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David A Degoey,
David A Betebenner,
David J Grampovnik,
Dachun Liu,
John K Pratt,
Michael D Tufano,
Wenping He,
Preethi Krishnan,
Tami J Pilot-Matias,
Kennan C Marsh,
Akhteruzzaman Molla, Dale J Kempf,
Clarence J Maring
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ABSTRACT: Efforts to improve the genotype 1a potency and pharmacokinetics of earlier naphthyridine-based HCV NS5A inhibitors resulted in the discovery of a novel series of pyrido[2,3-d]pyrimidine compounds, which displayed potent inhibition of HCV genotypes 1a and 1b in the replicon assay. SAR in this system revealed that the introduction of amides bearing an additional 'E' ring provided compounds with improved potency and pharmacokinetics. Introduction of a chiral center on the amide portion resulted in the observation of a stereochemical dependence for replicon potency and provided a site for the attachment of functional groups useful for improving the solubility of the series. Compound 21 was selected for administration in an HCV-infected chimpanzee. Observation of a robust viral load decline provided positive proof of concept for inhibition of HCV replication in vivo for the compound series.
Bioorganic & medicinal chemistry letters 04/2013; · 2.65 Impact Factor
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A Chris Krueger,
Darold L Madigan,
David W Beno,
David A Betebenner,
Robert Carrick,
Brian E Green,
Wenping He,
Dachun Liu,
Clarence J Maring,
Keith F McDaniel,
Hongmei Mo,
Akhteruzzaman Molla,
Christopher E Motter,
Tami J Pilot-Matias,
Michael D Tufano, Dale J Kempf
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ABSTRACT: The synthesis of several pyrido[2,3-d]pyrimidine and pyrimido[4,5-d]pyrimidine analogs is described with one such analog possessing subnanomolar potency in both genotype 1a and 1b cell culture HCV replicon assays.
Bioorganic & medicinal chemistry letters 03/2012; 22(6):2212-5. · 2.65 Impact Factor
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Douglas K Hutchinson,
Charles A Flentge,
Pamela L Donner,
Rolf Wagner,
Clarence J Maring,
Warren M Kati,
Yaya Liu,
Sherie V Masse,
Tim Middleton,
Hongmei Mo,
Debra Montgomery,
Wen W Jiang,
Gennadiy Koev,
David W A Beno,
Kent D Stewart,
Vincent S Stoll,
Akhteruzzaman Molla, Dale J Kempf
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ABSTRACT: A series of quinoline derivatives was synthesized as potential bioisosteric replacements for the benzothiadiazine moiety of earlier Hepatitis C NS5B polymerase inhibitors. Several of these compounds exhibited potent activity in enzymatic and replicon assays.
Bioorganic & medicinal chemistry letters 01/2011; 21(6):1876-9. · 2.65 Impact Factor
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ABSTRACT: Patterns of HIV-1 protease inhibitor (PI) resistance-associated mutations (RAMs) and effects on PI susceptibility associated with the L76V mutation were studied in a large database. Of 20,501 sequences with ≥1 PI RAM, 3.2% contained L76V; L76V was alone in 0.04%. Common partner mutations included M46I, I54V, V82A, I84V, and L90M. L76V was associated with a 2- to 6-fold decrease in susceptibility to lopinavir, darunavir, amprenavir, and indinavir and a 7- to 8-fold increase in susceptibility to atazanavir and saquinavir.
Antimicrobial Agents and Chemotherapy 11/2010; 54(11):4903-6. · 4.84 Impact Factor
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Yi Yang,
Annette J Dahly-Vernon,
Eric A G Blomme,
Jie Lai-Zhang, Dale J Kempf,
Kennan C Marsh,
Yvette A Harrington,
Steven H Nye,
Darin L Evans,
Richard J Roman,
Howard J Jacob,
Jeffrey F Waring
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ABSTRACT: Ritonavir (RTV) and other protease inhibitors (PIs) used for the treatment of human immunodeficiency virus (HIV) infection are associated with elevated serum triglycerides (TG) and cholesterol in some patients. A rat strain (Sprague-Dawley or SD) commonly used in toxicology studies is not sensitive to RTV-induced hyperlipidemia, making mechanistic studies and the identification of novel, lipid-neutral PIs challenging. The objective of this study was to identify a rat strain that mirrors human PI-associated hyperlipidemia. RTV was administered at 100 mg/kg/day for 5 days to a panel of 14 rat strains estimated to cover approximately 86% of the known genetic variance in rats. Increased serum TG and cholesterol levels occurred only in two rat strains, including LEW x BN rats. Livers from LEW x BN (sensitive) and SD (resistant) rats were then evaluated using microarrays to investigate differences in the transcriptomic response to RTV. Several genes, including some involved in bile acid biosynthesis, gluconeogenesis, and carbohydrate metabolism, were differentially regulated between the two strains. In particular, cytochrome P450 7A1 (CYP7A1), a key enzyme for cholesterol metabolism, was down-regulated in the sensitive and up-regulated in resistant rats. Collectively, these results demonstrate the utility of a genetically diverse rat panel to identify strains with clinical relevance for a particular adverse effect. Furthermore, the genome-wide transcriptomic analysis suggests that RTV-induced hyperlipidemia is at least in part due to changes in hepatic lipid biosynthesis and metabolism. These findings will facilitate the discovery of novel, lipid-neutral HIV PIs and the identification of relevant biomarkers for this adverse event.
The Veterinary Journal 07/2010; 185(1):75-82. · 2.24 Impact Factor
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ABSTRACT: Patients treated with highly active antiretroviral therapy may develop metabolic side effects such as hyperlipidemia, insulin resistance, lipoatrophy and lactic acidosis. The pathophysiology of these metabolic abnormalities is unknown, although some, e.g., lactic acidosis and lipoatrophy, are more associated with nucleoside use while protease inhibitors (PIs) have been shown to contribute to hyperlipidemia and insulin resistance. Identifying new PIs that are not associated with dyslipidemia has been hindered by the lack of mechanistic information and the unavailability of relevant animal models. In order to understand the molecular mechanism behind the hyperlipidemia associated with other protease inhibitors, and to develop a more effective, faster screen for compounds with this liability, we have analyzed expression profiles from PI-treated animals. Previously, we have shown that treatment of rats with ritonavir results in increases in the expression of proteasomal subunit genes in the liver. We show this increase is similar in rats treated with bortezomib, a proteasome inhibitor. In addition, we have treated rats with additional protease inhibitors, including atazanavir, which is associated with lower rates of lipid elevations in the clinic when administered in the absence of ritonavir. Our results indicate a strong correlation between proteasomal induction and lipid elevations, and have allowed us to develop a rapid screen for identifying novel PIs that do not induce the proteasome.
Archive für Toxikologie 03/2010; 84(4):263-70. · 4.67 Impact Factor
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Koushi Hidaka,
Tooru Kimura,
Hamdy M Abdel-Rahman,
Jeffrey-Tri Nguyen,
Keith F McDaniel,
William E Kohlbrenner,
Akhteruzzaman Molla,
Motoyasu Adachi,
Taro Tamada,
Ryota Kuroki,
Noriko Katsuki,
Yoshiaki Tanaka,
Hikaru Matsumoto,
Jun Wang,
Yoshio Hayashi, Dale J Kempf,
Yoshiaki Kiso
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ABSTRACT: A series of HIV protease inhibitor based on the allophenylnorstatine structure with various P(2)' moieties were synthesized. Among these analogues, we discovered that a small allyl group would maintain potent enzyme inhibitory activity compared to the o-methylbenzyl moiety in clinical candidate 1 (KNI-764, also known as JE-2147, AG-1776, or SM-319777). Introduction of an anilinic amino group to 2 (KNI-727) improved water-solubility and anti-HIV-1 activity. X-ray crystallographic analysis of 13k (KNI-1689) with a beta-methallyl group at P(2)' position revealed hydrophobic interactions with Ala28, Ile84, and Ile50' similar to that of 1. The presence of an additional methyl group on the allyl group in compound 13k significantly increased anti-HIV activity over 1 while providing a rational drug design for structural minimization and improving membrane permeability.
Journal of Medicinal Chemistry 12/2009; 52(23):7604-17. · 4.80 Impact Factor
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Kent D Stewart,
Jeffrey R Huth,
Teresa I Ng,
Keith McDaniel,
Rebecca Newlin Hutchinson,
Vincent S Stoll,
Renaldo R Mendoza,
Edmund D Matayoshi,
Robert Carrick,
Hongmei Mo, [......],
Karl Walter,
Paul L Richardson,
Leo W Barrett,
Robert Meadows,
Steve Anderson,
William Kohlbrenner,
Clarence Maring, Dale J Kempf,
Akhter Molla,
Edward T Olejniczak
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ABSTRACT: The ectodomain of HIV-1 gp41 mediates the fusion of viral and host cellular membranes. The peptide-based drug Enfuvirtide(1) is precedent that antagonists of this fusion activity may act as anti HIV-agents. Here, NMR screening was used to discover non-peptide leads against this target and resulted in the discovery of a new benzamide 1 series. This series is non-peptide, low molecular weight, and analogs have activity in a cell fusion assay with EC50 values ranging 3-41microM. Structural work on the gp41/benzamide 1 complex was determined by NMR spectroscopy using a designed model peptide system that mimics an open pocket of the fusogenic form of the protein.
Bioorganic & medicinal chemistry letters 11/2009; 20(2):612-7. · 2.65 Impact Factor
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ABSTRACT: The HIV protease inhibitor ritonavir (RTV) is also a potent inhibitor of the metabolizing enzyme cytochrome P450 3A (CYP3A) and is clinically useful in HIV therapy in its ability to enhance human plasma levels of other HIV protease inhibitors (PIs). A novel series of CYP3A inhibitors was designed around the structural elements of RTV believed to be important to CYP3A inhibition, with general design features being the attachment of groups that mimic the P2-P3 segment of RTV to a soluble core. Several analogs were found to strongly enhance plasma levels of lopinavir (LPV), including 8, which compares favorably with RTV in the same model. Interestingly, an inverse correlation between in vitro inhibition of CYP3A and elevation of LPV was observed. The compounds described in this study may be useful for enhancing the pharmacokinetics of drugs that are metabolized by CYP3A.
Bioorganic & medicinal chemistry letters 08/2009; 19(18):5444-8. · 2.65 Impact Factor
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David A DeGoey,
David J Grampovnik,
William J Flosi,
Kennan C Marsh,
Xiu C Wang,
Larry L Klein,
Keith F McDaniel,
Yaya Liu,
Michelle A Long,
Warren M Kati,
Akhteruzzaman Molla, Dale J Kempf
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ABSTRACT: We studied the synthesis, cleavage rates, and oral administration of prodrugs of the HIV protease inhibitors (PIs) lopinavir and ritonavir. Phosphate esters attached directly to the central hydroxyl groups of these PIs did not demonstrate enzyme-mediated cleavage in vitro and did not provide measurable plasma levels of the parent drugs in vivo. However, oxymethylphosphate (OMP) and oxyethylphosphate (OEP) prodrugs provided improved rates of cleavage, high levels of aqueous solubility, and high plasma levels of the parent drugs when dosed orally in rats and dogs. Dosing unformulated capsules containing the solid prodrugs led to plasma levels equivalent to those observed for dosing formulated solutions of the parent drugs. A direct synthetic process for the preparation of OMP and OEP prodrugs was developed, and the improved synthetic method may be applicable to the preparation of analogous soluble prodrugs of other drug classes with limited solubility.
Journal of Medicinal Chemistry 05/2009; 52(9):2964-70. · 4.80 Impact Factor
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John T Randolph,
Charles A Flentge,
Peggy P Huang,
Douglas K Hutchinson,
Larry L Klein,
Hock B Lim,
Rubina Mondal,
Thomas Reisch,
Debra A Montgomery,
Wen W Jiang,
Sherie V Masse,
Lisa E Hernandez,
Rodger F Henry,
Yaya Liu,
Gennadiy Koev,
Warren M Kati,
Kent D Stewart,
David W A Beno,
Akhteruzzaman Molla, Dale J Kempf
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ABSTRACT: Benzothiadiazine inhibitors of the HCV NS5B RNA-dependent RNA polymerase are an important class of non-nucleoside inhibitors that have received considerable attention in the search for novel HCV therapeutics. Research in our laboratories has identified a novel series of tetracyclic benzothiadiazine inhibitors of HCV polymerase bearing a benzylamino substituent on the B-ring. Compounds in this series exhibit low-nanomolar activities in both genotypes 1a and 1b polymerase inhibition assays and subgenomic replicon assays. Optimization of pharmacokinetic properties in rat led to compound 30, which has good oral bioavailability (F = 56%) and a favorable tissue distribution drug profile, with high liver to plasma ratios. Compound 30 is a potent inhibitor in replicon assays, with EC(50) values of 10 and 6 nM against genotypes 1a and 1b, respectively.
Journal of Medicinal Chemistry 05/2009; 52(10):3174-83. · 4.80 Impact Factor
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David A Degoey,
David J Grampovnik,
Charles A Flentge,
William J Flosi,
Hui-Ju Chen,
Clinton M Yeung,
John T Randolph,
Larry L Klein,
Tatyana Dekhtyar,
Lynn Colletti, [......],
Vincent Stoll,
Mulugeta Mamo,
David C Morfitt,
Bach Nguyen,
James M Schmidt,
Sue J Swanson,
Hongmei Mo,
Warren M Kati,
Akhteruzzaman Molla, Dale J Kempf
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ABSTRACT: A series of symmetry-based HIV protease inhibitors was designed and synthesized. Modification of the core regiochemistry and stereochemistry significantly affected the potency, metabolic stability, and oral bioavailability of the inhibitors, as did the variation of a pendent arylmethyl P3 group. Optimization led to the selection of two compounds, 10c (A-790742) and 9d (A-792611), for advancement to preclinical studies. Both compounds displayed low nanomolar potency against wild type HIV in the presence of human serum, low rates of metabolism in human liver microsomes, and high oral bioavailability in animal models. The compounds were examined in a preclinical model for the hyperbilirubinemia observed with some HIV PIs, and both exhibited less bilirubin elevation than comparator compounds. X-ray crystallographic analyses of the new cores were used to examine differences in their binding modes. The antiviral activity of the compounds against protease inhibitor resistant strains of HIV was also determined.
Journal of Medicinal Chemistry 04/2009; 52(8):2571-86. · 4.80 Impact Factor
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Rolf Wagner,
Daniel P Larson,
David W A Beno,
Todd D Bosse,
John F Darbyshire,
Yi Gao,
Bradley D Gates,
Wenping He,
Rodger F Henry,
Lisa E Hernandez, [......],
Yaya Liu,
Michelle A Long,
Clarence J Maring,
Sherie V Masse,
Tim Middleton,
Debra A Montgomery,
John K Pratt,
Patricia Stuart,
Akhteruzzaman Molla, Dale J Kempf
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ABSTRACT: The hepatitis C virus (HCV) NS5B polymerase is essential for viral replication and has been a prime target for drug discovery research. Our efforts directed toward the discovery of HCV polymerase inhibitors resulted in the identification of unsymmetrical dialkyl-hydroxynaphthalenoyl-benzothiadiazines 2 and 3. The most active compound displayed activity in genotypes 1a and 1b polymerase and replicon cell culture inhibition assays at subnanomolar and low nanomolar concentrations, respectively. It also displayed an excellent pharmacokinetic profile in rats, with a plasma elimination half-life after intravenous dosing of 4.5 h, oral bioavailability of 77%, and a peak liver concentration of 21.8 microg/mL.
Journal of Medicinal Chemistry 03/2009; 52(6):1659-69. · 4.80 Impact Factor
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Douglas K Hutchinson,
Teresa Rosenberg,
Larry L Klein,
Todd D Bosse,
Daniel P Larson,
Wenping He,
Wen W Jiang,
Warren M Kati,
William E Kohlbrenner,
Yaya Liu,
Sherie V Masse,
Tim Middleton,
Akhteruzzaman Molla,
Debra A Montgomery,
David W A Beno,
Kent D Stewart,
Vincent S Stoll, Dale J Kempf
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ABSTRACT: 4,4-Dialkyl-1-hydroxy-3-oxo-3.4-dihydronaphthalene-3-yl benzothiadiazine derivatives were synthesized and evaluated as inhibitors of genotypes 1a and 1b HCV NS5B polymerase. A number of these compounds exhibited potent activity against genotypes 1a and 1b HCV polymerase in both enzymatic and cell culture activities. A representative compound also showed favorable pharmacokinetics in the rat.
Bioorganic & medicinal chemistry letters 08/2008; 18(14):3887-90. · 2.65 Impact Factor
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ABSTRACT: BILN 2061 is a macrocyclic tripeptide inhibitor of hepatitis C virus NS3-4A protease that has shown efficacy in the clinic for treating patients infected with HCV. We have synthesized a P3 aza-peptide analog of a potent macrocyclic tripeptide inhibitor closely related to BILN 2061. This aza-derivative was found to be >2 orders of magnitude less active than the parent macrocycle in both isolated enzyme (HCV NS3-4A) and HCV subgenomic replicon assays. NMR studies of P3 aza-peptides revealed these compounds adopt a beta-turn conformation stabilized by an intramolecular H-bonding interaction. Molecular models of these structures indicate a D-like configuration of the P3 aza-residue. Thus, the configurationally undefined nature at P3 in the aza-peptide allows the compound to adopt an H-bond stabilized conformation that is substantially different from that necessary for tight binding to the active site of HCV NS3 protease.
Bioorganic & medicinal chemistry letters 05/2008; 18(8):2745-50. · 2.65 Impact Factor
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Pamela L Donner,
Qinghua Xie,
John K Pratt,
Clarence J Maring,
Warren Kati,
Wen Jiang,
Yaya Liu,
Gennadiy Koev,
Sherie Masse,
Debra Montgomery,
Akhter Molla, Dale J Kempf
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ABSTRACT: In our program to discover non-nucleoside, small molecule inhibitors of genotype 1 HCV polymerase, we investigated a series of promising analogs based on a benzothiadiazine screening hit that contains an ABCD ring system. After demonstrating that a methylsulfonylamino D-ring substituent increased the enzyme potency into the low nanomolar range, we explored a minimum core required for activity by truncating to a three-ring system. Described herein are the syntheses and structure-activity relationship of a set of inhibitors lacking the A-ring of an ABCD ring system. We observed that small aromatic rings and alkenyl groups appended to the 5-position of the B-ring were optimal, resulting in inhibitors with low nanomolar potencies.
Bioorganic & medicinal chemistry letters 05/2008; 18(8):2735-8. · 2.65 Impact Factor
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ABSTRACT: A-790742 is a potent human immunodeficiency virus type 1 (HIV-1) protease inhibitor, with 50% effective concentrations ranging from 2 to 7 nM against wild-type HIV-1. The activity of this compound is lowered by approximately sevenfold in the presence of 50% human serum. A-790742 maintained potent antiviral activity against lopinavir-resistant variants generated in vitro as well as against a panel of molecular clones containing proteases derived from HIV-1 patient isolates with multiple protease mutations. During in vitro selection, A-790742 selected two primary mutations (V82L and I84V) along with L23I, L33F, K45I, A71V/A, and V77I in the pNL4-3 background and two other mutations (A71V and V82G) accompanied by M46I and L63P in the HIV-1 RF background. HIV-1 pNL4-3 clones with a single V82L or I84V mutation were phenotypically resistant to A-790742 and ritonavir. Taking these results together, A-790742 displays a favorable anti-HIV-1 profile against both the wild type and a large number of mutants resistant to other protease inhibitors. The selection of the uncommon V82L and V82G mutations in protease by A-790742 suggests the potential for an advantageous resistance profile with this protease inhibitor.
Antimicrobial Agents and Chemotherapy 05/2008; 52(4):1337-44. · 4.84 Impact Factor
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ABSTRACT: The synthesis of several pyrrolidine inhibitor analogs is described that possess nanomolar in vitro potencies against the neuraminidase enzymes expressed by the B/Memphis/3/89 and A/N1/PR/8/34 influenza strains.
Bioorganic & medicinal chemistry letters 04/2008; 18(5):1692-5. · 2.65 Impact Factor
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ABSTRACT: Drug-drug interactions involving induction of cytochrome P450 enzymes (P450s) can lead to loss of drug efficacy. Certain drugs, particularly those used to treat mycobacterial and human immunodeficiency virus (HIV) infections, are especially prone to induce P450s. During studies to examine drug-interaction potential of compounds in cultured human hepatocytes, exposure with (S)-1-[(1S,3S,4S)-4-[(S)-2-(3-benzyl-2-oxo-imidazolidin-1-yl)-3,3-dimethyl-butyrylamino]-3-hydroxy-5-phenyl-1-(4-pyridin-2-yl-benzyl)-pentylcarbamoyl]-2,2-dimethyl-propyl-carbamic acid methyl ester (A-792611), a novel HIV protease inhibitor (PI) previously under investigation for the treatment of HIV infection, resulted in significant down-regulation of constitutive CYP3A4 expression. Furthermore, coadministration of A-792611 was found to attenuate CYP3A4 induction mediated by known inducers rifampin and efavirenz. A-792611 also attenuated the rifampin and ritonavir-mediated activation of the human pregnane X receptor (PXR) in luciferase reporter assays. Microarray analysis on cultured human hepatocytes revealed that A-792611 treatment down-regulated the expression of PXR target genes CYP3A4, CYP2B6, CYP2C8, and CYP2C9, whereas there was a lack of inductive effect observed in treated rat hepatocytes. A-792611 did not interact with other ligand-activated nuclear receptors that regulate P450 expression such as constitutive androstane receptor, farnesoid X receptor, vitamin D receptor, and peroxisome proliferator-activated receptor alpha. These data suggest that A-792611 is a functional and effective human PXR inhibitor. Among the class of HIV-PIs, which are typically PXR activators, A-792611 seems to have a unique property for PXR antagonism and could be a useful tool for studying nuclear receptor pathway regulation.
Drug metabolism and disposition: the biological fate of chemicals 04/2008; 36(3):500-7. · 3.74 Impact Factor
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ABSTRACT: Residual viremia can be detected in most HIV-1-infected patients on antiretroviral therapy despite suppression of plasma RNA to <50 copies per ml, but the source and duration of this viremia is currently unknown. Therefore, we analyzed longitudinal plasma samples from 40 patients enrolled in the Abbott M97-720 trial at baseline (pretherapy) and weeks 60 to 384 by using an HIV-1 RNA assay with single-copy sensitivity. All patients were on therapy (lopinavir/ritonavir, stavudine, and lamivudine) with plasma HIV RNA <50 copies per ml by week 96 of the study and thereafter. Single-copy assay results revealed that 77% of the patient samples had detectable low-level viremia (>/=1 copy per ml), and all patients had at least one sample with detectable viremia. A nonlinear mixed effects model revealed a biphasic decline in plasma RNA levels occurring over weeks 60 to 384: an initial phase of decay with a half-life of 39 weeks and a subsequent phase with no perceptible decay. The level of pretherapy viremia extrapolated for each phase of decay was significantly correlated with total baseline viremia for each patient (R(2) = 0.27, P = 0.001 and R(2) = 0.19, P < 0.005, respectively), supporting a biological link between the extent of overall baseline viral infection and the infection of long-lived reservoirs. These data suggest that low-level persistent viremia appears to arise from at least two cell compartments, one in which viral production decays over time and a second in which viral production remains stable for at least 7 years.
Proceedings of the National Academy of Sciences 04/2008; 105(10):3879-84. · 9.68 Impact Factor
