# Inducing Off-pathway Assembly of HIV Gag Polyprotein with Computationally Designed Peptides

> **NIH NIH DP2** · UNIVERSITY OF ILLINOIS AT CHICAGO · 2024 · $475,447

## Abstract

Viruses are inanimate biomolecular assemblages constructed inside host cells for the tasks of
transmission and infection. Despite the high degree of fidelity required to produce functional infectious
particles, viruses are adept at developing resistance to natural and vaccine-induced immune responses
through escape mutations. This is due to the presence of multiple redundant self-assembly signals,
resulting in a fitness landscape with vast regions of favorable sequence space. Viruses can sample
extensively from this space to arrive at escape variants, while retaining the capacity to properly
assemble.
We propose a transformative approach that aims to target large regions of viral fitness
landscapes, with the goal of overcoming antiviral drug resistance. In this approach, various viral
self-assembly signals will be exploited to induce the mis-assembly of viral components toward non-
infectious endpoints. Computationally designed peptides will steer the self-assembly process toward
trapped states accessible to large numbers of genetic variants. Peptides are ideal for this task for a
number of reasons. Firstly, peptides can target large surface areas of proteins, allowing for binding to
targets that lack deep binding pockets. Secondly, peptides can be designed to self-assemble into
diverse supramolecular structures, such as fibers, two-dimensional arrays, and liquid condensates. We
will leverage the ability of peptides to form these types of structures to induce the formation of non-
infectious viral mis-assemblies. Finally, peptides can be optimized for membrane permeability, allowing
for the targeting of viral replication inside host cells.
Drug-induced mis-assembly of HIV viral capsid has been suggested as one of several possible
mechanisms of action of the small-molecule drug PF74. We aim to develop a rationally-guided design
approach to enable the wide-spread application of this novel mechanism of anti-viral action. We will
target three domains of the HIV Gag protein known to play distinct roles in viral assembly for directed
mis-assembly by computationally designed peptides.
The resulting peptides will incorporate design elements that direct the trapping of viral components
within one-dimensional fibers, two-dimensional arrays, and three-dimensional liquid condensates. Self-
assembly will be monitored at the single-molecule level using Interferometric Mass Spectrometry, and
at the bulk level with Bio-layer Interferometry and Dynamic Light Scattering, while Electron Microscopy
and Fluorescence Microscopy will be used to visualize the induced assemblies. This project paves the
way for development of antiviral therapies through mechanisms that pose high barriers to antiviral
resistance.

## Key facts

- **NIH application ID:** 10894759
- **Project number:** 5DP2AI177928-02
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT CHICAGO
- **Principal Investigator:** Jose Abraham Villegas
- **Activity code:** DP2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $475,447
- **Award type:** 5
- **Project period:** 2023-08-01 → 2028-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10894759

## Citation

> US National Institutes of Health, RePORTER application 10894759, Inducing Off-pathway Assembly of HIV Gag Polyprotein with Computationally Designed Peptides (5DP2AI177928-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10894759. Licensed CC0.

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