Antiviral Chemistry & Chemotherapy 16:295–302 In vitro activity of SPD754, a new deoxycytidine nucleoside reverse transcriptase inhibitor (NRTI), against 215 HIV-1 isolates resistant to other NRTIs Richard C. Bethell1*, Yolanda S. Lie2 and Neil T. Parkin2 1 Shire BioChem Inc., Ville St. Laurent, Québec, Canada. Presently: Boehringer Ingelheim (Canada) Ltd, Laval, Québec, Canada 2 ViroLogic, Inc., South San Francisco, CA, USA *Corresponding author: Tel: +1 450 682 4641 ext. 4332; Fax: +1 450 682 4642; Email: rbethell@lav.boehringer-ingelheim.com This work was presented in part at the 12th International HIV Drug Resistance Workshop, Cabo San Lucas, Mexico, June 10–14 2003 (Abstract 3). SPD754 (also known as AVX-754) is a deoxycytidine analogue nucleoside reverse transcriptase inhibitor (NRTI) with antiretroviral activity against HIV-1 and HIV-2 in vitro and against recombinant viruses containing thymidine analogue mutations (TAMs). In order to better establish the activity of SPD754 against HIV-1 containing TAMs, twelve panels of up to twenty clinical isolates with defined TAM combinations were selected from the ViroLogic database. Phenotypic viral susceptibility to SPD754 and five other NRTIs was tested using the PhenoSense HIV assay and expressed as median fold-change compared with a reference strain. In total, 215 isolates were selected, representing four TAM patterns in both pathways by which TAMs accumulate clinically. The presence of five TAMs in the 41, 215 pathway, at codons 41, 67, 210, 215, and 219 of reverse transcriptase (RT), produced a median 1.8-fold reduction in SPD754 susceptibility, compared with fold reductions to zidovudine, lamivudine, abacavir, didanosine and tenofovir of 438, 4.8, 4.5, 1.4 and 3.6, respectively. Five TAMs in the 67, 70, 219 pathway (at codons 41, 67, 70, 215 and 219) reduced SPD754 susceptibility by a median 1.3-fold, compared with fold reductions for the aforementioned NRTIs of 108, 3.2, 3.0, 1.3 and 2.5, respectively. M184V addition reduced SPD754 susceptibility by 1.8-fold in the presence or absence of TAMs. SPD754 retains a substantial proportion of its antiviral activity against HIV-1 containing multiple TAMs, with or without the M184V mutation. These data suggest that SPD754 is a promising new NRTI for the treatment of NRTIexperienced HIV-infected patients. Keywords: Antiretroviral agents, antiviral drug resistance, human immunodeficiency virus, HIV-1 reverse transcriptase, reverse transcriptase inhibitors, SPD754 Introduction Nucleoside reverse transcriptase inhibitors (NRTIs) are the backbone of highly active antiretroviral therapy (HAART) regimens recommended for the treatment of patients with HIV infection (Dybul et al., 2002; Panel on Clinical Practices for Treatment of HIV Infection, 2003). HAART regimens have substantially reduced morbidity and mortality associated with HIV disease (Palella et al., 1998; Murphy et al., 2001). However, resistance to antiretrovirals, including NRTIs, is increasingly common and is an important cause of virological treatment failure (Deeks, 2004). A longitudinal study in France found that 78% of HIV samples collected from treated patients ©2005 International Medical Press 0956-3202 between 1997 and 2000 had mutations in the reverse transcriptase (RT) genome conferring resistance to at least one NRTI (Tamalet et al., 2003). A quarter of isolates were genotypically resistant to all three major antiretroviral classes, that is NRTIs, non-nucleoside reverse transcriptase inhibitors and protease inhibitors. Similar data have been reported from the United States (Kagan et al., 2000; Richman et al., 2004). Primary infection with NRTI-resistant HIV is also of increasing concern in some countries, including the United States (Salomon et al., 2000; UK Collaborative Group, 2001; Little et al., 2002). 295 R Bethell et al. NRTIs share a common mechanism of action: following intracellular activation to the triphosphate (TP) form, they compete with endogenous phosphonated nucleotides for binding to viral RT. RT incorporates NRTI-monophosphates into nascent DNA chains during replication, causing chain termination. Resistance to NRTIs occurs primarily via two mechanisms: increased rates of phosphorylysis of the incorporated NRTI-monophosphate and improved specificity of the RT for the natural nucleoside triphosphate relative to the triphosphorylated NRTI (de Mendoza et al., 2002). Mutations at codons 41, 67, 70, 210, 215 and 219 of the RT genome – collectively known as ‘thymidine analogue mutations’ (TAMs) because of their initial association with resistance to zidovudine and stavudine – act to increase the rate of phosphorylysis. HIV-1 acquires these mutations sequentially during NRTI treatment, and the accumulation of these mutations leads to progressive decreases in susceptibility to all NRTIs (Whitcomb et al., 2003). This accumulation occurs via two pathways determined by the first TAM present at first treatment failure, which is itself determined by the treatment regimen. One pathway originates through mutations at codons 41 or 215 (predominantly 215Y ). After both of these mutations have been selected, mutations at codons 210, 67 and 219 are accumulated sequentially. The other pathway is characterized by the accumulation of three mutations at codons 67, 70 and 219. Once these three mutations have been selected, mutations at codons 215 (predominantly 215F) and 41 are accumulated sequentially (Flandre et al., 2003, Marcelin et al., 2004). Other mutations, such as the M184V mutation, alter the structure of the NRTI binding site upon RT. Such mutations result in better discrimination between the nucleoside triphosphate substrate and the NRTI-triphosphate, diminishing the probability of a chain termination event during reverse transcription. M184V is rapidly selected during lamivudine-containing HAART (Descamps et al., 2000; Maguire et al., 2000) and causes high-level resistance to lamivudine and reduced susceptibilty to didanosine, zalcitabine and abacavir (Whitcomb et al., 2003). Because of the large number of patients who received sequential monotherapy or dual NRTI therapy with zidovudine or stavudine and lamivudine prior to the introduction of triple drug combination therapy, and the large numbers of patients who take lamivudine with zidovudine or stavudine in HAART regimens, many treatment-experienced patients harbour viruses that contain both TAMs and the M184V mutation. SPD754 (also known as AVX-754, and formerly as BCH-10618) is a novel deoxycytidine analogue NRTI in clinical development. SPD754 is the (–)-enantiomer of 2′-deoxy-3′-oxa-4′-thiocytidine (dOTC or BCH-10652) (de Muys et al., 1999; Taylor et al., 2000). SPD754 showed 296 good antiviral activity against HIV-1 isolates in vitro, both alone and in combination with other NRTIs (De Muys et al., 1999; Taylor et al., 2000), good antiviral activity against viruses with a range of NRTI-resistant genotypes (De Muys et al., 1999; Taylor et al., 2000), and a low potential for cellular and mitochondrial toxicity (Bethell RC, de Rooj ER, Smolders KGM, van Schijndel HB, Timmermans EC & de Baar MP (2004) Comparison of the in vitro mitochondrial toxicity of SPD754 and HepG2 cells with nine other nucleoside reverse transcriptase inhibitors. 44th Interscience Conference on Antimicrobial Agents & Chemotherapy. Washington DC, USA. 30 October–2 November 2004. Abstract H-207). SPD754 showed promising efficacy in a Phase II study of antiretroviralnaive, HIV-infected patients (Cahn P, Lange J, Cassetti I, Sawyer J, Zala C, Rolon M, Bologna R & Shiveley L (2003) Anti-HIV-1 activity of SPD754, a new NRTI: results of a 10 day monotherapy study in treatment-naïve HIV patients. 2nd International Aids Society Conference. Paris, France, 13–16 July 2003. Abstract LB-15). In order to further characterize the activity of SPD754 against clinical isolates of HIV-1 containing TAMs and the M184V mutation, SPD754 has been tested against a large panel of HIV1 clinical isolates with defined genotypic profiles associated with NRTI resistance. Materials and methods Compounds SPD754 was synthesized at Shire Pharmaceuticals (Laval, Quebec, Canada) as described previously (Mansour et al., 1995). Zidovudine and didanosine were sourced from Sigma Chemical (MO, USA), lamivudine from Roxanne Labs (CT, USA), abacavir from GlaxoSmithKline (NC, USA) and tenofovir from Gilead Sciences (CA, USA). The structures of all the antiviral compounds used in the present study are shown in Figure 1. Viruses and cells Studies were performed using a panel of HIV-1 strains with specific TAM patterns based on the data on pathways for the selection of TAMs from the studies of Marcelin et al. (2004) and Flandre et al. (2003). TAMs were defined as M41L, D67N, K70R, L210W, T215F or Y, and K219E, H, N, Q, R. Panels of clinical HIV-1 isolates with these genotypic patterns were then selected from the ViroLogic library of genotyped clinical isolates. Ten to twenty samples with each genotype were selected. Mutations at codons 44 (E44A or D) and 118 were allowed within groups. Samples with mixtures at codons 41, 67, 70, 184, 210, 215 and 219 were excluded. Viruses containing insertions at codon 69 or the Q151M mutation were excluded, as were those with other mutations not ©2005 International Medical Press SPD754 versus NRTI-resistant HIV Figure 1. Chemical structures of SPD754, lamivudine, tenofovir, zidovudine, abacavir and didanosine NH2 NH2 NH2 N N O N N N S S HO P O SPD754 N O HO HO HO O N O N O Tenofovir Lamivudine O O HN HN N O O N HO N N N N N NH2 HO O NH N HO N3 Zidovudine Abacavir typically included among TAMs (for example K65R, L74I or V, and V75A, M, S, or T). Repeat samples from the same patient with different genotypes were included, but only one isolate from any given patient within any genotypic group was permitted. None of the viruses contained mutations known to confer resistance to either non-nucleoside reverse transcriptase inhibitors or protease inhibitors. The effect of the M184V mutation on the antiviral activity of NRTIs was determined by constructing similar panels of viruses. Six such panels measured the effect of the presence of the M814V mutation on the NRTI sensitivity of wild-type virus and viruses with mutations TAMs at codons 41 and 215, or codons 67, 70 and 219. In all tests, NRTI susceptibility in the clinical isolates was compared with that of a reference virus (strain CNDO) containing the RT (and protease) sequences of the NL4-3 HIV-1. Cells were cultured as previously described for the automated PhenoSense HIV assay (Petropoulos et al., 2000). Antiviral assay Phenotypic viral susceptibility to the aforementioned NRTIs was assessed using the PhenoSense HIV assay (Petropoulos et al. 2000). The results were expressed as Antiviral Chemistry & Chemotherapy 16.5 Didanosine median fold-change in 50% inhibitory concentration (IC50) in clinical isolates, as compared with the reference strain. Statistical methods Analysis of the effect of M184V mutation on viral susceptibility to NRTIs was performed using pair-wise comparisons and plotted as bivariate scattergrams with linear regression lines for the whole dataset or for the groups with or without M184V. Pair-wise regression analysis of log-transformed median fold-changes in susceptibility was undertaken to evaluate the level of cross resistance between SPD754 and the other NRTIs tested. Results A total of 215 isolates were selected (Table 1). These isolates exhibited eight genotypic patterns containing only TAMs, four in each of the two TAM pathways. Consistent with previous results (Marcelin et al., 2004), viruses in the 41, 215 pathway contained predominantly Y at codon 215, whereas viruses in the 67, 70, 219 pathway contained predominantly F. A further three panels contained viruses with M184V together with mutations with no TAMs or 297 298 20 20 20 20 20 20 15 10 20 20 15 15 Wild type Wild type+M184V 41, 215 path 41, 215 41, 215+M184V 41, 210, 215 41, 67, 210, 215 41, 67, 210, 215, 219 67, 70, 219 path 67, 70 67, 70, 219 67, 70, 219+M184V 67, 70, 215, 219 41, 67, 70, 215, 219 5 4 – – – 15 19 20 18 19 – – Y 10 11 – – – 0 1 0 2 1 – – F 33 27 – – – 100 95 100 90 95 – – %Y Codon 215 1.3 (0.9–1.9) 1.4 (1.0–1.7) 1.8 (1.6–2.7) 1.0 (0.6–1.9) 1.0 (0.8–1.2) 1.8 (1.2–2.6) 1.7 (1.2–2.4) 1.4 (1.1–1.9) 2.1 (1.3–3.1) 1.2 (0.7–1.7) 1.6 (1.2–2.1) 0.9 (0.7–1.1) IC50 FC* (range) SPD754 – – 1.9 – – – – – 1.7 – 1.8 – ∆184† 0.6 – ∆184† – 0.2 108 – (13.0–827) 44 – (4.2–404) 3.4 0.2 (1.5–12.0) 21 – (2.9–326) 5.5 – (2.5–10.0) 438.0 – (7.2–1000) 271 – (5.6–1000) 91 (11–852) 6.0 (0.6–15) 33.1 – (4.1–246) 0.5 (0.3–1.0) 0.7 (0.2–1.3) IC50 FC* (range) Zidovudine – ∆184† – – – – – – 3.2 (1.7–5.1) 3.8 (1.9–9.8) – – 200 116.2 (200–200) 1.7 (1.0–3.8) 1.6 (1.2–2.8) 4.8 (2.2–7.6) 4.2 (2.7–6.4) 1.9 (1.3–4.4) 200 138.5 (200–200) 1.4 (0.9–2.7) 200 214.4 (138–200) 0.9 (0.7–1.1) IC50 FC* (range) Lamivudine 3.0 (1.5–5.3) 2.3 (1.5–4.0) 3.1 (2.5–5.5) 1.5 (0.8–3.2) 1.2 (0.9–1.6) 4.5 (1.8–6.7) 3.3 (1.8–4.7) 2.5 (1.3–3.8) 4.5 (2.6–6.2) 1.7 (1.3–3.1) 2.7 (1.8–3.3) 0.9 (0.6–1.1) IC50 FC* (range) Abacavir – – 2.1 – – – – – 2.6 – 3.1 – ∆184† 1.3 (0.9–1.7) 1.1 (1.0–1.6) 1.3 (1.1–1.8) 0.9 (0.6–1.3) 1.0 (0.8–1.1) 1.4 (1.1–2.0) 1.3 (1.0–1.8) 1.2 (0.9–1.7) 1.5 (1.0–1.9) 1.0 (0.9–1.4) 1.3 (1.0–1.6) 1.0 (0.7–1.1) IC50 FC* (range) – – 1.4 – – – – – 1.5 – 1.3 – ∆184† Didanosine 2.5 (1.5–5.0) 2.0 (1.0–3.6) 0.9 (0.6–1.6) 1.8 (1.1–4.6) 1.2 (0.9–1.7) 3.6 (1.1–9.1) 3.0 (1.0–5.7) 2.6 (1.4–5.9) 1.0 (0.4–1.4) 2.2 (1.3–4.7) 0.5 (0.4–0.6) 0.8 (0.4–0.9) IC50 FC* (range) – – 0.5 – – – – – 0.4 – 0.7 – ∆184† Tenofovir *Median (range) of the individual fold change (FC) values of the 50% inhibitory concentration (IC50) for clinical isolates relative to the standard reference strain (NL4-3). Data shown are rounded values from the raw data. Upper limit of assay =200-fold for lamivudine. †Median FC value of isolates containing M184V relative to the median FC value of isolates with the same genotype without M184V. n Genotype Table 1. Effect of thymidine analogue mutations (TAMs) in the 41, 215 and 67, 70, 219 pathways, in the presence and absence of M184V mutations, on HIV-1 in vitro susceptibility to SPD754 and other nucleotide reverse transcriptase inhibitors. R Bethell et al. ©2005 International Medical Press SPD754 versus NRTI-resistant HIV with TAMs at either codons 41 and 215, or 67, 70 and 219. A further panel contained viruses with no nucleosideassociated mutations (NAMs). Effect of TAMs on the antiviral activity of SPD754 and other NRTIs Viruses with no NAMs had a median 0.9-fold change in susceptibility to SPD754 (range 0.7–1.1) relative to the reference strain. The median fold-changes for all the other NRTIs against this panel of viruses were also close to 1.0. Mutations at codons 41 and 215 conferred a median 33-fold change in susceptibility to zidovudine relative to wild-type HIV-1. The sequential addition of mutations at codons 210, 67 and 219 progressively reduced susceptibility to zidovudine until a median 438-fold reduction was observed in the presence of all five mutations (Table 1). Mutations at codons 67 and 70 conferred a median 5.0-fold change in susceptibility to zidovudine. A progressive decrease in susceptibility occurred with the accumulation of further mutations at codons 210, 67 and 219 until a median 108-fold reduction occurred in the presence of all five mutations (Table 1). In contrast, mutations at codons 41 and 215 produced a limited 1.2-fold (range 0.7–1.7) reduction in susceptibility to SPD754. The incremental effects of further TAMs in this pathway reached a 1.8-fold reduction (range 1.2–2.6) when all five were present (Table 1). Similar fold-changes in susceptibility to didanosine were observed, while reductions in susceptibility to lamivudine, abacavir and tenofovir in the presence of all five TAMs were 4.8 (range 2.2–7.6), 4.5 (range 1.8–6.7) and 3.6 (range 1.1–9.1), respectively. These levels of resistance to didanosine, abacavir and tenofovir and lamivudine are consistent with the results of a previous study (Whitcomb et al. 2003). Mutations at codons 67 and 70 had no effect on susceptibility to SPD754 (median fold-change 1.0; range 0.8–1.2). Accumulation of additional TAMs within this pathway resulted in minimal changes in SPD754 susceptibility, which reached 1.3-fold change (0.9–1.9) when all five TAMs were present (Table 1). Again, similar changes in viral susceptibility to didanosine were observed, while fold reductions in susceptibility to lamivudine, abacavir and tenofovir in the presence of all five TAMs were 3.2 (range 1.7–5.1), 3.0 (range 1.5–5.3) and 2.5 (range 1.5–5.0), respectively. Effect of M184V mutation on the antiviral activity of SPD754 and other NRTIs Susceptibility to NRTIs was assessed in the presence and absence of the M184V mutation in wild-type HIV-1 and isolates with mutations at codons 41 and 215, or 67, 70 and 219. As expected, the presence of the M184V mutation reduced median viral susceptibility to lamivudine to such a Antiviral Chemistry & Chemotherapy 16.5 large extent that the IC50 value could not be determined on any virus containing this mutation, regardless of the background genotype. Pair-wise comparisons showed that M184V addition was associated with an approximate 1.8-fold reduction in susceptibility to SPD754 in all genotypes (Table 1). In comparison, M184V reduced abacavir susceptibility 2.1 to 3.1-fold and didanosine susceptibility by 1.3 to 1.5-fold. M184V slightly increased viral susceptibility to tenofovir, and this effect appeared slightly greater in the groups of viruses containing TAMs than in the group lacking TAMs (2.1 and 2.3-fold increased susceptibility in the 67, 70, 219 and 41, 215 groups respectively, compared with 1.5-fold in the viruses lacking TAMs). Cross resistance between NRTIs Pair-wise regression analyses for SPD754 indicated that, as for all other NRTIs (Whitcomb et al., 2003), there is significant cross resistance between SPD754 and the other NRTIs tested (r2 approximately 0.5–0.75) as shown in Figure 2. The extent of cross resistance with zidovudine and tenofovir was only apparent when samples with or without M184V were analysed separately, whereas correlations between SPD754 and abacavir or didanosine were evident with or without splitting the samples by the presence of M184V. However, in both subgroups, the extent of cross resistance was substantial. In addition, there was significant cross resistance between SPD754 and lamivudine in samples lacking M184V (r2=0.70; data not shown). Discussion Previous studies have demonstrated that TAM accumulation progressively decreases HIV susceptibility to all NRTIs (Whitcomb et al., 2003). While measurable in vitro resistance does not always result in reduced clinical susceptibility, clinical ‘cut off ’ thresholds for resistance assigned for various NRTIs indicate that clinically significant reductions in susceptibility to a number of NRTIs can occur in isolates with sufficient numbers of TAMs (Whitcomb et al., 2003). Data from the present study confirm that TAMs incrementally increase resistance to all of the NRTIs tested in the present study, namely zidovudine, lamivudine, abacavir, didanosine, tenofovir and SPD754. SPD754, along with didanosine, showed a decrease in susceptibility of <50% in the presence of up to five TAMs. The presence of five mutations at codons 41, 67, 210, 215, and 219 conferred a median 1.8-fold reduction in susceptibility to SPD754. Similarly the presence of TAMs at codons 41, 67, 70, 215 and 219 conferred a median 1.3-fold reduction in susceptibility to SPD754. Until studies are performed to determine the clinically relevant threshold for SPD754, we cannot 299 R Bethell et al. Figure 2. Scattergrams based on pair-wise regression analysis showing potential level of in vitro cross resistance between SPD754 and: A) abacavir, B) didanosine, C) tenofovir and D) zidovudine. A B 10 r2=0.76 r2=0.64 Didanosine FC Abacavir FC 10 1 0 1 SPD754 FC 0 r2=0.70 r2=0.64 1 0 10 C 0 1 SPD754 FC 10 D 10 1000 2 r =0.53 r2=0.50 r2=0.59 r2=0.50 Zidovudine FC Tenofovir FC 100 1 0 0 1 SPD754 FC 10 1 0 10 0 1 SPD754 FC 10 Values for r 2 indicate correlation co-efficients for the groups defined by the absence (M184 wt) or presence of the M184V mutation. determine whether or not these modest reductions in susceptibility will impact virological response rates. Nonetheless, the relatively low magnitude of the susceptibility reductions suggest that SPD754 will be useful in the treatment of NRTI-experienced HIV-infected patients, in whom cross resistance among NRTIs limits the available options for salvage therapy (Deeks, 2004). The structural basis of the very high level of resistance to lamivudine conferred by the M184V and M184I mutations has been attributed to steric interactions between the branched side-chain of these amino acids and thiomethylene group of lamivudine, which is very much larger than the oxygen atom of the natural substrates of the reverse transcriptase (Sarafianos et al., 1999). The very 300 much lower magnitude of the decrease in susceptibility to SPD754 conferred by M184V is therefore likely to result from the much smaller size of a single sulphur atom of SPD754 when compared to the corresponding thiomethylene group of lamivudine, as is shown in Figure 1. Whitcomb et al. (2003) have proposed that NRTIs can be divided into two groups according to the effect of the M184V mutation in vitro: susceptibility to ‘Group 1’ agents (zidovudine, stavudine, tenofovir and adefovir) is increased by M184V, while susceptibility to Group 2 agents (lamivudine, emtricitabine, didanosine, zalcitabine and abacavir) is decreased (Whitcomb et al., 2003). The clinical relevance of these in vitro observations will vary according to the clinical cut off for individual agents. The effect of the ©2005 International Medical Press SPD754 versus NRTI-resistant HIV M184V mutation on SPD754 susceptibility was consistent regardless of the background genotype: the mutation produced a small (1.8-fold) decrease in susceptibility to SPD754 in the presence of TAMs accumulated via either pathway. Clearly, SPD754 belongs in the second category of NRTIs, although its activity was affected less than that of many other members. In common with previous reports (Miller et al., 2003), M184V slightly increased viral susceptibility to tenofovir in the present study. M184V-positive HIV-1 mutants show reduced replicative fitness owing to enhanced fidelity and/or impaired processivity in the RT enzyme (Back et al., 1996; Naeger et al., 2001; Diallo et al., 2003). Furthermore, there was a 0.5 log10 reduction in viral load relative to baseline viral load among patients who received lamivudine monotherapy and in whom the M184V was rapidly selected (Kuritzkes et al. 1996). These observations have led some to propose that lamivudine administration should be continued in patients with the M184V mutation in order to maintain a reduced replicative capacity. However, an NRTI with potent clinical antiretroviral activity [Bethell RC & Collins P (2004) Genotypic and phenotypic analysis of HIV-1 isolates from patients after 10 days monotherapy with SPD754. 44th Interscience Conference on Antimicrobial Agents and Chemotherapy. 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