Selection of HIV-1 for resistance to fifth generation protease inhibitors reveals two independent pathways to high-level resistance
- University of North Carolina at Chapel Hill, United States
- University of Massachusetts Medical School, United States
Abstract
Darunavir (DRV) is exceptional among potent HIV-1 protease inhibitors (PIs) in high drug concentrations that are achived in vivo. Little is known about the de novo resistance pathway for DRV. We selected for resistance to high drug concentrations against ten PIs and their structural precursor DRV. Mutations accumulated through two pathways (anchored by protease mutations I50V or I84V). Small changes in the inhibitor P1'-equivalent position led to preferential use of one pathway over the other. Changes in the inhbitor P2'-equivalent position determined differences in potency that were retained in the resistant viruses and that impacted the selected mutations. Viral variants from the two pathways showed differential selection of compensatory mutations in Gag cleavage sites. These results reveal the high level of selective pressure that is attainable with fifth generation PIs, and how features of the inhibitor affect both the resistance pathway and the residual potency in the face of resistance.
Data availability
The sequencing data (Figure 2, 3, and 4) is available at NIH Sequencing Read Archive (SRA) under BioProject ID PRJNA853351.All source data files for enzymatic Ki and Km (Table 1, Figure 2 and 5) have been uploaded to the Carolina Digital Repository: Swanstrom, Ron, and Ean Spielvogel. Km and Ki Dataset for Selection of Hiv-1 for Resistance to Fifth Generation Protease Inhibitors Reveals Two Independent Pathways to High-level Resistance. 2022.All source data files for EC50 inhibition curves (Figure 2 and 6) have been uploaded to the Carolina Digital Repository: Swanstrom, Ron, and Ean Spielvogel. Ec50 Dataset for Selection of Hiv-1 for Resistance to Fifth Generation Protease Inhibitors Reveals Two Independent Pathways to High-level Resistance. 2022.
Article and author information
Author details
Funding
National Institute of General Medical Sciences (1P01GM109767-01A`)
- Ean Spielvogel
- Sook-Kyung Lee
- Shuntai Zhou
- Gordon J Lockbaum
- Mina Henes
- Amy Sondgeroth
- Klajdi Kosovrasti
- Ellen A Nalivaika
- Akbar Ali
- Nese Kurt Yilmaz
- Celia A Schiffer
- Ronald Swanstrom
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2023, Spielvogel et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 946
- views
-
- 129
- downloads
-
- 11
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Selection of HIV-1 for resistance to fifth generation protease inhibitors reveals two independent pathways to high-level resistance
eLife 12:e80328.
https://doi.org/10.7554/eLife.80328
Further reading
-
- Biochemistry and Chemical Biology
- Stem Cells and Regenerative Medicine
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling. In this study, we characterise the proteomes of multiple hiPSC and hESC lines derived from independent donors and find that while they express a near-identical set of proteins, they show consistent quantitative differences in the abundance of a subset of proteins. hiPSCs have increased total protein content, while maintaining a comparable cell cycle profile to hESCs, with increased abundance of cytoplasmic and mitochondrial proteins required to sustain high growth rates, including nutrient transporters and metabolic proteins. Prominent changes detected in proteins involved in mitochondrial metabolism correlated with enhanced mitochondrial potential, shown using high-resolution respirometry. hiPSCs also produced higher levels of secreted proteins, including growth factors and proteins involved in the inhibition of the immune system. The data indicate that reprogramming of fibroblasts to hiPSCs produces important differences in cytoplasmic and mitochondrial proteins compared to hESCs, with consequences affecting growth and metabolism. This study improves our understanding of the molecular differences between hiPSCs and hESCs, with implications for potential risks and benefits for their use in future disease modelling and therapeutic applications.
-
- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
Dynamic conformational and structural changes in proteins and protein complexes play a central and ubiquitous role in the regulation of protein function, yet it is very challenging to study these changes, especially for large protein complexes, under physiological conditions. Here, we introduce a novel isobaric crosslinker, Qlinker, for studying conformational and structural changes in proteins and protein complexes using quantitative crosslinking mass spectrometry. Qlinkers are small and simple, amine-reactive molecules with an optimal extended distance of ~10 Å, which use MS2 reporter ions for relative quantification of Qlinker-modified peptides derived from different samples. We synthesized the 2-plex Q2linker and showed that the Q2linker can provide quantitative crosslinking data that pinpoints key conformational and structural changes in biosensors, binary and ternary complexes composed of the general transcription factors TBP, TFIIA, and TFIIB, and RNA polymerase II complexes.
