scholarly journals The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

2014 ◽  
Vol 10 (8) ◽  
pp. e1003776 ◽  
Author(s):  
Jaclyn K. Mann ◽  
John P. Barton ◽  
Andrew L. Ferguson ◽  
Saleha Omarjee ◽  
Bruce D. Walker ◽  
...  
Keyword(s):  
Fitness Landscape ◽  
In Vitro Testing ◽  
Modeling Approaches ◽  
Model Predictions ◽  
Hiv 1

scholarly journals Modelling and in vitro testing of the HIV-1 Nef fitness landscape

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
John P Barton ◽  
Erasha Rajkoomar ◽  
Jaclyn K Mann ◽  
Dariusz K Murakowski ◽  
Mako Toyoda ◽  
...  
Keyword(s):  
Clinical Data ◽  
Fitness Landscape ◽  
Effective Vaccine ◽  
In Vitro Testing ◽  
Multifunctional Protein ◽  
Model Predictions ◽  
The Cost ◽  
Hiv 1

Abstract An effective vaccine is urgently required to curb the HIV-1 epidemic. We have previously described an approach to model the fitness landscape of several HIV-1 proteins, and have validated the results against experimental and clinical data. The fitness landscape may be used to identify mutation patterns harmful to virus viability, and consequently inform the design of immunogens that can target such regions for immunological control. Here we apply such an analysis and complementary experiments to HIV-1 Nef, a multifunctional protein which plays a key role in HIV-1 pathogenesis. We measured Nef-driven replication capacities as well as Nef-mediated CD4 and HLA-I down-modulation capacities of thirty-two different Nef mutants, and tested model predictions against these results. Furthermore, we evaluated the models using 448 patient-derived Nef sequences for which several Nef activities were previously measured. Model predictions correlated significantly with Nef-driven replication and CD4 down-modulation capacities, but not HLA-I down-modulation capacities, of the various Nef mutants. Similarly, in our analysis of patient-derived Nef sequences, CD4 down-modulation capacity correlated the most significantly with model predictions, suggesting that of the tested Nef functions, this is the most important in vivo. Overall, our results highlight how the fitness landscape inferred from patient-derived sequences captures, at least in part, the in vivo functional effects of mutations to Nef. However, the correlation between predictions of the fitness landscape and measured parameters of Nef function is not as accurate as the correlation observed in past studies for other proteins. This may be because of the additional complexity associated with inferring the cost of mutations on the diverse functions of Nef.

scholarly journals Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease

2019 ◽  
Author(s):  
Tian-hao Zhang ◽  
Lei Dai ◽  
John P. Barton ◽  
Yushen Du ◽  
Yuxiang Tan ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Fitness Landscape ◽  
Sequence Data ◽  
Fitness Cost ◽  
Resistance Mutations ◽  
Human T Cells ◽  
Multiple Cycles ◽  
Replication Fitness ◽  
Hiv 1

AbstractDrug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance.

Urokinase Evaluated with the Experimental Radioactive Embolus

1967 ◽  
Vol 17 (03/04) ◽  
pp. 405-411
Author(s):  
M Hume
Keyword(s):  
Animal Experiment ◽  
Blood Clot ◽  
In Vitro Testing ◽  
Effective Agent

SummaryUrokinase and urokinase-activated plasmin have been given to the dog and rabbit. A thrombolytic state has been induced. Purified urokinase has induced lysis of the experimental radioactive blood clot embolus in the circulation. Demonstration of effectiveness in this animal experiment is hampered by inhibition of the agents in the circulation to a degree much greater than was noted in previous experiments with streptokinase. In vitro testing indicates that under proper conditions urokinase will be an effective agent in the treatment of human thromboembolism.

DEVELOPMENT OF APPROACHES FOR DETECTION OF GENOME-INTEGRATED PROVIRAL DNA OF THE HUMAN IMMUNODEFICIENCY VIRUS (HIV-1) IN ULTRA LOW CONCENTRATIONS USING THE CRISPR/CAS SYSTEM

2020 ◽  
Author(s):  
M.A. Tyumentseva ◽  
◽  
A.I. Tyumentsev ◽  
V.G. Akimkin ◽  
◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Health Monitoring ◽  
Biological Samples ◽  
Proviral Dna ◽  
Guide Rnas ◽  
Ribonucleoprotein Complexes ◽  
Low Concentrations ◽  
Immunodeficiency Virus ◽  
Hiv 1

For the effective functioning of supervisory and health monitoring services, it is necessary to introduce modern molecular technologies into their practice. Therefore, the task of developing new effective methods for detecting pathogen, for example HIV, based on CRISPR/CAS genome editing systems, remains urgent. In the present work, guide RNAs and specific oligonucleotides were developed for preliminary amplification of highly conserved regions of the HIV-1 genome. The developed guide RNAs make it possible to detect single copies of HIV-1 proviral DNA in vitro as part of CRISPR/CAS ribonucleoprotein complexes in biological samples after preliminary amplification.

In vitro binding activity between HCK SH3 domain and HIV-1 Nef protein

2011 ◽  
Vol 31 (3) ◽  
pp. 262-265
Author(s):  
Xiao-lin QIN ◽  
Chao-qi LIU ◽  
Dong-ming REN ◽  
Yong-qin ZHOU
Keyword(s):  
Sh3 Domain ◽  
Binding Activity ◽  
Hiv 1

Anti HIV-1 Agents 7. Discovery of 1-Hydroxy-4-chloro-9,10-anthraquinone Derivatives as New HIV-1 Inhibitors in Vitro

2011 ◽  
Vol 8 (7) ◽  
pp. 602-605
Author(s):  
Ning Huang ◽  
Qin Wang ◽  
Liu-Meng Yang ◽  
Hui Xu ◽  
Yong-Tang Zheng
Keyword(s):  
Anthraquinone Derivatives ◽  
Anti Hiv ◽  
Hiv 1

scholarly journals 1592U89, a novel carbocyclic nucleoside analog with potent, selective anti-human immunodeficiency virus activity.

1997 ◽  
Vol 41 (5) ◽  
pp. 1082-1093 ◽  
Author(s):  
S M Daluge ◽  
S S Good ◽  
M B Faletto ◽  
W H Miller ◽  
M H St Clair ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Oral Bioavailability ◽  
Human Peripheral Blood ◽  
Cross Resistance ◽  
Immunodeficiency Virus ◽  
Carbocyclic Nucleoside ◽  
Hiv 1 ◽  
In Cells

1592U89, (-)-(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]-2-cyclo pentene-1-methanol, is a carbocyclic nucleoside with a unique biological profile giving potent, selective anti-human immunodeficiency virus (HIV) activity. 1592U89 was selected after evaluation of a wide variety of analogs containing a cyclopentene substitution for the 2'-deoxyriboside of natural deoxynucleosides, optimizing in vitro anti-HIV potency, oral bioavailability, and central nervous system (CNS) penetration. 1592U89 was equivalent in potency to 3'-azido-3'-deoxythymidine (AZT) in human peripheral blood lymphocyte (PBL) cultures against clinical isolates of HIV type 1 (HIV-1) from antiretroviral drug-naive patients (average 50% inhibitory concentration [IC50], 0.26 microM for 1592U89 and 0.23 microM for AZT). 1592U89 showed minimal cross-resistance (approximately twofold) with AZT and other approved HIV reverse transcriptase (RT) inhibitors. 1592U89 was synergistic in combination with AZT, the nonnucleoside RT inhibitor nevirapine, and the protease inhibitor 141W94 in MT4 cells against HIV-1 (IIIB). 1592U89 was anabolized intracellularly to its 5'-monophosphate in CD4+ CEM cells and in PBLs, but the di- and triphosphates of 1592U89 were not detected. The only triphosphate found in cells incubated with 1592U89 was that of the guanine analog (-)-carbovir (CBV). However, the in vivo pharmacokinetic, distribution, and toxicological profiles of 1592U89 were distinct from and improved over those of CBV, probably because CBV itself was not appreciably formed from 1592U89 in cells or animals (<2%). The 5'-triphosphate of CBV was a potent, selective inhibitor of HIV-1 RT, with Ki values for DNA polymerases (alpha, beta, gamma, and epsilon which were 90-, 2,900-, 1,200-, and 1,900-fold greater, respectively, than for RT (Ki, 21 nM). 1592U89 was relatively nontoxic to human bone marrow progenitors erythroid burst-forming unit and granulocyte-macrophage CFU (IC50s, 110 microM) and human leukemic and liver tumor cell lines. 1592U89 had excellent oral bioavailability (105% in the rat) and penetrated the CNS (rat brain and monkey cerebrospinal fluid) as well as AZT. Having demonstrated an excellent preclinical profile, 1592U89 has progressed to clinical evaluation in HIV-infected patients.

In vitro synthesis of enzymatically active HIV-1 protease for rapid phenotypic resistance profiling

2005 ◽  
Vol 32 (4) ◽  
pp. 294-299 ◽  
Author(s):  
Dieter Hoffmann ◽  
Bernd Buchberger ◽  
Cordula Nemetz
Keyword(s):  
In Vitro Synthesis ◽  
Phenotypic Resistance ◽  
Hiv 1
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