---
title: "IN C-terminal Domain Mutations Alter HIV-1 Sensitivity to ALLINIs"
id: "biorxiv-3-hiv-1-integrase-c-terminal-domain-mutations-regulate-allini-sensitivity"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-3-hiv-1-integrase-c-terminal-domain-mutations-regulate-allini-sensitivity"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.22.761050v1?rss=1"
published_at: "2026-10-24T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# IN C-terminal Domain Mutations Alter HIV-1 Sensitivity to ALLINIs
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-3-hiv-1-integrase-c-terminal-domain-mutations-regulate-allini-sensitivity
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.22.761050v1?rss=1)
- **Published At:** 2026-10-24T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The study examined how mutations in the C-terminal domain (CTD) of **HIV-1 integrase** (IN) change sensitivity to allosteric integrase inhibitors (**ALLINI**). - IN performs two lifecycle roles: catalyzing viral DNA integration and promoting correct virion maturation through **gRNA** binding via basic CTD residues. - ALLINIs bind a V-shaped pocket at the catalytic core domain (CCD) dimer interface and drive CTD engagement from adjacent dimers, blocking **gRNA** binding. - Prior virological data linking CTD residues directly to ALLINI activity were limited because many CTD mutations produce noninfectious virus. - Investigators studied CTD mutants that carried compensatory substitutions restoring infectivity; these restored viruses showed altered ALLINI sensitivity. - R269A/K273A substitutions in the CTD produced approximately 100-fold enhanced sensitivity to ALLINIs, according to the authors. - Enhanced sensitivity correlated with loss of IN–**gRNA** binding at low ALLINI concentrations, while IN multimerization measured in vitro and in virions showed minimal change. - By contrast, the I268T substitution (a suppressor of I268A) conferred partial resistance to ALLINI-mediated inhibition of **gRNA** binding. - The study team interpreted these results as direct genetic evidence that CTD residues, although distal to the primary CCD drug-binding pocket, modulate ALLINI sensitivity and support IN–**gRNA** binding as a key functional target of these inhibitors. - The preprint did not report details such as experimental sample sizes, specific ALLINI compounds tested by name in the abstract, or exact assay conditions; those methodological details are not provided in the abstract text.
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Abhishek Kumar 1 Washington University in St. Louis School of Medicine; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Abhishek%2BKumar%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kumar%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAbhishek%2BKumar%2B) Tung Dinh 2 University of Colorado School of Medicine; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Tung%2BDinh%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Dinh%20T&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ATung%2BDinh%2B) Christian Shema Mugisha 3 Washington University in St Louis School of Medicine; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Christian%2BShema%2BMugisha%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Mugisha%20CS&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AChristian%2BShema%2BMugisha%2B) Anthony Twumasi Boateng 4 Washington University School of Medicine in St Louis Continuing Medical Education; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Anthony%2BTwumasi%2BBoateng%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Boateng%20AT&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAnthony%2BTwumasi%2BBoateng%2B) Qianzi Zhou 3 Washington University in St Louis School of Medicine; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Qianzi%2BZhou%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Zhou%20Q&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AQianzi%2BZhou%2B) Mamuka Kvaratskhelia 5 University of Colorado Anschutz Medical Campus * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Mamuka%2BKvaratskhelia%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kvaratskhelia%20M&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AMamuka%2BKvaratskhelia%2B) * [ORCID record for Mamuka Kvaratskhelia](http://orcid.org/0000-0003-3800-0033 "Open in new tab") Sebla Bulent Kutluay 3 Washington University in St Louis School of Medicine; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Sebla%2BBulent%2BKutluay%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kutluay%20SB&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ASebla%2BBulent%2BKutluay%2B) * [ORCID record for Sebla Bulent Kutluay](http://orcid.org/0000-0001-5549-7032 "Open in new tab") * For correspondence: kutluay@wustl.edu * [Abstract](https://www.biorxiv.org/content/10.64898/2026.10.22.761050v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5901200/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.10.22.761050v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5901200/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.10.22.761050v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5901200/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.10.22.761050v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5901200/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract HIV-1 integrase (IN) performs two essential functions in virus replication: catalyzing the integration of reverse-transcribed viral cDNA into host DNA and promoting proper virion maturation. The latter is mediated by IN binding to the genomic RNA (gRNA) through basic residues in its C-terminal domain (CTD), thereby ensuring correct repackaging of the gRNA inside the remodeled capsid lattice. Allosteric integrase inhibitors (ALLINIs) bind within a V-shaped pocket at the interface of the catalytic core domain (CCD) of IN dimers, promote the engagement of the CTDs from adjacent dimers, and thereby occlude gRNA binding. However, virological evidence supporting a role for the IN-CTD in ALLINI mechanism of action is lacking, as mutations in CTD residues implicated in ALLINI-induced multimerization typically yield non-infectious viruses. Here we demonstrate that IN-CTD mutants bearing compensatory substitutions that restore infectivity exhibit markedly altered sensitivity to ALLINIs. Specifically, we show that R269A/K273A substitutions within the IN-CTD confer ~100-fold enhanced sensitivity to ALLINIs. This correlates with a loss of IN-gRNA binding at low ALLINI concentrations, while exerting minimal effects on IN multimerization in vitro and in virions. In contrast, we found that the IN I268T substitution which arose as a suppressor mutation of I268A confers partial resistance to ALLINI-induced inhibition of gRNA binding. Collectively, these findings provide the first direct genetic evidence that CTD residues, despite being distal to the primary drug binding site at the CCD dimer, modulate sensitivity to ALLINIs and highlights IN-gRNA binding as a central target of ALLINIs. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-NC-ND 4.0 International license](http://creativecommons.org/licenses/by-nc-nd/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.10.22.761050v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.22.761050.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) HIV-1 Integrase C-terminal Domain Mutations Regulate ALLINI Sensitivity Abhishek Kumar, Tung Dinh, Christian Shema Mugisha, Anthony Twumasi Boateng, Qianzi Zhou, Mamuka Kvaratskhelia, Sebla Bulent Kutluay bioRxiv 2026.10.22.761050; doi: https://doi.org/10.64898/2026.10.22.761050 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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