# Targeting Viral RNA Using a Sequence Programmable Small Molecule-Oligonucleotide Conjugate

> **NIH NIH U19** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $5,450,416

## Abstract

PROJECT 1: TARGETING VIRAL RNA USING A SEQUENCE PROGRAMMABLE SMALL MOLECULE-
OLIGONUCLEOTIDE CONJUGATE
SUMMARY
We propose to merge small molecule and antisense oligonucleotide (ASO) approaches to specifically inhibit viral
RNA translation without inhibiting the translation of endogenous cellular mRNAs. Rocaglate natural products,
such as rocaglamide A (Roc), demonstrate a unique RNA-targeting mechanism by which small molecule binding
to a bimolecular cavity between eIF4A helicase and polypurine RNA (stretches of A and G) generates a steric
clamp on the 5’ untranslated regions (UTRs) of target mRNAs. Due to obstruction of the scanning ribosome, this
rocaglamide-mediated clamp results in translational inhibition of polypurine tract-containing mRNAs, including
that of SARS-CoV-2 and other positive-sense RNA viruses. While pre-clinical viral replication assays indicate
that zotatifin, a clinical candidate based on rocaglamide, may demonstrate a promising therapeutic window as
an anti-viral, it is anticipated that the simultaneous inhibition of multiple polypurine tract-containing mRNAs within
the cell could result in dose-limiting toxicities.
We position rocaglamide as a unique protein-RNA molecular glue that can be directed to specific viral target
sequences through the appendage of an additional RNA-targeting chemical element. We have designed
rocaglamide-ASO (RocASO) molecules which link rocaglamide to an ASO whose binding is dependent upon
complementary base-pairing with target RNA sequences. A model that juxtaposes the two therapeutic modalities
reveals a permissible disposition of the two binding elements approximately 20 Å apart, which will be traversed
by a variable chemical tether of sufficient length. RocASOs designed against the 5’ UTR of SARS-CoV-2 will be
tested using biochemical ternary complex formation assays with eIF4A and viral RNA, as well as assayed using
cellular reporters of SARS-CoV-2 5’ UTR translation and RNA stability. Finally, we will apply RocASOs in a
SARS-CoV-2 replicon system to determine the relative tolerance of RocASOs to polypurine tract or ASO
recognition sequence mutations. These experiments will also evaluate whether potentially emergent alterations
to target sequences could be addressed by introducing concomitant modifications to RocASOs, assessing the
platform as an adaptable RNA targeting modality for novel SARS-CoV-2 variants and other viral 5’ UTR
sequences.

## Key facts

- **NIH application ID:** 10512627
- **Project number:** 1U19AI171110-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** KEVAN M. SHOKAT
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $5,450,416
- **Award type:** 1
- **Project period:** 2022-05-16 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10512627

## Citation

> US National Institutes of Health, RePORTER application 10512627, Targeting Viral RNA Using a Sequence Programmable Small Molecule-Oligonucleotide Conjugate (1U19AI171110-01). Retrieved via AI Analytics 2026-05-29 from https://api.ai-analytics.org/grant/nih/10512627. Licensed CC0.

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