ArticleThe journal of physical chemistry. B2019
Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase.
Article in The journal of physical chemistry. B, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Discovery of a potent ROR1 inhibitor using μs-scale MD simulations, wt-metadynamics, and absolute binding free energy calculations.Journal of molecular modeling · 2025Article
- Thermodynamics and Kinetics of the Deintercalation of a Novel Anthracycline from Double-Stranded Oligonucleotide DNA.The journal of physical chemistry. B · 2025Article
- Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations.Journal of chemical information and modeling · 2023Article
- Collective variable discovery in the age of machine learning: reality, hype and everything in between.RSC advances · 2022Review
- Human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT) structure and biochemistry reveals remarkable similarities to HIV-1 RT and opportunities for HERV-K-specific inhibition.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Exploring the Binding Mechanism of a Supramolecular Tweezer CLR01 to 14-3-3σ ProteinFrontiers in chemistry · 2022Article
- Molecular dynamics of the viral life cycle: progress and prospects.Current opinion in virology · 2021Review
- Metadynamics as a Postprocessing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2.Journal of chemical information and modeling · 2020Article
- Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance.Current opinion in structural biology · 2020Review
- Improving the positional adaptability: structure-based design of biphenyl-substituted diaryltriazines as novel non-nucleoside HIV-1 reverse transcriptase inhibitors.Acta pharmaceutica Sinica. B · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs), which bind to an allosteric site 10-15 Å from the polymerase active site, play a central role in anti-HIV chemotherapy. Though NNRTIs have been known for 30 years, the pathways by which they bind and unbind from HIV-RT have not been characterized. In crystal structures for complexes, three channels are found to extend from the NNRTI binding site to the exterior of the protein, while added mystery comes from the fact that the binding site is collapsed in the unliganded protein. To address this issue, metadynamics simulations have been performed to elucidate the unbinding of four NNRTIs from HIV-RT. A general and transferable collective variable defined by the distance between the center-of-mass (COM) of the binding pocket and COM of the ligand is used to follow the dynamics while minimizing the bias. The metadynamics also allows computation of the barriers to unbinding, which are compared with the observed potencies of the compounds in an antiviral assay.
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Registered trials
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