HIV reverse transcriptase: Structural interpretation of drug resistant genetic variants from India




Abraham J. Kandathil1,$, Agnel P. Joseph2,$, R. Kannangai1, N. Srinivasan2, Oriapadicakal C. Abraham3 , Susanne A. Pulimood4 and G. Sridharan1*




1Departments of Clinical Virology, Christian Medical College, Vellore, India; 2Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India; 3Internal Medicine and 4Dermatology, Christian Medical College, Vellore, India; $Joint first authors



Article Type





Received June 05, 2009; Revised June 18, 2009; Accepted July 15, 2009; Published August 20, 2009



The reverse transcriptase (RT) enzyme is the prime target of nucleoside/ nucleotide (NRTI) and non-nucleoside (NNRTI) reverse transcriptase inhibitors. Here we investigate the structural basis of effects of drug-resistance mutations in clade C RT using three-dimensional structural modeling. Apropos the expectation was for unique mechanisms in clade C based on interactions with amino acids of p66 subunit in RT molecule. 3-D structures of RT with mutations found in sequences from 2 treatment na´ve, 8 failed and one reference clade C have been modeled and analyzed. Models were generated by computational mutation of available crystal structures of drug bound homologous RT. Energy minimization of the models and the structural analyses were carried out using standard methods. Mutations at positions 75,101,118,190,230,238 and 318 known to confer drug resistance were investigated. Different mutations produced different effects such as alteration of geometry of the drugbinding pocket, structural changes at the site of entry of the drug (into the active site), repositioning the template bases or by discriminating the inhibitors from their natural substrates. For the mutations analyzed, NRTI resistance was mediated mainly by the ability to discriminate between inhibitors and natural substrate, whereas, NNRTI resistance affected either the drug entry or the geometry of the active site. Our analysis suggests that different mutations result in different structural effects affecting the ability of a given drug to bind to the RT. Our studies will help in the development of newer drugs taking into account the presence of these mutations and the structural basis of drug resistance.




Drug resistance, Genetic mutations, HIV-1, Reverse transcriptase, Structural modeling



Kandathil et al., Bioinformation 4(1): 36-45 (2009)

Edited by


P. Kangueane








Biomedical Informatics 





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