Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors
- Yale University, United States
- Shandong University, China
- KU Leuven, Belgium
Abstract
Rapid generation of drug-resistant mutations in HIV-1 reverse transcriptase (RT), a prime target for anti-HIV therapy, poses a major impediment to effective anti-HIV treatment. Our previous efforts have led to the development of two novel non-nucleoside reverse transcriptase inhibitors (NNRTIs) with piperidine-substituted thiophene[3,2-d]pyrimidine scaffolds, compounds K-5a2 and 25a, which demonstrate highly potent anti-HIV-1 activities and improved resistance profiles compared with etravirine and rilpivirine, respectively. Here, we have determined the crystal structures of HIV-1 wild-type (WT) RT and seven RT variants bearing prevalent drug-resistant mutations in complex with K-5a2 or 25a at ~2 Å resolution. These high-resolution structures illustrate the molecular details of the extensive hydrophobic interactions and the network of main chain hydrogen bonds formed between the NNRTIs and the RT inhibitor binding pocket, and provide valuable insights into the favorable structural features that can be employed for designing NNRTIs that are broadly active against drug-resistant HIV-1 variants.
Data availability
Diffraction data and atomic coordinates have been deposited in the Protein Data Bank under the accession codes 6C0J, 6C0K, 6C0L, 6CGF, 6C0N, 6C0O, 6C0P, 6C0R, 6DUF, 6DUG, and 6DUH.
-
Crystal structure of HIV-1 reverse transcriptase in complex with nonnucleoside inhibitor K-5a2Publicly available at the RCSB Protein Data Bank (accession no. 6C0J).
-
Crystal structure of HIV-1 K103N mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5a2Publicly available at the RCSB Protein Data Bank (accession no. 6C0K).
-
Crystal structure of HIV-1 E138K mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5a2Publicly available at the RCSB Protein Data Bank (accession no. 6C0L).
-
Crystal structure of HIV-1 Y188L mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5a2Publicly available at the RCSB Protein Data Bank (accession no. 6CGF).
-
Crystal structure of HIV-1 reverse transcriptase in complex with non-nucleoside inhibitor 25aPublicly available at the RCSB Protein Data Bank (accession no. 6C0N).
-
Crystal structure of HIV-1 K103N mutant reverse transcriptase in complex with non-nucleoside inhibitor 25aPublicly available at the RCSB Protein Data Bank (accession no. 6C0O).
-
Crystal structure of HIV-1 E138K mutant reverse transcriptase in complex with non-nucleoside inhibitor 25aPublicly available at the RCSB Protein Data Bank (accession no. 6C0P).
-
Crystal structure of HIV-1 K103N/Y181C mutant reverse transcriptase in complex with non-nucleoside inhibitor 25aPublicly available at the RCSB Protein Data Bank (accession no. 6C0R).
-
Crystal structure of HIV-1 reverse transcriptase V106A/F227L mutant in complex with non-nucleoside inhibitor 25aPublicly available at the RCSB Protein Data Bank (accession no. 6DUF).
-
Crystal structure of HIV-1 reverse transcriptase K101P mutant in complex with non-nucleoside inhibitor 25aPublicly available at the RCSB Protein Data Bank (accession no. 6DUG).
-
Crystal structure of HIV-1 reverse transcriptase Y181I mutant in complex with non-nucleoside inhibitor 25aPublicly available at the RCSB Protein Data Bank (accession no. 6DUH).
-
Crystal structure of HIV-1 reverse transcriptase (RT) in complex with Rilpivirine (TMC278, Edurant), a non-nucleoside rt-inhibiting drugPublicly available at the RCSB Protein Data Bank (accession no. 4G1Q).
-
HIV-1 Reverse Transcriptase in Complex with TMC125Publicly available at the RCSB Protein Data Bank (accession no. 3MEC).
Article and author information
Author details
Funding
Howard Hughes Medical Institute (Investigator Program)
- Thomas A Steitz
National Institute of General Medical Sciences (GM022778)
- Thomas A Steitz
National Natural Science Foundation of China (81273354)
- Xinyong Liu
Key research and development project of Shandong Province (2017CXGC1401)
- Xinyong Liu
Major Project of Science and Technology of Shandong Province (2015ZDJS04001)
- Xinyong Liu
Young Scholars Program of Shandong University (2016WLJH32)
- Peng Zhan
Key Project of National Natural Science Foundation of China for International Cooperation (81420108027)
- Xinyong Liu
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Axel T Brunger, Stanford University, United States
Version history
- Received: March 2, 2018
- Accepted: July 18, 2018
- Accepted Manuscript published: July 25, 2018 (version 1)
- Version of Record published: August 7, 2018 (version 2)
Copyright
© 2018, Yang 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
-
- 2,261
- views
-
- 393
- downloads
-
- 58
- 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)
Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors
eLife 7:e36340.
https://doi.org/10.7554/eLife.36340
Further reading
-
- Microbiology and Infectious Disease
The target of rapamycin (TOR) signaling pathway is highly conserved and plays a crucial role in diverse biological processes in eukaryotes. Despite its significance, the underlying mechanism of the TOR pathway in Aspergillus flavus remains elusive. In this study, we comprehensively analyzed the TOR signaling pathway in A. flavus by identifying and characterizing nine genes that encode distinct components of this pathway. The FK506-binding protein Fkbp3 and its lysine succinylation are important for aflatoxin production and rapamycin resistance. The TorA kinase plays a pivotal role in the regulation of growth, spore production, aflatoxin biosynthesis, and responses to rapamycin and cell membrane stress. As a significant downstream effector molecule of the TorA kinase, the Sch9 kinase regulates aflatoxin B1 (AFB1) synthesis, osmotic and calcium stress response in A. flavus, and this regulation is mediated through its S_TKc, S_TK_X domains, and the ATP-binding site at K340. We also showed that the Sch9 kinase may have a regulatory impact on the high osmolarity glycerol (HOG) signaling pathway. TapA and TipA, the other downstream components of the TorA kinase, play a significant role in regulating cell wall stress response in A. flavus. Moreover, the members of the TapA-phosphatase complexes, SitA and Ppg1, are important for various biological processes in A. flavus, including vegetative growth, sclerotia formation, AFB1 biosynthesis, and pathogenicity. We also demonstrated that SitA and Ppg1 are involved in regulating lipid droplets (LDs) biogenesis and cell wall integrity (CWI) signaling pathways. In addition, another phosphatase complex, Nem1/Spo7, plays critical roles in hyphal development, conidiation, aflatoxin production, and LDs biogenesis. Collectively, our study has provided important insight into the regulatory network of the TOR signaling pathway and has elucidated the underlying molecular mechanisms of aflatoxin biosynthesis in A. flavus.
-
- Microbiology and Infectious Disease
The microbiota is a key determinant of the physiology and immunity of animal hosts. The factors governing the transmissibility of viruses between susceptible hosts are incompletely understood. Bacteria serve as food for Caenorhabditis elegans and represent an integral part of the natural environment of C. elegans. We determined the effects of bacteria isolated with C. elegans from its natural environment on the transmission of Orsay virus in C. elegans using quantitative virus transmission and host susceptibility assays. We observed that Ochrobactrum species promoted Orsay virus transmission, whereas Pseudomonas lurida MYb11 attenuated virus transmission relative to the standard laboratory bacterial food Escherichia coli OP50. We found that pathogenic Pseudomonas aeruginosa strains PA01 and PA14 further attenuated virus transmission. We determined that the amount of Orsay virus required to infect 50% of a C. elegans population on P. lurida MYb11 compared with Ochrobactrum vermis MYb71 was dramatically increased, over three orders of magnitude. Host susceptibility was attenuated even further in the presence of P. aeruginosa PA14. Genetic analysis of the determinants of P. aeruginosa required for attenuation of C. elegans susceptibility to Orsay virus infection revealed a role for regulators of quorum sensing. Our data suggest that distinct constituents of the C. elegans microbiota and potential pathogens can have widely divergent effects on Orsay virus transmission, such that associated bacteria can effectively determine host susceptibility versus resistance to viral infection. Our study provides quantitative evidence for a critical role for tripartite host-virus-bacteria interactions in determining the transmissibility of viruses among susceptible hosts.
