# Novel mechanism of integrase (IN) resistance to Dolutegravir through epistatic interactions between IN and the nucleocapsid and polypurine tract regions of HIV-1

> **NIH NIH R01** · EMORY UNIVERSITY · 2020 · $506,986

## Abstract

PROJECT SUMMARY
Integration is essential for HIV-1 replication and is completed by integrase (IN). A class of drugs which inhibit the
strand transfer (ST) function of HIV integrase, called IN strand transfer inhibitors (INSTIs), includes approved
drugs raltegravir (RAL), elvitegravir (EVG) (1st generation) and dolutegravir (DTG), bictegravir (BIC) (2nd
generation). DTG has a higher genetic barrier to resistance than RAL or EVG, and is recommended by the World
Health Organization as an alternative to efavirenz in first-line regimens in low- and middle-income countries
(LMICs). Selection for DTG resistance is rare, but does exist and is currently not well understood. There is
mounting evidence for failure of DTG-based treatment in clinical trials (VIKING-3 study) in the absence of
mutations in the targeted IN gene. Our overarching hypothesis is that mutations outside IN can impart drug
resistance to IN-targeting drugs through indirect interactions that we call epistatic. The scientific premise for
studying these interactions is soundly grounded on two key pieces of evidence: First, in surprising preliminary
data from in vitro serial passage experiments in the presence of increasing amounts of DTG, a DTG resistance
mutation located outside IN was discovered. Experiments with recombinant viruses validated DTG resistance of
this mutation and showed enhanced resistance in the presence of the E157Q IN polymorphism. Moreover, deep
sequencing analyses showed that compared to infection by wild-type, mutant–containing viruses resulted in
more insertions, deletions, and non-canonical long terminal repeat (LTR) ends in 2-LTR circles and integrated
viral DNA. Second, a recent independent study based on similar serial passage experiments, identified changes
at the general G-tract region of the 3’-polypurine tract (3’-PPT) in a DTG-resistant virus (Malet et al., 2017).
Subsequently, different 3’-PPT changes were reported in a patient that failed DTG therapy. However, the
mechanism of DTG resistance through mutations at the 3’-PPT remains unclear due to conflicting hypotheses
and lack of experimental validation. Our hypothesis is that mutations outside IN can affect DTG resistance by
altering the LTR ends at the INSTI binding site. This hypothesis will be tested by a team of experts that includes
PIs Sarafianos (biochemical, virological drug resistance mechanisms), PI Lyumkis (single particle cryo-EM on
intasome/drug complexes) and PI Hachiya (virology, drug resistance) with the support by HIV IN experts Hughes
(NCI) and Kvaratskhelia (U Colorado), using virological, biochemical, and structural tools to address the aims to
investigate the virological, biological, and structural mechanisms of DTG resistance through epistatic
interactions. These innovative studies will help elucidate the molecular mechanisms of INSTI resistance through
epistatic interactions via mutations that are outside the IN gene and affect the INSTI-binding site. They are
significant and will ...

## Key facts

- **NIH application ID:** 9894732
- **Project number:** 5R01AI146017-02
- **Recipient organization:** EMORY UNIVERSITY
- **Principal Investigator:** Atsuko Hachiya
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $506,986
- **Award type:** 5
- **Project period:** 2019-03-15 → 2024-02-29

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9894732

## Citation

> US National Institutes of Health, RePORTER application 9894732, Novel mechanism of integrase (IN) resistance to Dolutegravir through epistatic interactions between IN and the nucleocapsid and polypurine tract regions of HIV-1 (5R01AI146017-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9894732. Licensed CC0.

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