scholarly journals Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity

2016 ◽  
Vol 90 (15) ◽  
pp. 6906-6917 ◽  
Author(s):  
Pablo Garcia-Miranda ◽  
Jordan T. Becker ◽  
Bayleigh E. Benner ◽  
Alexander Blume ◽  
Nathan M. Sherer ◽  
...  
Keyword(s):  
Thermodynamic Stability ◽  
Virus Infectivity ◽  
Ribosomal Frameshift ◽  
Stem Loop ◽  
Assembly Mechanism ◽  
Polyprotein Precursor ◽  
The Stability ◽  
Hiv 1 ◽  
In Cells

ABSTRACTHuman immunodeficiency virus (HIV) replication is strongly dependent upon a programmed ribosomal frameshift. Here we investigate the relationships between the thermodynamic stability of the HIV type 1 (HIV-1) RNA frameshift site stem-loop, frameshift efficiency, and infectivity, using pseudotyped HIV-1 and HEK293T cells. The data reveal a strong correlation between frameshift efficiency and local, but not overall, RNA thermodynamic stability. Mutations that modestly increase the local stability of the frameshift site RNA stem-loop structure increase frameshift efficiency 2-fold to 3-fold in cells. Thus, frameshift efficiency is determined by the strength of the thermodynamic barrier encountered by the ribosome. These data agree with previousin vitromeasurements, suggesting that there are no virus- or host-specific factors that modulate frameshifting. The data also indicate that there are no sequence-specific requirements for the frameshift site stem-loop. A linear correlation between Gag-polymerase (Gag-Pol) levels in cells and levels in virions supports the idea of a stochastic virion assembly mechanism. We further demonstrate that the surrounding genomic RNA secondary structure influences frameshift efficiency and that a mutation that commonly arises in response to protease inhibitor therapy creates a functional but inefficient secondary slippery site. Finally, HIV-1 mutants with enhanced frameshift efficiencies are significantly less infectious, suggesting that compounds that increase frameshift efficiency by as little as 2-fold may be effective at suppressing HIV-1 replication.IMPORTANCEHIV, like many retroviruses, utilizes a −1 programmed ribosomal frameshift to generate viral enzymes in the form of a Gag-Pol polyprotein precursor. Thus, frameshifting is essential for viral replication. Here, we utilized a panel of mutant HIV strains to demonstrate that in cells, frameshifting efficiency is correlated with the stability of the local thermodynamic barrier to ribosomal translocation. Increasing the stability of the frameshift site RNA increases the frameshift efficiency 2-fold to 3-fold. Mutant viruses with increased frameshift efficiencies have significantly reduced infectivity. These data suggest that this effect might be exploited in the development of novel antiviral strategies.

scholarly journals 1592U89, a novel carbocyclic nucleoside analog with potent, selective anti-human immunodeficiency virus activity.

1997 ◽  
Vol 41 (5) ◽  
pp. 1082-1093 ◽  
Author(s):  
S M Daluge ◽  
S S Good ◽  
M B Faletto ◽  
W H Miller ◽  
M H St Clair ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Oral Bioavailability ◽  
Human Peripheral Blood ◽  
Cross Resistance ◽  
Immunodeficiency Virus ◽  
Carbocyclic Nucleoside ◽  
Hiv 1 ◽  
In Cells

1592U89, (-)-(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]-2-cyclo pentene-1-methanol, is a carbocyclic nucleoside with a unique biological profile giving potent, selective anti-human immunodeficiency virus (HIV) activity. 1592U89 was selected after evaluation of a wide variety of analogs containing a cyclopentene substitution for the 2'-deoxyriboside of natural deoxynucleosides, optimizing in vitro anti-HIV potency, oral bioavailability, and central nervous system (CNS) penetration. 1592U89 was equivalent in potency to 3'-azido-3'-deoxythymidine (AZT) in human peripheral blood lymphocyte (PBL) cultures against clinical isolates of HIV type 1 (HIV-1) from antiretroviral drug-naive patients (average 50% inhibitory concentration [IC50], 0.26 microM for 1592U89 and 0.23 microM for AZT). 1592U89 showed minimal cross-resistance (approximately twofold) with AZT and other approved HIV reverse transcriptase (RT) inhibitors. 1592U89 was synergistic in combination with AZT, the nonnucleoside RT inhibitor nevirapine, and the protease inhibitor 141W94 in MT4 cells against HIV-1 (IIIB). 1592U89 was anabolized intracellularly to its 5'-monophosphate in CD4+ CEM cells and in PBLs, but the di- and triphosphates of 1592U89 were not detected. The only triphosphate found in cells incubated with 1592U89 was that of the guanine analog (-)-carbovir (CBV). However, the in vivo pharmacokinetic, distribution, and toxicological profiles of 1592U89 were distinct from and improved over those of CBV, probably because CBV itself was not appreciably formed from 1592U89 in cells or animals (<2%). The 5'-triphosphate of CBV was a potent, selective inhibitor of HIV-1 RT, with Ki values for DNA polymerases (alpha, beta, gamma, and epsilon which were 90-, 2,900-, 1,200-, and 1,900-fold greater, respectively, than for RT (Ki, 21 nM). 1592U89 was relatively nontoxic to human bone marrow progenitors erythroid burst-forming unit and granulocyte-macrophage CFU (IC50s, 110 microM) and human leukemic and liver tumor cell lines. 1592U89 had excellent oral bioavailability (105% in the rat) and penetrated the CNS (rat brain and monkey cerebrospinal fluid) as well as AZT. Having demonstrated an excellent preclinical profile, 1592U89 has progressed to clinical evaluation in HIV-infected patients.

scholarly journals Screening of a Focused Ubiquitin-Proteasome Pathway Inhibitor Library Identifies Small Molecules as Novel Modulators of Botulinum Neurotoxin Type A Toxicity

2021 ◽  
Vol 12 ◽  
Author(s):  
Edanur Sen ◽  
Krishna P. Kota ◽  
Rekha G. Panchal ◽  
Sina Bavari ◽  
Erkan Kiris
Keyword(s):  
Small Molecules ◽  
Ubiquitin Proteasome Pathway ◽  
Lead Compounds ◽  
Botulinum Neurotoxins ◽  
Ubiquitin Proteasome ◽  
Proteasome Pathway ◽  
The Stability ◽  
Dose Dependent ◽  
In Cells

Botulinum neurotoxins (BoNTs) are known as the most potent bacterial toxins, which can cause potentially deadly disease botulism. BoNT Serotype A (BoNT/A) is the most studied serotype as it is responsible for most human botulism cases, and its formulations are extensively utilized in clinics for therapeutic and cosmetic applications. BoNT/A has the longest-lasting effect in neurons compared to other serotypes, and there has been high interest in understanding how BoNT/A manages to escape protein degradation machinery in neurons for months. Recent work demonstrated that an E3 ligase, HECTD2, leads to efficient ubiquitination of the BoNT/A Light Chain (A/LC); however, the dominant activity of a deubiquitinase (DUB), VCIP135, inhibits the degradation of the enzymatic component. Another DUB, USP9X, was also identified as a potential indirect contributor to A/LC degradation. In this study, we screened a focused ubiquitin-proteasome pathway inhibitor library, including VCIP135 and USP9X inhibitors, and identified ten potential lead compounds affecting BoNT/A mediated SNAP-25 cleavage in neurons in pre-intoxication conditions. We then tested the dose-dependent effects of the compounds and their potential toxic effects in cells. A subset of the lead compounds demonstrated efficacy on the stability and ubiquitination of A/LC in cells. Three of the compounds, WP1130 (degrasyn), PR-619, and Celastrol, further demonstrated efficacy against BoNT/A holotoxin in an in vitro post-intoxication model. Excitingly, PR-619 and WP1130 are known inhibitors of VCIP135 and USP9X, respectively. Modulation of BoNT turnover in cells by small molecules can potentially lead to the development of effective countermeasures against botulism.

scholarly journals Robust cullin-RING ligase function is established by a multiplicity of poly-ubiquitylation pathways

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Spencer Hill ◽  
Kurt Reichermeier ◽  
Daniel C Scott ◽  
Lorena Samentar ◽  
Jasmin Coulombe-Huntington ◽  
...  
Keyword(s):  
Chain Extension ◽  
Genome Wide ◽  
A Genome ◽  
Crispr Screen ◽  
Extension Activity ◽  
The Stability ◽  
Genetic Buffering ◽  
Ligase Function ◽  
In Cells

The cullin-RING ligases (CRLs) form the major family of E3 ubiquitin ligases. The prototypic CRLs in yeast, called SCF enzymes, employ a single E2 enzyme, Cdc34, to build poly-ubiquitin chains required for degradation. In contrast, six different human E2 and E3 enzyme activities, including Cdc34 orthologs UBE2R1 and UBE2R2, appear to mediate SCF-catalyzed substrate polyubiquitylation in vitro. The combinatorial interplay of these enzymes raises questions about genetic buffering of SCFs in human cells and challenges the dogma that E3s alone determine substrate specificity. To enable the quantitative comparisons of SCF-dependent ubiquitylation reactions with physiological enzyme concentrations, mass spectrometry was employed to estimate E2 and E3 levels in cells. In combination with UBE2R1/2, the E2 UBE2D3 and the E3 ARIH1 both promoted SCF-mediated polyubiquitylation in a substrate-specific fashion. Unexpectedly, UBE2R2 alone had negligible ubiquitylation activity at physiological concentrations and the ablation of UBE2R1/2 had no effect on the stability of SCF substrates in cells. A genome-wide CRISPR screen revealed that an additional E2 enzyme, UBE2G1, buffers against the loss of UBE2R1/2. UBE2G1 had robust in vitro chain extension activity with SCF, and UBE2G1 knockdown in cells lacking UBE2R1/2 resulted in stabilization of the SCF substrates p27 and CYCLIN E as well as the CUL2-RING ligase substrate HIF1α. The results demonstrate the human SCF enzyme system is diversified by association with multiple catalytic enzyme partners.

scholarly journals Strong In Vivo Inhibition of HIV-1 Replication by Nullbasic, a Tat Mutant

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Hongping Jin ◽  
Yifan Sun ◽  
Dongsheng Li ◽  
Min-Hsuan Lin ◽  
Mary Lor ◽  
...  
Keyword(s):  
Mutant Form ◽  
Mrna Levels ◽  
Functional Cure ◽  
Fold Reduction ◽  
Infected Cells ◽  
Hiv 1 ◽  
Transcription And Replication ◽  
In Cells

ABSTRACT Nullbasic is a mutant form of the HIV-1 transcriptional activator protein (Tat) that strongly inhibits HIV-1 transcription and replication in lymphocytes in vitro. To investigate Nullbasic inhibition in vivo, we employed an NSG mouse model where animals were engrafted with primary human CD4+ cells expressing a Nullbasic-ZsGreen1 (NB-ZSG) fusion protein or ZSG. NB-ZSG and ZSG were delivered by using a retroviral vector where CD4+ cells were transduced either prior to (preinfection) or following (postinfection) HIV-1 infection. The transduced cells were analyzed in vitro up to 10 days postinfection (dpi) and in vivo up to 39 dpi. Compared to ZSG, NB-ZSG strongly inhibited HIV-1 replication both in vitro and in vivo using preinfection treatment. In vitro, HIV-1 mRNA levels in cells were reduced by up to 60-fold. In vivo, HIV-1 RNA was undetectable in plasma samples during the course of the experiment, and HIV-1 mRNA levels in resident CD4+ cells in organ tissue were reduced up to 2,800-fold. Postinfection treatment of HIV-1-infected cells with NB-ZSG attenuated HIV-1 infection for up to 14 days. In vitro, a 25-fold reduction of viral mRNA in cells was observed but diminished to a <2-fold reduction by 10 dpi. In vivo, HIV-1 RNA was undetectable in plasma of NB-ZSG mice at 14 dpi but afterwards was not significantly different between NB-ZSG mice and control mice. However, we observed higher levels of CD4+ cells in NB-ZSG mice than in control mice, suggesting that NB-ZSG imparted a survival advantage to HIV-1-infected animals. IMPORTANCE HIV-1 infection is effectively controlled by antiviral therapy that inhibits virus replication and reduces viral loads below detectable levels in patients. However, therapy interruption leads to viral rebound due to latently infected cells, which serve as a source of continued viral infection. Interest in strategies leading to a functional cure for HIV-1 infection by long-term or permanent viral suppression is growing. Here, we show that a mutant form of the HIV-1 Tat protein, referred to as Nullbasic, inhibits HIV-1 transcription in infected CD4+ cells in vivo. Analysis shows that stable expression of Nullbasic in CD4+ cells could lead to durable anti-HIV-1 activity. Nullbasic, as a gene therapy candidate, could be a part of a functional-cure strategy to suppress HIV-1 transcription and replication.

scholarly journals HSF1 inhibition attenuates HIV-1 latency reversal mediated by several candidate LRAs In Vitro and Ex Vivo

2020 ◽  
Vol 117 (27) ◽  
pp. 15763-15771 ◽  
Author(s):  
Andrew Timmons ◽  
Emily Fray ◽  
Mithra Kumar ◽  
Fengting Wu ◽  
Weiwei Dai ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Ex Vivo ◽  
In Vitro Models ◽  
Model Systems ◽  
Heat Shock Factor 1 ◽  
Primary Cells ◽  
Major Barrier ◽  
Hiv 1 ◽  
In Cells

HIV-1 latency is a major barrier to cure. Identification of small molecules that destabilize latency and allow immune clearance of infected cells could lead to treatment-free remission. In vitro models of HIV-1 latency involving cell lines or primary cells have been developed for characterization of HIV-1 latency and high-throughput screening for latency-reversing agents (LRAs). We have shown that the majority of LRAs identified to date are relatively ineffective in cells from infected individuals despite activity in model systems. We show here that, for diverse LRAs, latency reversal observed in model systems involves a heat shock factor 1 (HSF1)-mediated stress pathway. Small-molecule inhibition of HSF1 attenuated HIV-1 latency reversal by histone deactylase inhibitors, protein kinase C agonists, and proteasome inhibitors without interfering with the known mechanism of action of these LRAs. However, latency reversal by second mitochondria-derived activator of caspase (SMAC) mimetics was not affected by inhibition of HSF1. In cells from infected individuals, inhibition of HSF1 attenuated latency reversal by phorbol ester+ionomycin but not by anti-CD3+anti-CD28. HSF1 promotes elongation of HIV-1 RNA by recruiting P-TEFb to the HIV-1 long terminal repeat (LTR), and we show that inhibition of HSF1 attenuates the formation of elongated HIV-1 transcripts. We demonstrate that in vitro models of latency have higher levels of the P-TEFb subunit cyclin T1 than primary cells, which may explain why many LRAs are functional in model systems but relatively ineffective in primary cells. Together, these studies provide insights into why particular LRA combinations are effective in reversing latency in cells from infected individuals.

Effect of Derivatized Nucleotide Antiviral Drugs on HIV-1 Replication in Cells of T-Lymphoblastoid and Monocyte/Macrophage Lineage in Vitro

1990 ◽  
Vol 616 (1 AIDS) ◽  
pp. 508-510
Author(s):  
M. I. DAWSON ◽  
H. ABRAMS ◽  
A. SATYAM ◽  
S. TORKELSON ◽  
B. ROSS ◽  
...  
Keyword(s):  
Antiviral Drugs ◽  
Hiv 1 ◽  
Macrophage Lineage ◽  
In Cells

scholarly journals Alpha-Cyclodextrin Sulphate, an anti-HIV Agent, Retains its Antiviral Effect in the Presence of Hydrocortisol Phosphate

1993 ◽  
Vol 4 (1) ◽  
pp. 65-66 ◽  
Author(s):  
J. Pitha ◽  
R. Anand
Keyword(s):  
Mononuclear Cells ◽  
Human Peripheral Blood ◽  
Antiviral Effect ◽  
Simultaneous Treatment ◽  
Peripheral Blood Mononuclear ◽  
Antiviral Compound ◽  
Cytopathic Effects ◽  
The Stability ◽  
Hiv 1

Cyclodextrin sulphates alpha (a) and beta (b) were found to be inhibitors of replication of human immunodeficiency virus (HIV-1) in phytohaemagglutinin (PHA)-stimulated human peripheral blood mononuclear cells (PBMC); the same cells were also stimulated to proliferate (Anand et al., 1990). B-Cyclodextrin sulphate was also found to stimulate another, more complex, cell proliferation-neovascularization process in rabbit cornea (Folkman et al., 1989). Since the process of neovascularization is generally associated with progression of tumour growth and other pathologies, it is obvious that its stimulation by an antiviral compound may be a serious side effect. Nevertheless endotoxin-induced neovascularization can be suppressed by simultaneous treatment with b-cyclodextrin sulphate and glucocorticoids (Folkman et al., 1989). The same co-treatment may possibly be used to improve antiviral action of cyclodextrin sulphates, but such a combination therapy may not be free of complications. Glucocorticoids also affect the stability of various cellular membranes. Treatment of cells in vitro by glucocorticoids is known to stabilize their lysozymes. Glucocorticoids affect both the proliferative capacity of the cells (Cristofalo, 1972) and cytopathic effects of rabies viral infection. Furthermore, it has been reported that the cytopathic effects of rabies and of yellow fever viruses were inhibited while those of the polio virus were only mildly affected (Hannoun et al., 1965). Consequently, in this work we evaluated effects of a glucocorticoid and of glucocorticoid-a-cyclodextrin sulphate combination on HIV-1 replication.

scholarly journals The secrets of the stability of the HIV-1 capsid

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Martin Obr ◽  
Hans-Georg Kräusslich
Keyword(s):  
Small Molecule ◽  
Biophysical Studies ◽  
The Stability ◽  
Capsid Stability ◽  
Hiv 1

Structural and biophysical studies help to follow the disassembly of the HIV-1 capsid in vitro, and reveal the role of a small molecule called IP6 in regulating capsid stability.

scholarly journals Maraviroc and Other HIV-1 Entry Inhibitors Exhibit a Class-Specific Redistribution Effect That Results in Increased Extracellular Viral Load

2012 ◽  
Vol 56 (8) ◽  
pp. 4154-4160 ◽  
Author(s):  
Victor G. Kramer ◽  
Susan M. Schader ◽  
Maureen Oliveira ◽  
Susan P. Colby-Germinario ◽  
Daniel A. Donahue ◽  
...  
Keyword(s):  
Viral Load ◽  
Clinical Success ◽  
Antiretroviral Drugs ◽  
Virus Infectivity ◽  
Reverse Transcriptase Enzyme ◽  
Entry Inhibitors ◽  
Hiv 1 ◽  
Entry Inhibition ◽  
Redistribution Effect

ABSTRACTHIV entry inhibitors, such as maraviroc (MVC), prevent cell-free viruses from entering the cells. In clinical trials, patients who were treated with MVC often displayed viral loads that were above the limit of conventional viral load detection compared to efavirenz-based regimens. We hypothesize that viruses blocked by entry inhibitors may be redistributed to plasma, where they artificially increase viral load measurements compared to those with the use of antiretroviral drugs (ARVs) that act intracellularly. We infected PM-1 cells with CCR5-tropic HIV-1 BaL or CXCR4-tropic HIV-1 NL4-3 in the presence of inhibitory concentrations of efavirenz, raltegravir, enfuvirtide, maraviroc, and AMD3100, the latter three being entry inhibitors. Supernatant viral load, reverse transcriptase enzyme activity, and intracellular nucleic acid levels were measured at times up to 24 h postinfection. Infectivity of redistributed dual-tropic HIV-1 was assessed using TZM-bl cells. Extracellular viral load analysis revealed that entry inhibitor-treated cells had higher levels of virus in the supernatant than the cells treated with other ARVs at 8 h postinfection. By 24 h, the supernatant viral load was still higher for entry inhibitors than other ARVs. We observed a correlation between viral load and the step of entry inhibition. Dual-tropic virus infectivity was undiminished utilizing the CCR5 coreceptor following redistribution by CXCR4 entry inhibition. Thisin vitromodel indicates that entry inhibitors exhibit a redistribution effect unseen with intracellular ARV drugs. Based on these results, the effectiveness of some entry inhibitors may be underestimated if plasma viral load is used as a sole indicator of clinical success.

scholarly journals PF74 and Its Novel Derivatives Stabilize Hexameric Lattice of HIV-1 Mature-Like Particles

Molecules ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 1895
Author(s):  
Alžběta Dostálková ◽  
Kryštof Škach ◽  
Filip Kaufman ◽  
Ivana Křížová ◽  
Romana Hadravová ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Early Stage ◽  
Protein A ◽  
Protein Protein Interactions ◽  
Particle Assembly ◽  
Gag Polyprotein ◽  
Polyprotein Precursor ◽  
Hiv 1 ◽  
Ca Protein

A major structural retroviral protein, capsid protein (CA), is able to oligomerize into two different hexameric lattices, which makes this protein a key component for both the early and late stages of HIV-1 replication. During the late stage, the CA protein, as part of the Gag polyprotein precursor, facilitates protein–protein interactions that lead to the assembly of immature particles. Following protease activation and Gag polyprotein processing, CA also drives the assembly of the mature viral core. In the early stage of infection, the role of the CA protein is distinct. It controls the disassembly of the mature CA hexameric lattice i.e., uncoating, which is critical for the reverse transcription of the single-stranded RNA genome into double stranded DNA. These properties make CA a very attractive target for small molecule functioning as inhibitors of HIV-1 particle assembly and/or disassembly. Of these, inhibitors containing the PF74 scaffold have been extensively studied. In this study, we reported a series of modifications of the PF74 molecule and its characterization through a combination of biochemical and structural approaches. Our data supported the hypothesis that PF74 stabilizes the mature HIV-1 CA hexameric lattice. We identified derivatives with a higher in vitro stabilization activity in comparison to the original PF74 molecule.

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