Fragment based search for small molecule inhibitors of HIV-1 Tat-TAR

Zeiger, Mirco; Stark, Sebastian; Kalden, Elisabeth; Ackermann, Bettina; Ferner, Jan; Scheffer, Ute; Shoja-Bazargani, Fatemeh; Erdel, Veysel; Schwalbe, Harald; Göbel, Michael

doi:10.1016/j.bmcl.2014.11.004

Cited by 34 publications

(37 citation statements)

References 29 publications

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“…49-52 High-throughput and fragment-based screens have yielded small molecules that bind TAR in the micromolar range and inhibit Tat interactions. 53-57 Recently, small molecule microarrays have been employed by Schneekloth and coworkers to discover a TAR-binding probe that inhibits the HIV-induced cell death of T-lymphocytes at 28 μM without measured toxicity. 17 Importantly, this thienopyridine-based probe was charge neutral and bound TAR with a dissociation constant of 2.4 μM.…”

Section: Introductionmentioning

confidence: 99%

Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR

et al. 2017

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Diversification of RNA-targeted scaffolds offers great promise in the search for selective ligands of therapeutically relevant RNA such as HIV-1 TAR. We herein report the establishment of amiloride as a novel RNA-binding scaffold along with synthetic routes for combinatorial C(5)- and C(6)-diversification. Iterative modifications at the C(5)- and C(6)- positions yielded derivative 24, which demonstrated a 100-fold increase in activity over the parent dimethylamiloride in peptide displacement assays. NMR chemical shift mapping was performed using the 2D SOFAST- [1H-13C] HMQC NMR method, which allowed for facile and rapid evaluation of binding modes for all library members. Cheminformatic analysis revealed distinct differences between selective and non-selective ligands. In this study, we evolved dimethylamiloride from a weak TAR ligand to one of the tightest binding selective TAR ligands reported to date through a novel combination of synthetic methods and analytical techniques. We expect these methods to allow for rapid library expansion and tuning of the amiloride scaffold for a range of RNA targets and for SOFAST NMR to allow unprecedented evaluation of small molecule:RNA interactions.

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Section: Introductionmentioning

confidence: 99%

Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR

et al. 2017

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“…Their combination led to 2,4,6-triaminoquinazoline (Fig. 7) as the compound with the highest affinity to TAR RNA (IC 50 ¼ 40 μM) [107]. Further investigation of the interaction between 2,4,6-triaminoquinazoline and TAR RNA by 1 H-NMR titrations revealed that this fragment has two distinctive binding sites.…”

Section: Ligands Discovered By Fragment Screening On Rna Targetsmentioning

confidence: 97%

Structure-Based Discovery of Small Molecules Binding to RNA

Wehler

Brenk

2017

Topics in Medicinal Chemistry

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Ribonucleic acids (RNAs) constitute attractive drug targets. The wealth of structural information about RNAs is steadily increasing making it possible to use this information for the design of new ligands. Two methods that make heavy use of structural knowledge for ligand discovery are molecular docking and fragment screening. In molecular docking the structure of the binding site is used as a template for the design of new ligands using computational methods whereas in fragment screening biophysical methods are used for the detection of weak binding ligands which are subsequently elaborated into tighter binding molecules. In this chapter, we give an overview of both methods in the context of ligand discovery for RNA targets and illustrate their applications for hit discovery.

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“…Next, we tested the ability of the compounds to displace peptides mimics of the cognate proteins that bind TAR and RREIIB using fluorescence-based assays. These assays have previously been used in screening for an evaluating TAR and RRE binders (Matsumoto et al 2000;Hamasaki and Ueno 2001;Patwardhan et al 2017Patwardhan et al , 2019Zeiger et al 2014). The TAR assay measures fluorescence resonance energy transfer (FRET) of a dual-labeled arginine rich motif (ARM) Tat-mimic peptide (Matsumoto et al 2000;Ganser et al 2018), and the RRE assay measures fluorescence anisotropy of an ARM Rev-mimic peptide (Luedtke and Tor 2003;Chu et al 2019).…”

Section: Assaying Binding Using Rna-peptide Displacement Assaysmentioning

confidence: 99%

Revealing the high propensity of RNAs to non-specifically bind drug-like small molecules

Kelly

Chu²,

Shi

et al. 2020

Preprint

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Identifying small molecules that selectively bind a single RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to non-specific binding of aminoglycosides and intercalators to a variety of RNAs. Many such compounds have been reported to bind RNAs and inhibit their cellular activities, however the ability of such compounds to discriminate against RNA stem-loops commonly found in the transcriptome has not been thoroughly assessed in all cases. Here, we examined the propensities of three drug-like compounds, previously shown to bind and inhibit the cellular activity of three distinct RNAs, to non-specifically bind two HIV-1 stem-loop RNAs: the transactivation response element (TAR) and stem IIB in the rev response element (RREIIB). All three compounds bound to TAR and RREIIB in vitro, and two inhibited TAR-dependent transactivation and RRE-dependent viral export in cell-based assays while also exhibiting substantial off-target interactions consistent with non-specific cellular activity. A survey of X-ray and NMR structures of RNA-small molecule complexes revealed that drug-like molecules form hydrogen bonds with functional groups commonly accessible in canonical stem-loop RNA motifs, much like aminoglycosides, and in contrast to ligands that specifically bind riboswitches. Our results support extending the group of non-selective RNA-binders beyond aminoglycosides and intercalators to encompass drug-like compounds with capacity for non-specific hydrogen-bonding and reinforce the importance of assaying for off-target interactions and RNA selectivity in vitro and in cells when assessing novel RNA-binders.

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Fragment based search for small molecule inhibitors of HIV-1 Tat-TAR

Cited by 34 publications

References 29 publications

Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR

Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR

Structure-Based Discovery of Small Molecules Binding to RNA

Revealing the high propensity of RNAs to non-specifically bind drug-like small molecules

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