Antiviral Chemistry & Chemotherapy 13:115–128 1 ©2002 International Medical Press 0956-3202/02/$17.00 Introduction The reverse transcriptase (RT) of HIV-1 is a multifunc- tional enzyme that catalyzes the conversion of viral genomic RNA into double-stranded proviral DNA. RT is an important target for antiviral chemotherapy because it is essential for viral replication. Two classes of inhibitors are currently being used in the management of HIV infection. Non-nucleoside RT inhibitors (NNRTIs) bind directly to a hydrophobic pocket adjacent to the polymerase active site of RT. Nucleoside RT inhibitors (NRTIs) such as zidovu- dine (AZT) and lamivudine (3TC), which are being wide- ly used in the treatment of HIV infection, act by compet- ing with natural substrates at the HIV RT active site, lead- ing to incorporation and termination of the DNA chain. Unlike most cellular DNA polymerases, RT exhibits lower fidelity and processivity than cellular DNA polymerases and lacks a 3′- to 5′- proofreading activity, resulting in a high mutation rate and drug resistance (Preston et al., 1988; Roberts et al., 1988; Huber et al., 1989; Kellam et al., 1992; Yu & Goodman, 1992). Anti-HIV therapy is limit- ed because of a number of factors, including development of viral drug resistance and significant host toxicity often observed following long-term exposure to antiviral drugs (Table 1) (Larder & Kemp, 1989; Gao et al., 1992). Consequently, efforts continue to identify potent antiviral agents effective against drug resistant virus. (–)-β-D- Dioxolane guanine (DXG) and its prodrug, 2,6-diaminop- urine (DAPD), have been reported to be potent inhibitors of HIV-1 (Kim et al., 1993; Siddiqui et al., 1993; Furman et al., 2001). When recombinant or clinical variants of HIV-1 were used to assess the efficacy of this purine nucle- oside analogue against drug-resistant HIV-1, it was observed that AZT-resistant and 3TC-resistant virus Molecular mechanism of DAPD/DXG against zidovu- dine- and lamivudine- drug resistant mutants: a molecular modelling approach Youhoon Chong 1 , Katyna Borroto-Esoda 2 , Phillip A Furman 2 , Raymond F Schinazi 3 and Chung K Chu 1 * 1 Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Ga., USA 2 Triangle Pharmaceuticals, Durham, NC, USA 3 Emory University School of Medicine/ Veterans Affairs Medical Center, Decatur, Ga., USA Corresponding author: Tel: +706 542 5379; Fax: +1 706 542 5381; E-mail: dchu@rx.uga.edu In order to understand molecular mechanism of antiviral drug resistance of HIV-1 reverse tran- scriptase (RT) as well as potent antiviral activity of 2,6-diaminopurine dioxolane (DAPD) [prodrug of (–)-β-D-dioxolane guanine (DXG)] against drug- resistant RTs, molecular modelling studies of three structurally distinct nucleoside RT inhibitor (NRTI)- triphosphates (TP) [zidovudine (AZT)-TP, lamivu- dine (3TC)-TP and DXG-TP] complexed with the wild-type (WT) and mutated RT were conducted. The computational analyses indicated that the antiviral activity and the calculated relative bind- ing energy of the RT inhibitor triphosphates can be correlated, and the minimized structures gave information on the molecular mechanism of drug resistance conferred by mutations. The interac- tions between the NRTI-TP and adjacent amino acid residues (Lys65, Lys70, Arg72, Tyr115 and/or Gln151) played important roles in stabilizing the enzyme–inhibitor complex. Particularly, Arg72 was found to stabilize the dioxolane and oxathiolane sugar moiety through hydrogen bonding, which was responsible for favourable binding affinity of DXG-TP to AZT- as well as 3TC-resistant mutants. The conformational changes in these amino acid residues caused by mutation always affected the changes in the tertiary structures of enzyme–inhibitor complexes through either clos- ing or opening the gap between the fingers and palm domains. The enzyme-inhibitor complexes with good binding affinity showed tight binding modes by closing the gap between the two domains, whereas weak inhibitors gave open and loose complexes. Keywords: HIV-1 RT, drug resistance, molecular modelling, DAPD, DXG, 3TC, AZT