Probing the geometric constraints of RNA binding via dynamic covalent chemistry

McAnany, John D.; Reichert, John P.; Miller, Benjamin L.

doi:10.1016/j.bmc.2016.02.029

“…Incubation of this library with HIV-1 FSS RNA caused it to collapse to a dimer-only library, and in particular selection of 5 ( C–C , inset). Adapted with permission from ref . Copyright 2021 Elsevier.…”

Section: Establishing On-target Activity: Bioassaysmentioning

confidence: 99%

“…53 Finally, to expand DCC beyond hit identification, we tested the ability of small libraries incorporating 5 to "evolve" into more complex structures using dithiols such as 12 (Figure 7). 54 Interestingly, although compounds incorporating 12 (such as 13) were observed in mass spectral analysis of libraries formed in the absence of HIV-1 FSS RNA (Figure 7, inset), selection in the presence of the RNA yielded only 5 and related dimers. While not the expected outcome, this provided validation of our initial 2007 screen and served as proof-of-concept for implementing more complex DCC systems with other targets.…”

Section: ■ Introductionmentioning

confidence: 99%

Targeting Ribosomal Frameshifting as an Antiviral Strategy: From HIV-1 to SARS-CoV-2

Anokhina

¹

,

Miller

²

2021

Self Cite

View full text Add to dashboard Cite

Metrics & MoreArticle Recommendations CONSPECTUS: Treatment of HIV-1 has largely involved targeting viral enzymes using a cocktail of inhibitors. However, resistance to these inhibitors and toxicity in the long term have pushed the field to identify new therapeutic targets. To that end, −1 programmed ribosomal frameshifting (−1 PRF) has gained attention as a potential node for therapeutic intervention. In this process, a ribosome moves one nucleotide backward in the course of translating a mRNA, revealing a new reading frame for protein synthesis.In HIV-1, −1 PRF allows the virus to regulate the ratios of enzymatic and structural proteins as needed for correct viral particle assembly. Two RNA structural elements are central to −1 PRF in HIV: a slippery sequence and a highly conserved stable hairpin called the HIV-1 frameshifting stimulatory signal (FSS). Dysregulation of −1 PRF is deleterious for the virus. Thus, −1 PRF is an attractive target for new antiviral development. It is important to note that HIV-1 is not the only virus exploiting −1 PRF for regulating production of its proteins. Coronaviruses, including the COVID-19 pandemic virus SARS-CoV-2, also rely on −1 PRF. In SARS-CoV-2 and other coronaviruses, −1 PRF is required for synthesis of RNA-dependent RNA polymerase and several other nonstructural proteins. Coronaviruses employ a more complex RNA structural element for regulating −1 PRF called a pseudoknot. The purpose of this Account is primarily to review the development of molecules targeting HIV-1 −1 PRF. These approaches are case studies illustrating how the entire pipeline from screening to the generation of high-affinity leads might be implemented. We consider both target-based and function-based screening, with a particular focus on our group's approach beginning with a resinbound dynamic combinatorial library (RBDCL) screen. We then used rational design approaches to optimize binding affinity, selectivity, and cellular bioavailability. Our tactic is, to the best of our knowledge, the only study resulting in compounds that bind specifically to the HIV-1 FSS RNA and reduce infectivity of laboratory and drug-resistant strains of HIV-1 in human cells. Lessons learned from strategies targeting −1 PRF HIV-1 might provide solutions in the development of antivirals in areas of unmet medical need. This includes the development of new frameshift-altering therapies for SARS-CoV-2, approaches to which are very recently beginning to appear.

show abstract

Ternary Complex‐Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo‐PROTACs

Diehl,

Salerno,

Ciulli

2024

Angewandte Chemie

0

View full text Add to dashboard Cite

Dynamic combinatorial chemistry (DCC) leverages a reversible reaction to generate compound libraries from constituting building blocks under thermodynamic control. The position of this equilibrium can be biased by addition of a target macromolecule towards enrichment of bound ligands. While DCC has been applied to select ligands for a single target protein, its application to identifying chimeric molecules inducing proximity between two proteins is unprecedented. In this proof‐of‐concept study, we develop a DCC approach to select bifunctional proteolysis targeting chimeras (PROTACs) based on their ability to stabilize the ternary complex. We focus on VHL‐targeting Homo‐PROTACs as model system, and show that the formation of a VHL2:Homo‐PROTAC ternary complex reversibly assembled using thiol‐disulfide exchange chemistry leads to amplification of potent VHL Homo‐PROTACs with degradation activities which correlated well with their biophysical ability to dimerize VHL. Ternary complex templated dynamic combinatorial libraries allowed identification of novel Homo‐PROTAC degraders. We anticipate future applications of ternary‐complex directed DCC to early PROTAC screenings and expansion to other proximity‐inducing modalities beyond PROTACs.

show abstract

Ternary Complex‐Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo‐PROTACs

Diehl,

Salerno,

Ciulli

2024

Angew Chem Int Ed

1

0

View full text Add to dashboard Cite

Dynamic combinatorial chemistry (DCC) leverages a reversible reaction to generate compound libraries from constituting building blocks under thermodynamic control. The position of this equilibrium can be biased by addition of a target macromolecule towards enrichment of bound ligands. While DCC has been applied to select ligands for a single target protein, its application to identifying chimeric molecules inducing proximity between two proteins is unprecedented. In this proof‐of‐concept study, we develop a DCC approach to select bifunctional proteolysis targeting chimeras (PROTACs) based on their ability to stabilize the ternary complex. We focus on VHL‐targeting Homo‐PROTACs as model system, and show that the formation of a VHL2:Homo‐PROTAC ternary complex reversibly assembled using thiol‐disulfide exchange chemistry leads to amplification of potent VHL Homo‐PROTACs with degradation activities which correlated well with their biophysical ability to dimerize VHL. Ternary complex templated dynamic combinatorial libraries allowed identification of novel Homo‐PROTAC degraders. We anticipate future applications of ternary‐complex directed DCC to early PROTAC screenings and expansion to other proximity‐inducing modalities beyond PROTACs.

show abstract

Probing the geometric constraints of RNA binding via dynamic covalent chemistry

Cited by 6 publications

References 22 publications

Targeting Ribosomal Frameshifting as an Antiviral Strategy: From HIV-1 to SARS-CoV-2

Targeting Ribosomal Frameshifting as an Antiviral Strategy: From HIV-1 to SARS-CoV-2

Ternary Complex‐Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo‐PROTACs

Ternary Complex‐Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo‐PROTACs

Contact Info

Product

Resources

About