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.
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
-
- 2,341
- views
-
- 406
- downloads
-
- 63
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Further reading
-
- Microbiology and Infectious Disease
Saprolegnia parasitica is one of the most virulent oomycete species in freshwater aquatic environments, causing severe saprolegniasis and leading to significant economic losses in the aquaculture industry. Thus far, the prevention and control of saprolegniasis face a shortage of medications. Linalool, a natural antibiotic alternative found in various essential oils, exhibits promising antimicrobial activity against a wide range of pathogens. In this study, the specific role of linalool in protecting S. parasitica infection at both in vitro and in vivo levels was investigated. Linalool showed multifaceted anti-oomycetes potential by both of antimicrobial efficacy and immunomodulatory efficacy. For in vitro test, linalool exhibited strong anti-oomycetes activity and mode of action included: (1) Linalool disrupted the cell membrane of the mycelium, causing the intracellular components leak out; (2) Linalool prohibited ribosome function, thereby inhibiting protein synthesis and ultimately affecting mycelium growth. Surprisingly, meanwhile we found the potential immune protective mechanism of linalool in the in vivo test: (1) Linalool enhanced the complement and coagulation system which in turn activated host immune defense and lysate S. parasitica cells; (2) Linalool promoted wound healing, tissue repair, and phagocytosis to cope with S. parasitica infection; (3) Linalool positively modulated the immune response by increasing the abundance of beneficial Actinobacteriota; (4) Linalool stimulated the production of inflammatory cytokines and chemokines to lyse S. parasitica cells. In all, our findings showed that linalool possessed multifaceted anti-oomycetes potential which would be a promising natural antibiotic alternative to cope with S. parasitica infection in the aquaculture industry.
-
- Genetics and Genomics
- Microbiology and Infectious Disease
Polyamines are biologically ubiquitous cations that bind to nucleic acids, ribosomes, and phospholipids and, thereby, modulate numerous processes, including surface motility in Escherichia coli. We characterized the metabolic pathways that contribute to polyamine-dependent control of surface motility in the commonly used strain W3110 and the transcriptome of a mutant lacking a putrescine synthetic pathway that was required for surface motility. Genetic analysis showed that surface motility required type 1 pili, the simultaneous presence of two independent putrescine anabolic pathways, and modulation by putrescine transport and catabolism. An immunological assay for FimA—the major pili subunit, reverse transcription quantitative PCR of fimA, and transmission electron microscopy confirmed that pili synthesis required putrescine. Comparative RNAseq analysis of a wild type and ΔspeB mutant which exhibits impaired pili synthesis showed that the latter had fewer transcripts for pili structural genes and for fimB which codes for the phase variation recombinase that orients the fim operon promoter in the ON phase, although loss of speB did not affect the promoter orientation. Results from the RNAseq analysis also suggested (a) changes in transcripts for several transcription factor genes that affect fim operon expression, (b) compensatory mechanisms for low putrescine which implies a putrescine homeostatic network, and (c) decreased transcripts of genes for oxidative energy metabolism and iron transport which a previous genetic analysis suggests may be sufficient to account for the pili defect in putrescine synthesis mutants. We conclude that pili synthesis requires putrescine and putrescine concentration is controlled by a complex homeostatic network that includes the genes of oxidative energy metabolism.
