves cholesterol efflux from HIV-infected cells. Through virtual screening of the NCI library of compounds, we identified a compound, 1[(7-Oxo-7H-benz[de]anthracene-3-yl)amino]anthraquinone, which blocked Nef-calnexin interaction, partially restored ABCA1 activity in HIV-infected cells, and reduced foam cell formation in a culture of HIV-infected macrophages. Conclusion This study identifies potential targets that can be exploited to block the pathogenic effect of HIV infection on cholesterol metabolism and prevent atherosclerosis in HIV-infected subjects.

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“…The RNase H active site is located at the C terminus in close contact with the p51 subunit and contains a highly conserved and essential DEDD motif comprising the carboxylate residues D443, E478, D498, and D549, which coordinate two Mg 2 + cations that are required as cofactors for the hydrolysis reaction. [5] Whereas no RNase H inhibitor has reached clinical trials, a limited number of compounds have been reported, and they can be classified into two classes: metal-chelating active-site inhibitors, which bind and coordinate the two Mg 2 + ion cofactors, and allosteric inhibitors, which induce a conformational change in the active site that disables the RNA:DNA hybrid substrate binding. [6][7][8][9][10] Allosteric inhibitors could be attractive both to counteract the development of resistant strains and to avoid the inhibition of related host enzymes, such as the human RNase H1.…”

Section: Introductionmentioning

confidence: 99%

Studies on Cycloheptathiophene‐3‐carboxamide Derivatives as Allosteric HIV‐1 Ribonuclease H Inhibitors

et al. 2016

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Despite the significant progress achieved with combination antiretroviral therapy in the fight against human immunodeficiency virus (HIV) infection, the difficulty to eradicate the virus together with the rapid emergence of multidrug-resistant strains clearly underline a pressing need for innovative agents, possibly endowed with novel mechanisms of action. In this context, owing to its essential role in HIV genome replication, the reverse transcriptase associated ribonuclease H (RNase H) has proven to be an appealing target. To identify new RNase H inhibitors, an in-house cycloheptathiophene-3-carboxamide library was screened; this led to compounds endowed with inhibitory activity, the structural optimization of which led to the catechol derivative 2-(3,4-dihydroxybenzamido)-N-(pyridin-2-yl)-5,6,7,8-tetrahydro-4H-cyclohepta[b]thiophene-3-carboxamide (compound 33) with an IC50 value on the RNase H activity in the nanomolar range. Mechanistic studies suggested selective inhibition of the RNase H through binding to an innovative allosteric site, which could be further exploited to enrich this class of inhibitors.

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New Anthraquinone Derivatives as Inhibitors of the HIV-1 Reverse Transcriptase-Associated Ribonuclease H Function

Cited by 27 publications

References 49 publications

Inhibition of Foamy Virus Reverse Transcriptase by Human Immunodeficiency Virus Type 1 RNase H Inhibitors

Inhibition of Foamy Virus Reverse Transcriptase by Human Immunodeficiency Virus Type 1 RNase H Inhibitors

Interaction Between HIV-1 Nef and Calnexin

Studies on Cycloheptathiophene‐3‐carboxamide Derivatives as Allosteric HIV‐1 Ribonuclease H Inhibitors

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