# Structure-based design of stapled peptides to target Gag-Pol and INI1 interaction to block assembly

> **NIH NIH R21** · ALBERT EINSTEIN COLLEGE OF MEDICINE · 2021 · $271,500

## Abstract

Abstract:
 This application is in response to RFA-AI-19-072, “Novel Therapeutics Directed to Intracellular HIV
Targets”. The long term goal of this application is to develop stapled peptide inhibitors to disrupt intracellular
protein-protein interactions (PPI) between the host and the virus to curb HIV-1 replication. PPI surfaces are hard
to disrupt because of their large and flat surface of interactions. However, recent success in the development of
larger biologics such as hydrocarbon stapled peptides allows targeting of PPIs. The stapled peptides are a
helices from binding interfaces of PPI that are locked into their bioactive forms. Our goal is to intracellularly
disrupt HIV-1 integrase (IN) interaction with the host factor INI1/hSNF5 using stapled peptides, to inhibit HIV-1
assembly, particle production and/or particle morphogenesis.
 It has been established that perturbing IN without affecting its enzymatic activity can inhibit late stages of
HIV-1 replication such as assembly, particle production and/or particle morphogenesis. Several class II IN
mutations and allosteric inhibitors of IN (ALLINI), inhibit late events and they do so by perturbing IN/IN
multimerization, IN/host factor interaction or IN/RNA interactions. INI1/hSNF5 is the first IN-binding host factor
to be identified. We have extensively studied its role in HIV-1 replication and found that it is required for HIV-1
late events. We found that expression of a minimal-IN-binding domain of INI1 (INI1183-292) termed S6, disrupts
IN/INI1 interaction in vivo and potently inhibits HIV-1 particle production. Knocking down INI1 and use of INI1-/-
cell lines also inhibit HIV-1 particle production. Interestingly, IN mutants that are defective for binding to INI1 lead
to the production of morphologically defective particles. These studies together indicate that targeting IN/INI1
interaction is an effective strategy to inhibit HIV-1 particle production. However, lack of structure of INI1 and
IN/INI1 interactions have precluded our ability to develop inhibitors to target this interaction. Recent
developments in our laboratory in solving the NMR structure of the IN-binding Repeat 1 (Rpt1) domain of INI1,
and molecular docking studies of IN/INI1 interaction have helped to overcome this knowledge gap. These
structural studies have been validated by mutational, biochemical and virological studies that establish the
significance of IN/INI1 interactions.
 During our structural studies we made an unprecedented novel discovery that INI1 Rpt1 and Trans
Activating Response element (TAR) of HIV-1 genomic RNA structurally mimic each other. Nucleic acid mimicry
by proteins exists in nature, but mimicry of Rpt1 to TAR is novel and has not been reported earlier. We found
that both Rpt1 and TAR bind to same surface of IN C-terminal domain (CTD) and compete with each other for
binding to IN with identical IC50 value of 0.005 µM. Furthermore, INI1-interaction-defective mutants of IN resulted
in impairment of ...

## Key facts

- **NIH application ID:** 10140004
- **Project number:** 1R21AI156932-01
- **Recipient organization:** ALBERT EINSTEIN COLLEGE OF MEDICINE
- **Principal Investigator:** GANJAM V KALPANA
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $271,500
- **Award type:** 1
- **Project period:** 2020-11-13 → 2022-10-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10140004

## Citation

> US National Institutes of Health, RePORTER application 10140004, Structure-based design of stapled peptides to target Gag-Pol and INI1 interaction to block assembly (1R21AI156932-01). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10140004. Licensed CC0.

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