Prediction of drug-resistance in HIV-1 subtype C based on protease sequences from ART naive and first-line treatment failures in North India using genotypic and docking analysis Jaideep S. Toor a , Aman Sharma b , Rajender Kumar c , Pawan Gupta c , Prabha Garg c , Sunil K. Arora a,⇑ a Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India b Department of Internal Medicine, Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India c Computer Centre, National Institute of Pharmaceutical Education & Research, S.A.S. Nagar, Punjab, India article info Article history: Received 26 April 2011 Revised 1 August 2011 Accepted 8 August 2011 Available online xxxx Keywords: First-line treatment failure HIV-1 subtype C Drug resistance Protease inhibitors Molecular modelling Stanford drug resistance database abstract Genotyping reveal emergence of drug resistance (DR)-related mutations in HIV-1 protease (PR) gene in the first-line treatment failure patients as per Stanford DR database. In order to have a subtype C specific prediction model, a three dimensional structure of local wild type C variant is created and the identified mutations were introduced to assess the mutational effects on protease inhibitors (PI) in a homology model. We estimated viral load, CD4 count and conducted DR genotyping in HIV isolates from 129 therapy naive and 20 first-line treatment failure individuals. Several genotypic variations, as compared to subtype B sequence in the Stanford gene database were detected in HIV-1 subtype C isolates from treatment naive individuals. Among these, nine mutations (12S, 15V, 19I, 36I, 41K, 63P, 69K, 89M, 93L) occurred in more than 60% of the isolates and were considered as local wild type for molecular modelling studies. No major mutations were seen in the PR sequences in isolates from treatment-naive individuals, although isolates from two patients had T74S mutation, known to be associated with reduced susceptibility to nelfinavir (NFV) and a combination of M36I, H69K and L89M mutations found in isolates from 77 patients (59.7%), considered to be conferring resistance to tipranavir (TPV) according to ANRS algorithm. Among the first-line treatment failures, an isolate from one patient showed L33F, I47T, M46G, and G48E muta- tions conferring intermediate resistance to saquinavir (SQV) and lopinavir (LPV). Though the docking energy scores are in agreement with this interpretation for SQV, it, however, indicated these mutations to be causing intermediate to high level resistance to atazanavir (ATV) and tipranavir (TPV) but making it susceptible to LPV. The patient finally responded to a second-line regimen containing 3TC, AZT and LPV with significant viral suppression. All the DR genotyping studies analyse the results using available databases which are all based on sub- type B specific sequences. The proposed homology model in this study is unique, as it may predict sub- type C specific susceptibility criteria for the available PIs. Ó 2011 Elsevier B.V. All rights reserved. 1. Introduction Drug resistance (DR) is inevitable consequence of incomplete suppression of Human Immunodeficiency virus (HIV) replication. The rapid turnover of HIV-1 RNA and its genetic variability leads to the production of many variants with decreased drug suscepti- bility (Ho et al., 1995; Perrin and Telenti, 1998). With the emer- gence of failure to first-line treatment consisting a combination of Nucleoside Reverse Transcriptase Inhibitors (NRTIs) and Non- Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) in India, Na- tional AIDS Control Organisation (Government of India) introduced second-line treatment in 2009 which includes one protease inhib- itor (PI) and two NRTIs in triple drug combination therapy. Protease inhibitors (PIs), originally designed and tested against the subtype B viruses are currently also made available in other parts of the world including Indian subcontinent where the epi- demic is dominated by subtype C (Arora et al., 2008; Deshpande et al., 2004; Sen et al., 2007). Importantly, the Stanford DR muta- tion database is mainly subtype B sequence based, and some re- ports including data (unpublished) from our own laboratory have indicated that protease (PR) gene in subtype C displays a reason- able level of sequence variability from subtype B and so rise the question of whether the DR mutations mentioned in the Stanford database will behave in a similar fashion for subtype C PR as well (Kinomoto et al., 2005)? Further, the mutations like M36I and I15V 0166-3542/$ - see front matter Ó 2011 Elsevier B.V. All rights reserved. doi:10.1016/j.antiviral.2011.08.005 ⇑ Corresponding author. Tel.: +91 172 2755192; fax: +91 172 2744401. E-mail address: skarora_in@yahoo.com (S.K. Arora). Antiviral Research xxx (2011) xxx–xxx Contents lists available at SciVerse ScienceDirect Antiviral Research journal homepage: www.elsevier.com/locate/antiviral Please cite this article in press as: Toor, J.S., et al. Prediction of drug-resistance in HIV-1 subtype C based on protease sequences from ART naive and first- line treatment failures in North India using genotypic and docking analysis. Antiviral Res. (2011), doi:10.1016/j.antiviral.2011.08.005