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Comprehensive model of wild-type and mutant HIV-1 reverse transciptases

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Abstract

An enhanced version of COMBINE that uses both ligand-based and structure-based alignment of ligands has been used to build a comprehensive 3-D QSAR model of wild-type HIV-1 reverse transcriptase and drug-resistant mutants. The COMBINEr model focused on 7 different RT enzymes complexed with just two HIV-RT inhibitors, niverapine (NVP) and efavirenz (EFV); therefore, 14 inhibitor/enzyme complexes comprised the training set. An external test set of chiral 2-(alkyl/aryl)amino-6-benzylpyrimidin-4(3H)-ones (DABOs) was used to test predictability. The COMBINEr model MC4, although developed using only two inhibitors, predicted the experimental activities of the test set with an acceptable average absolute error of prediction (0.89 pK i). Most notably, the model was able to correctly predict the right eudismic ratio for two R/S pairs of DABO derivatives. The enhanced COMBINEr approach was developed using only software freely available to academics.

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Acknowledgments

The authors thank the research group (Rotili et al. [5]) of Prof. Antonello Mai for sharing their data about the separation and activity of their DABO derivatives prior to publication. In addition, Garland R. Marshall acknowledges financial support from the Dipartimento di Chimica e Tecnologie del Farmaco, Facoltà di Farmacia e Medicina, Sapienza Università di Roma, which made his visiting professorship in Rome feasible.

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Authors and Affiliations

  1. Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P. le A. Moro 5, 00185, Rome, Italy

    Flavio Ballante, Ira Musmuca, Garland R. Marshall & Rino Ragno

  2. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA

    Garland R. Marshall

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  1. Flavio Ballante
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  2. Ira Musmuca
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  3. Garland R. Marshall
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  4. Rino Ragno
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Correspondence to Garland R. Marshall.

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Ballante, F., Musmuca, I., Marshall, G.R. et al. Comprehensive model of wild-type and mutant HIV-1 reverse transciptases. J Comput Aided Mol Des 26, 907–919 (2012). https://doi.org/10.1007/s10822-012-9586-6

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  • DOI: https://doi.org/10.1007/s10822-012-9586-6

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