Targeting RNA–Protein Interactions within the Human Immunodeficiency Virus Type 1 Lifecycle

Bell, Neil M.; L’Hernault, Anne; Murat, Pierre; Richards, John O.; Lever, Andrew; Balasubramanian, Shankar

doi:10.1021/bi401270d

Cited by 33 publications

(38 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Macrophages secrete virions from virus-containing intracellular vacuoles (41). Late endosomes are the principal locations for HIV assembly (42)(43)(44)(45)(46). Importantly, nanoATV retains full antiretroviral activity in late endosomes, as RT activity was substantially decreased in Rab7 and Rab11 vesicles.…”

Section: Discussionmentioning

confidence: 99%

Endosomal Trafficking of Nanoformulated Antiretroviral Therapy Facilitates Drug Particle Carriage and HIV Clearance

Guo

Zhang

Wysocki

et al. 2014

J Virol

View full text Add to dashboard Cite

Limitations of antiretroviral therapy (ART) include poor patient adherence, drug toxicities, viral resistance, and failure to penetrate viral reservoirs. Recent developments in nanoformulated ART (nanoART) could overcome such limitations. To this end, we now report a novel effect of nanoART that facilitates drug depots within intracellular compartments at or adjacent to the sites of the viral replication cycle. Poloxamer 407-coated nanocrystals containing the protease inhibitor atazanavir (ATV) were prepared by high-pressure homogenization. These drug particles readily accumulated in human monocyte-derived macrophages (MDM). NanoATV concentrations were ϳ1,000 times higher in cells than those that could be achieved by the native drug. ATV particles in late and recycling endosome compartments were seen following pulldown by immunoaffinity chromatography with Rab-specific antibodies conjugated to magnetic beads. Confocal microscopy provided cross validation by immunofluorescent staining of the compartments. Mathematical modeling validated drug-endosomal interactions. Measures of reverse transcriptase activity and HIV-1 p24 levels in culture media and cells showed that such endosomal drug concentrations enhanced antiviral responses up to 1,000-fold. We conclude that late and recycling endosomes can serve as depots for nanoATV. The colocalization of nano-ATV at endosomal sites of viral assembly and its slow release sped antiretroviral activities. Long-acting nanoART can serve as a drug carrier in both cells and subcellular compartments and, as such, can facilitate viral clearance. IMPORTANCEThe need for long-acting ART is significant and highlighted by limitations in drug access, toxicity, adherence, and reservoir penetrance. We propose that targeting nanoformulated drugs to infected tissues, cells, and subcellular sites of viral replication may improve clinical outcomes. Endosomes are sites for human immunodeficiency virus assembly, and increasing ART concentrations in such sites enhances viral clearance. The current work uncovers a new mechanism by which nanoART can enhance viral clearance over native drug formulations.

show abstract

Section: Discussionmentioning

confidence: 99%

Endosomal Trafficking of Nanoformulated Antiretroviral Therapy Facilitates Drug Particle Carriage and HIV Clearance

Guo

Zhang

Wysocki

et al. 2014

J Virol

View full text Add to dashboard Cite

show abstract

“…A FRET based SL3 RNA melting assay, similar to the cTAR DNA melting assay (Shvadchak et al, 2009) where the 3’ and 5’ ends of the oligonucleotide are labeled with a TET fluorophore and a black hole quencher (BHQ1), was used by Bell et al to identify a SL3-Gag interaction to identify compound 18 (Fig 5) (Bell et al, 2013). Using NMR studies, compound 18 was shown to interact with the tetraloop of the RNA, which is the region that is required for NC binding.…”

Section: Rna Bindersmentioning

confidence: 99%

“…They had shown earlier that NC is sufficient to bind SL3 RNA, however, the chaperoning effect is significant only in the presence of the flanking domains of the Gag polyprotein (Bell et al, 2012). Bell and colleagues hypothesized that the specific ability of Gag polyprotein, rather than mature NC, could effect structural changes in SL3 which may aid in genomic viral RNA packaging into the virus particle though avoiding binding by prematurely cleaved NC (Bell et al, 2013). This is in contrast with the significant chaperoning of NC alone on the TAR/cTAR oligonucleotides (Godet and Mely, 2010; Levin et al, 2010; Shvadchak et al, 2009; Sosic et al, 2013).…”

Section: Rna Bindersmentioning

confidence: 99%

Advances in targeting nucleocapsid–nucleic acid interactions in HIV-1 therapy

Garg

Torbett

2014

Virus Research

View full text Add to dashboard Cite

The continuing challenge of HIV-1 treatment resistance in patients creates a need for the development of new antiretroviral inhibitors. The HIV nucleocapsid (NC) protein is a potential therapeutic target. NC is necessary for viral RNA packaging and in the early stages of viral infection. The high level of NC amino acid conservation among all HIV-1 clades suggests a low tolerance for mutations. Thus, NC mutations that could arise during inhibitor treatment to provide resistance may render the virus less fit. Disruption of NC function provides a unique opportunity to strongly dampen replication at multiple points during the viral life cycle with a single inhibitor. Although NC exhibits desirable features for a potential antiviral target, the structural flexibility, size, and the presence of two zinc fingers makes small molecule targeting of NC a challenging task. In this review, we discuss the recent advances in strategies to develop inhibitors of NC function and present a perspective on potential novel approaches that may help to overcome some of the current challenges in the field.

show abstract

“…3D). These include TAR 154 and RRE, 155 but also the dimer initiation sequence (DIS), 156 the packaging signal (Ψ), 157 and the Gag/Pol frameshifting signal. 34 The TAR element resides within the 5′ UTR of the viral genome and serves as the binding site for the Tat protein.…”

Section: Viral Rna Motifsmentioning

confidence: 99%

Unveiling the druggable RNA targets and small molecule therapeutics

Sztuba-Solińska

Chávez-Calvillo

Cline

2019

Bioorganic & Medicinal Chemistry

View full text Add to dashboard Cite

Keywords:RNA structure and function RNA interactions Epitranscriptomics Small molecules RNA-based therapeutics RNA in disease Drug target A B S T R A C T The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets. RNA as a drug targetThe vast diversity of RNAs expanding beyond coding transcripts to several classes of ncRNAs that vary in length, biogenesis, polarity, and putative functions, increases the repertoire of druggable targets. 19,20 Here, specific RNA properties contribute to its attractive, yet challenging makeup as a target molecule. RNA can form complex three-dimensional structures through canonical Watson-Crick base pairing and complex tertiary interactions that are mediated by non-canonical bonds. Such structures can be as intricate and stable as those formed by proteins and can recognize small-molecule ligands, other nucleic acids, and/or proteins with high affinity and specificity. [21][22][23][24] At the same time, the highly dynamic conformation and repetitive character of its surface presents difficulties for drug design. 25,26 In addition, many putative small molecule-binding pockets in RNA are much more polar and solvent exposed than binding sites on proteins, complicating ligand design efforts. Compounding these issues, most target RNAs are expressed at low levels, with the exception of ribosomal (rRNA) and transfer (tRNA) RNAs, which constitute 80-90% and 10-15% of total cellular RNA, respectively. 27 Other abundant RNAs, such as messenger (mRNA), small nuclear (snRNA), and small nucleolar (snoRNA) are present at levels that are about 1-2 orders of magnitude lower than rRNA and tRNA. Certain small RNAs, such as micro (miRNA) and piwi (piRNAs) can be present at very high levels; however, this appears to be cell type dependent. One should keep in mind that if the RNA has catalytic activity or if it acts as a scaffold to regulate https://doi.

show abstract

Targeting RNA–Protein Interactions within the Human Immunodeficiency Virus Type 1 Lifecycle

Cited by 33 publications

References 37 publications

Endosomal Trafficking of Nanoformulated Antiretroviral Therapy Facilitates Drug Particle Carriage and HIV Clearance

Endosomal Trafficking of Nanoformulated Antiretroviral Therapy Facilitates Drug Particle Carriage and HIV Clearance

Advances in targeting nucleocapsid–nucleic acid interactions in HIV-1 therapy

Unveiling the druggable RNA targets and small molecule therapeutics

Contact Info

Product

Resources

About