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Related Experiment Video

Updated: Jun 6, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Efavirenz binding site in HIV-1 reverse transcriptase monomers.

Valerie A Braz¹, Mary D Barkley, Rebecca A Jockusch

¹Department of Chemistry, Case Western Reserve University,10900 Euclid Avenue, Cleveland, Ohio 44106, United States.

|November 25, 2010

Summary

Efavirenz (EFV) binding to HIV-1 reverse transcriptase (RT) monomers alters their conformations. This study reveals EFV

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Area of Science:

Biochemistry
Structural Biology
Drug Discovery

Background:

Efavirenz (EFV) is a key nonnucleoside reverse transcriptase inhibitor (NNRTI) for AIDS treatment.
NNRTIs target a hydrophobic pocket in the p66 subunit of reverse transcriptase (RT).
Monomeric p66 and p51 subunits of RT bind EFV with micromolar affinity.

Purpose of the Study:

To investigate the impact of EFV on the solution conformations of p66 and p51 RT monomers.
To compare the EFV binding site in monomers to the NNRTI pocket in the RT heterodimer.

Main Methods:

Hydrogen-deuterium exchange mass spectrometry (HXMS).
Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS).

Main Results:

HXMS showed reduced deuterium exchange for peptides in monomer-EFV complexes, indicating structural changes.
Peptide 232-246 exhibited slow unfolding-refolding in bound monomers, slower than in the RT heterodimer.
FT-ICR MS revealed EFV induces a more compact conformation in p51 and facilitates cleavage in p66.

Conclusions:

The EFV binding site on p66 and p51 monomers resembles the NNRTI pocket in the RT heterodimer.
EFV binding induces distinct conformational changes in p51 and p66 monomers.
Observed population shifts support a selected-fit binding mechanism for EFV.