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HIV-1 Resistance to the Capsid-Targeting Inhibitor PF74 Results in Altered Dependence on Host Factors Required for Virus Nuclear Entry.
Zhou J, Price AJ, Halambage UD, James LC, Aiken C
(2015) J Virol 89: 9068-79
MeSH Terms: Amino Acid Substitution, Anti-HIV Agents, Binding Sites, CD4-Positive T-Lymphocytes, Capsid, Capsid Proteins, Cell Line, Drug Resistance, Viral, HIV Infections, HIV-1, Host-Pathogen Interactions, Humans, Indoles, Macrophages, Molecular Chaperones, Nuclear Pore Complex Proteins, Phenylalanine, Protein Binding, Protein Conformation, RNA Interference, RNA, Small Interfering, Virus Internalization, Virus Replication, beta Karyopherins, mRNA Cleavage and Polyadenylation Factors
Show Abstract · Added February 4, 2016
UNLABELLED - During HIV-1 infection of cells, the viral capsid plays critical roles in reverse transcription and nuclear entry of the virus. The capsid-targeting small molecule PF74 inhibits HIV-1 at early stages of infection. HIV-1 resistance to PF74 is complex, requiring multiple amino acid substitutions in the viral CA protein. Here we report the identification and analysis of a novel PF74-resistant mutant encoding amino acid changes in both domains of CA, three of which are near the pocket where PF74 binds. Interestingly, the mutant virus retained partial PF74 binding, and its replication was stimulated by the compound. The mutant capsid structure was not significantly perturbed by binding of PF74; rather, the mutations inhibited capsid interactions with CPSF6 and Nup153 and altered HIV-1 dependence on these host factors and on TNPO3. Moreover, the replication of the mutant virus was markedly impaired in activated primary CD4(+) T cells and macrophages. Our results suggest that HIV-1 escapes a capsid-targeting small molecule inhibitor by altering the virus's dependence on host factors normally required for entry into the nucleus. They further imply that clinical resistance to inhibitors targeting the PF74 binding pocket is likely to be strongly limited by functional constraints on HIV-1 evolution.
IMPORTANCE - The HIV-1 capsid plays critical roles in early steps of infection and is an attractive target for therapy. Here we show that selection for resistance to a capsid-targeting small molecule inhibitor can result in viral dependence on the compound. The mutant virus was debilitated in primary T cells and macrophages--cellular targets of infection in vivo. The mutations also altered the virus's dependence on cellular factors that are normally required for HIV-1 entry into the nucleus. This work provides new information regarding mechanisms of HIV-1 resistance that should be useful in efforts to develop clinically useful drugs targeting the HIV-1 capsid.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.
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25 MeSH Terms
Compensatory substitutions in the HIV-1 capsid reduce the fitness cost associated with resistance to a capsid-targeting small-molecule inhibitor.
Shi J, Zhou J, Halambage UD, Shah VB, Burse MJ, Wu H, Blair WS, Butler SL, Aiken C
(2015) J Virol 89: 208-19
MeSH Terms: Amino Acid Substitution, Anti-HIV Agents, Cells, Cultured, Drug Resistance, Viral, HIV Core Protein p24, HIV-1, Humans, Indoles, Macrophages, Mutant Proteins, Mutation, Missense, Phenylalanine, Selection, Genetic, Suppression, Genetic, Virus Replication
Show Abstract · Added February 19, 2015
UNLABELLED - The HIV-1 capsid plays multiple roles in infection and is an emerging therapeutic target. The small-molecule HIV-1 inhibitor PF-3450074 (PF74) blocks HIV-1 at an early postentry stage by binding the viral capsid and interfering with its function. Selection for resistance resulted in accumulation of five amino acid changes in the viral CA protein, which collectively reduced binding of the compound to HIV-1 particles. In the present study, we dissected the individual and combinatorial contributions of each of the five substitutions Q67H, K70R, H87P, T107N, and L111I to PF74 resistance, PF74 binding, and HIV-1 infectivity. Q67H, K70R, and T107N each conferred low-level resistance to PF74 and collectively conferred strong resistance. The substitutions K70R and L111I impaired HIV-1 infectivity, which was partially restored by the other substitutions at positions 67 and 107. PF74 binding to HIV-1 particles was reduced by the Q67H, K70R, and T107N substitutions, consistent with the location of these positions in the inhibitor-binding pocket. Replication of the 5Mut virus was markedly impaired in cultured macrophages, reminiscent of the previously reported N74D CA mutant. 5Mut substitutions also reduced the binding of the host protein CPSF6 to assembled CA complexes in vitro and permitted infection of cells expressing the inhibitory protein CPSF6-358. Our results demonstrate that strong resistance to PF74 requires accumulation of multiple substitutions in CA to inhibit PF74 binding and compensate for fitness impairments associated with some of the sequence changes.
IMPORTANCE - The HIV-1 capsid is an emerging drug target, and several small-molecule compounds have been reported to inhibit HIV-1 infection by targeting the capsid. Here we show that resistance to the capsid-targeting inhibitor PF74 requires multiple amino acid substitutions in the binding pocket of the CA protein. Three changes in CA were necessary to inhibit binding of PF74 while maintaining viral infectivity. Replication of the PF74-resistant HIV-1 mutant was impaired in macrophages, likely owing to altered interactions with host cell factors. Our results suggest that HIV-1 resistance to capsid-targeting inhibitors will be limited by functional constraints on the viral capsid protein. Therefore, this work enhances the attractiveness of the HIV-1 capsid as a therapeutic target.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.
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15 MeSH Terms
Escape from neutralization by the respiratory syncytial virus-specific neutralizing monoclonal antibody palivizumab is driven by changes in on-rate of binding to the fusion protein.
Bates JT, Keefer CJ, Slaughter JC, Kulp DW, Schief WR, Crowe JE
(2014) Virology 454-455: 139-44
MeSH Terms: Antibodies, Monoclonal, Antibodies, Monoclonal, Humanized, Antibodies, Neutralizing, Drug Resistance, Viral, Humans, Kinetics, Mutation, Palivizumab, Protein Binding, Respiratory Syncytial Viruses, Viral Fusion Proteins
Show Abstract · Added February 2, 2015
The role of binding kinetics in determining neutralizing potency for antiviral antibodies is poorly understood. While it is believed that increased steady-state affinity correlates positively with increased virus-neutralizing activity, the relationship between association or dissociation rate and neutralization potency is unclear. We investigated the effect of naturally-occurring antibody resistance mutations in the RSV F protein on the kinetics of binding to palivizumab. Escape from palivizumab-mediated neutralization of RSV occurred with reduced association rate (Kon) for binding to RSV F protein, while alteration of dissociation rate (Koff) did not significantly affect neutralizing activity. Interestingly, linkage of reduced Kon with reduced potency mirrored the effect of increased Kon found in a high-affinity enhanced potency palivizumab variant (motavizumab). These data suggest that association rate is the dominant factor driving neutralization potency for antibodies to RSV F protein antigenic site A and determines the potency of antibody somatic variants or efficiency of escape of viral glycoprotein variants.
Copyright © 2014 Elsevier Inc. All rights reserved.
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11 MeSH Terms
The HIV Epidemic: High-Income Countries.
Vermund SH, Leigh-Brown AJ
(2012) Cold Spring Harb Perspect Med 2: a007195
MeSH Terms: Alcohol Drinking, Developed Countries, Drug Resistance, Viral, Epidemics, Female, HIV Infections, Heterosexuality, Homosexuality, Male, Humans, Income, Infectious Disease Transmission, Vertical, Male, Molecular Epidemiology, Needle Sharing, Risk Factors, Substance Abuse, Intravenous, Transfusion Reaction, Unsafe Sex
Show Abstract · Added March 5, 2014
The HIV epidemic in higher-income nations is driven by receptive anal intercourse, injection drug use through needle/syringe sharing, and, less efficiently, vaginal intercourse. Alcohol and noninjecting drug use increase sexual HIV vulnerability. Appropriate diagnostic screening has nearly eliminated blood/blood product-related transmissions and, with antiretroviral therapy, has reduced mother-to-child transmission radically. Affected subgroups have changed over time (e.g., increasing numbers of Black and minority ethnic men who have sex with men). Molecular phylogenetic approaches have established historical links between HIV strains from central Africa to those in the United States and thence to Europe. However, Europe did not just receive virus from the United States, as it was also imported from Africa directly. Initial introductions led to epidemics in different risk groups in Western Europe distinguished by viral clades/sequences, and likewise, more recent explosive epidemics linked to injection drug use in Eastern Europe are associated with specific strains. Recent developments in phylodynamic approaches have made it possible to obtain estimates of sequence evolution rates and network parameters for epidemics.
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18 MeSH Terms
Use of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in ART-naïve ACTG clinical trials participants.
Grady BJ, Torstenson ES, McLaren PJ, DE Bakker PI, Haas DW, Robbins GK, Gulick RM, Haubrich R, Ribaudo H, Ritchie MD
(2011) Pac Symp Biocomput : 253-64
MeSH Terms: ATP Binding Cassette Transporter, Subfamily B, Member 2, ATP-Binding Cassette Transporters, Alkynes, Anti-HIV Agents, Benzoxazines, Computational Biology, Cyclopropanes, Double-Blind Method, Drug Resistance, Viral, Epistasis, Genetic, Genome-Wide Association Study, HIV Infections, HIV-1, Humans, Polymorphism, Single Nucleotide, Potassium Channels, Inwardly Rectifying, Receptors, Drug, Risk Factors, Software, Sulfonylurea Receptors, Treatment Failure
Show Abstract · Added March 13, 2015
Personalized medicine is a high priority for the future of health care. The idea of tailoring an individual's wellness plan to their unique genetic code is one which we hope to realize through the use of pharmacogenomics. There have been examples of tremendous success in pharmacogenomic associations however there are many such examples in which only a small proportion of trait variance has been explained by the genetic variation. Although the increased use of GWAS could help explain more of this variation, it is likely that a significant proportion of the genetic architecture of these pharmacogenomic traits are due to complex genetic effects such as epistasis, also known as gene-gene interactions, as well as gene-drug interactions. In this study, we utilize the Biofilter software package to look for candidate epistasis contributing to risk for virologic failure with efavirenz-containing antiretroviral therapy (ART) regimens in treatment-naïve participants of AIDS Clinical Trials Group (ACTG) randomized clinical trials. A total of 904 individuals from three ACTG trials with data on efavirenz treatment are analyzed after race-stratification into white, black, and Hispanic ethnic groups. Biofilter was run considering 245 candidate ADME (absorption, distribution, metabolism, and excretion) genes and using database knowledge of gene and protein interaction networks to produce approximately 2 million SNP-SNP interaction models within each ethnic group. These models were evaluated within the PLATO software package using pair wise logistic regression models. Although no interaction model remained significant after correction for multiple comparisons, an interaction between SNPs in the TAP1 and ABCC9 genes was one of the top models before correction. The TAP1 protein is responsible for intracellular transport of antigen to MHC class I molecules, while ABCC9 codes for a transporter which is part of the subfamily of ABC transporters associated with multi-drug resistance. This study demonstrates the utility of the Biofilter method to prioritize the search for gene-gene interactions in large-scale genomic datasets, although replication in a larger cohort is required to confirm the validity of this particular TAP1-ABCC9 finding.
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21 MeSH Terms
Use of intravenous zanamivir after development of oseltamivir resistance in a critically Ill immunosuppressed child infected with 2009 pandemic influenza A (H1N1) virus.
Dulek DE, Williams JV, Creech CB, Schulert AK, Frangoul HA, Domm J, Denison MR, Chappell JD
(2010) Clin Infect Dis 50: 1493-6
MeSH Terms: Antiviral Agents, Compassionate Use Trials, Critical Illness, Drug Resistance, Viral, Female, Humans, Immunocompromised Host, Infant, Influenza A Virus, H1N1 Subtype, Influenza, Human, Injections, Intravenous, Oseltamivir, Treatment Outcome, Viral Load, Zanamivir
Show Abstract · Added February 3, 2014
Immunosuppressed patients receiving oseltamivir for 2009 novel H1N1 influenza A infection may develop drug resistance, leading to treatment failure. Intravenous zanamivir was administered on a compassionate-use basis to a profoundly immunosuppressed pediatric patient with severe oseltamivir-resistant novel H1N1 pneumonia. The regimen was well tolerated and was associated with a decrease in viral burden.
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15 MeSH Terms
Tenofovir disoproxil fumarate versus adefovir dipivoxil for chronic hepatitis B.
Marcellin P, Heathcote EJ, Buti M, Gane E, de Man RA, Krastev Z, Germanidis G, Lee SS, Flisiak R, Kaita K, Manns M, Kotzev I, Tchernev K, Buggisch P, Weilert F, Kurdas OO, Shiffman ML, Trinh H, Washington MK, Sorbel J, Anderson J, Snow-Lampart A, Mondou E, Quinn J, Rousseau F
(2008) N Engl J Med 359: 2442-55
MeSH Terms: Adenine, Adolescent, Adult, Aged, Alanine Transaminase, Antiviral Agents, DNA, Viral, Double-Blind Method, Drug Resistance, Viral, Female, Genotype, Hepatitis B Surface Antigens, Hepatitis B e Antigens, Hepatitis B virus, Hepatitis B, Chronic, Humans, Male, Middle Aged, Organophosphonates, Tenofovir, Viral Load
Show Abstract · Added March 5, 2014
BACKGROUND - Tenofovir disoproxil fumarate (DF) is a nucleotide analogue and a potent inhibitor of human immunodeficiency virus type 1 reverse transcriptase and hepatitis B virus (HBV) polymerase.
METHODS - In two double-blind, phase 3 studies, we randomly assigned patients with hepatitis B e antigen (HBeAg)-negative or HBeAg-positive chronic HBV infection to receive tenofovir DF or adefovir dipivoxil (ratio, 2:1) once daily for 48 weeks. The primary efficacy end point was a plasma HBV DNA level of less than 400 copies per milliliter (69 IU per milliliter) and histologic improvement (i.e., a reduction in the Knodell necroinflammation score of 2 or more points without worsening fibrosis) at week 48. Secondary end points included viral suppression (i.e., an HBV DNA level of <400 copies per milliliter), histologic improvement, serologic response, normalization of alanine aminotransferase levels, and development of resistance mutations.
RESULTS - At week 48, in both studies, a significantly higher proportion of patients receiving tenofovir DF than of those receiving adefovir dipivoxil had reached the primary end point (P<0.001). Viral suppression occurred in more HBeAg-negative patients receiving tenofovir DF than patients receiving adefovir dipivoxil (93% vs. 63%, P<0.001) and in more HBeAg-positive patients receiving tenofovir DF than patients receiving adefovir dipivoxil (76% vs. 13%, P<0.001). Significantly more HBeAg-positive patients treated with tenofovir DF than those treated with adefovir dipivoxil had normalized alanine aminotransferase levels (68% vs. 54%, P=0.03) and loss of hepatitis B surface antigen (3% vs. 0%, P=0.02). At week 48, amino acid substitutions within HBV DNA polymerase associated with phenotypic resistance to tenofovir DF or other drugs to treat HBV infection had not developed in any of the patients. Tenofovir DF produced a similar HBV DNA response in patients who had previously received lamivudine and in those who had not. The safety profile was similar for the two treatments in both studies.
CONCLUSIONS - Among patients with chronic HBV infection, tenofovir DF at a daily dose of 300 mg had superior antiviral efficacy with a similar safety profile as compared with adefovir dipivoxil at a daily dose of 10 mg through week 48. (ClinicalTrials.gov numbers, NCT00116805 and NCT00117676.)
2008 Massachusetts Medical Society
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21 MeSH Terms
Detection of nonnucleoside reverse-transcriptase inhibitor-resistant HIV-1 after discontinuation of virologically suppressive antiretroviral therapy.
Hare CB, Mellors J, Krambrink A, Su Z, Skiest D, Margolis DM, Patel SS, Barnas D, Frenkel L, Coombs RW, Aweeka F, Morse GD, Haas DW, Boltz V, Palmer S, Coffin J, Havlir DV
(2008) Clin Infect Dis 47: 421-4
MeSH Terms: Adult, Drug Administration Schedule, Drug Resistance, Viral, Female, HIV Infections, HIV-1, Humans, Male, Mutation, Reverse Transcriptase Inhibitors, Viral Load
Show Abstract · Added March 13, 2015
Using standard and ultrasensitive techniques, we detected nonnucleoside reverse-transcriptase inhibitor-associated resistance mutations in 11 (20%) of 54 subjects who discontinued virologically suppressive nonnucleoside reverse-transcriptase inhibitor-containing antiretroviral therapy. Resistance was detected in 45% and 14% of subjects with a baseline human immunodeficiency virus type 1 RNA level of 51-400 copies/mL and
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11 MeSH Terms
Acyclovir-resistant herpes simplex virus pneumonia post-unrelated stem cell transplantation: a word of caution.
Frangoul H, Wills M, Crossno C, Engel M, Domm J
(2007) Pediatr Transplant 11: 942-4
MeSH Terms: Acyclovir, Adolescent, Antiviral Agents, Child, Drug Resistance, Viral, Fatal Outcome, Female, Follow-Up Studies, Herpes Simplex, Humans, Pneumonia, Viral, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Stem Cell Transplantation
Show Abstract · Added March 27, 2014
HSV causes serious complications in immunocompromised patients, especially SCT recipients. Although ACV is an effective antiviral prophylaxis, the emergence of ACV resistance is a growing problem. The authors describe two cases of fatal ACV-resistant HSV in two pediatric patients following unrelated donor SCT. Despite the in vitro sensitivity of the HSV isolates to foscarnet, both patients failed to respond to foscarnet therapy. Other antiviral therapies should be considered in those patients who fail to show rapid clinical improvement.
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13 MeSH Terms
A randomized study of antiviral medication switch at lower- versus higher-switch thresholds: AIDS Clinical Trials Group Study A5115.
Riddler SA, Jiang H, Tenorio A, Huang H, Kuritzkes DR, Acosta EP, Landay A, Bastow B, Haas DW, Tashima KT, Jain MK, Deeks SG, Bartlett JA
(2007) Antivir Ther 12: 531-41
MeSH Terms: ADP-ribosyl Cyclase 1, Adult, Anti-HIV Agents, CD4 Lymphocyte Count, CD8-Positive T-Lymphocytes, Drug Administration Schedule, Drug Resistance, Viral, Drug Therapy, Combination, Female, HIV Infections, HIV-1, Humans, Male, Pilot Projects, RNA, Viral, Reverse Transcriptase Inhibitors, Treatment Outcome, Viremia
Show Abstract · Added March 13, 2015
BACKGROUND - Clinical stability has been observed with continued antiretroviral therapy (ART) in the setting of partial virological suppression. The optimal time to switch treatment in patients with low but detectable HIV-1 RNA is not known.
METHODS - Subjects on stable ART with HIV-1 RNA 200-10,000 copies/ml were randomized to an immediate treatment switch, or to a delayed switch when HIV-1 RNA increased to > or = 10,000 copies/ml or CD4+ T-cell count decreased by 20%. The primary outcome measures were immune activation (proportion of CD8+ T-cells expressing CD38 at week 48) and evolution of genotypic drug resistance.
RESULTS - The study failed to fully accrue the originally planned 108 subjects. Only 47 subjects were randomized to immediate- or delayed-switch arms. Of the subjects in the delayed-switch arm, 10/23 (43%) met the criteria for ART switch during the study (median follow-up 82 weeks). After 48 weeks of observation, the level of immune activation was comparable in the two arms. New resistance mutations were observed in 3/17 and 8/19 subjects in the immediate- and delayed-switch groups, respectively. The loss of future treatment options, however, was comparable in the delayed- and immediate-switch groups.
CONCLUSIONS - Individuals with partial viral suppression tend to remain immunologically stable, however, the accumulation of drug resistance mutations is an ongoing risk. Delayed switch in ART may be a reasonable short-term strategy for individuals with very limited treatment options.
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18 MeSH Terms