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

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

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

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 pKi). 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.

Original languageEnglish
Pages (from-to)907-919
Number of pages13
JournalJournal of Computer-Aided Molecular Design
Volume26
Issue number8
DOIs
StatePublished - Aug 2012

Keywords

  • 3-D-QSAR
  • COMBINEr
  • DABO inhibitors
  • Drug resistance
  • HIV-1 reverse transciptase
  • Molecular modeling
  • NNRTI
  • PLS
  • RT mutants

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