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Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase

Nature Chemistry volume 5, pages 174–181 (2013)Cite this article

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Abstract

The anti-AIDS drug rilpivirine undergoes conformational changes to bind HIV-1 reverse transcriptase (RT), which is an essential enzyme for the replication of HIV. These changes allow it to retain potency against mutations that otherwise would render the enzyme resistant. Here we report that water molecules play an essential role in this binding process. Femtosecond experiments and theory expose the molecular level dynamics of rilpivirine bound to HIV-1 RT. Two nitrile substituents, one on each arm of the drug, are used as vibrational probes of the structural dynamics within the binding pocket. Two-dimensional vibrational echo spectroscopy reveals that one nitrile group is unexpectedly hydrogen-bonded to a mobile water molecule, not identified in previous X-ray structures. Ultrafast nitrile–water dynamics are confirmed by simulations. A higher (1.51 Å) resolution X-ray structure also reveals a water–drug interaction network. Maintenance of a crucial anchoring hydrogen bond may help retain the potency of rilpivirine against pocket mutations despite the structural variations they cause.

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Figure 1: Experimental linear infrared spectra of rilpivirine in solution and in complex to the different RT enzymes.
Figure 2: Absorptive 2D-IR spectra of the two investigated mutant/rilpivirine complexes at different waiting times.
Figure 3: Experimental peak-shift decays extracted from 2D-IR data as a function of waiting time.
Figure 4: The calculated radial distribution function g(r) highlights differences between the two nitrile groups of rilpivirine.
Figure 5: Snapshot of rilpivirine in the NNRTI-binding pocket of the WT-RT complex as observed in our MD simulations and X-ray crystal structure.
Figure 6: Simulated peak-shift and absorptive 2D-IR spectra of the WT-RT/rilpivirine complex for different waiting times.

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Acknowledgements

We thank A. Roitberg for advice on the MD simulations. This research was supported by National Institutes of Health (NIH) Grants GM12592 (to R.M.H.) and NIH MERIT Award R37 AI27690 (to E.A.) by using instrumentation developed in the Ultrafast Optical Process Laboratory NIH Grant P41RR001348/9P41GM104605. We acknowledge the Brookhaven National Laboratory X29 beamline facility for X-ray data collection and R.S.K. Vijayan for helpful discussions.

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Author notes

  1. J. Reddy Challa

    Present address: Present address: Department of Chemistry, University of Rochester, Rochester, New Jersey 14627,

  2. Daniel G. Kuroda and Joseph D. Bauman: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Chemistry, Ultrafast Optical Processes Laboratory, University of Pennsylvania, Pennsylvania, 19067, USA

    Daniel G. Kuroda, J. Reddy Challa, Thomas Troxler & Robin M. Hochstrasser

  2. Center for Advanced Biotechnology and Medicine, Piscataway, 08854, New Jersey, USA

    Joseph D. Bauman, Disha Patel, Kalyan Das & Eddy Arnold

  3. Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, 08854, New Jersey, USA

    Joseph D. Bauman, Kalyan Das & Eddy Arnold

  4. Department of Medicinal Chemistry, Rutgers University, Piscataway, 08854, New Jersey, USA

    Disha Patel & Eddy Arnold

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Contributions

E.A. and R.M.H. conceived and designed the experiments. J.R.C. and T.T. performed the infrared experiments. D.G.K, J.R.C. and T.T. analysed the data. D.G.K. performed theoretical calculations and simulations. J.D.B. expressed and purified the protein samples and grew the crystals. J.D.B. and D.P. performed the X-ray data collection. J.D.B. and K.D. analysed and refined the crystal structure. D.G.K. and R.M.H. co-wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Robin M. Hochstrasser.

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Kuroda, D., Bauman, J., Challa, J. et al. Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase. Nature Chem 5, 174–181 (2013). https://doi.org/10.1038/nchem.1559

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