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25 results for “HIV-1 protease”
DRM-labeled HIV-1 protease sequence dataset
<p>An HIV-1 protease dataset with labeled DRMs derived from the Stanford HIV Drug Resistance Database<sup>1,2</sup> is provided. It is in <em>fasta</em> format with major protease drug resistance mutations (as defined by Wensing et al.<sup>3</sup>) provided in the sequence name section (following the ">" symbol) as a comma-separated list. The dataset was used in the following paper: "Ahmed A., de Souza D. R., Link R. W., Nonnemacher M. R., Wigdahl B., Dampier W. Design of a SHERLOCK-based low resource screening assay for HIV-1 drug resistance, in preparation, 2021. "</p>
X-ray structures of HIV-1 protease
<p>As of March 1, 2023, there were 233 X-ray structures of HIV-1 protease available in the RCSB PDB database (<a href="https://www.rcsb.org/">https://www.rcsb.org/</a>). Out of these structures, 219 had ligands bound in the active site while 14 did not have any ligands. To prepare the structures for analysis, we removed water, ions, and solvent molecules, extracted the ligands from the receptors, and aligned all the structures. Each HIV-1 protease structure is identified by its PDB ID (<pdbid>.pdb) while the corresponding ligand structures are named as ligs_<pdbdid>.pdb.</p>
dataset for bioRxiv preprint titled 'Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease'
<p>This data supports the Figures in the preprint titled</p> <p><strong>Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease</strong></p> <p><strong>working abstract</strong></p> <p>The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies. It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease, which is a critical dynamic region involved in non-specific polypeptide binding during invasion and infection of the host cell. In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV). We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.</p>
Improved production of HIV-1 subtype C protease from transgenic E coli
<p>The data set belongs to study carried out by Uraisha Ramlucken at Department of Biochemistry, University of KwaZulu-Natal, Durban, South Africa. This study was made possible through financial support from the National Research Foundation.</p>
Datasets for: The HIV-1 viral protease is activated during assembly and budding prior to particle release
<p>HIV-1 encodes a viral protease that is essential for the maturation of infectious viral particles. While protease inhibitors are effective antiretroviral agents, recent studies have shown that prematurely activating – rather than inhibiting – protease function leads to the pyroptotic death of infected cells, with exciting implications for efforts to eradicate viral reservoirs. Despite 40 years of research into the kinetics of protease activation, it remains unclear exactly when protease becomes activated. Recent reports have estimated that protease activation occurs minutes to hours after viral release, suggesting that premature protease activation may be challenging to induce efficiently. Here, combining a powerful FRET-based assay to monitor viral protease activity with sensitive techniques including nanoscale flow cytometry and instant structured illumination microscopy, we demonstrate that the viral protease is activated within cells prior to the release of free virions. Using genetic mutants that lock protease into a 'precursor' conformation, we further show that both the precursor and mature protease have rapid activation kinetics and that the activity of the precursor protease is sufficient for viral fusion with target cells. Our finding that HIV-1 protease is activated within producer cells prior to release of free virions helps resolve a long-standing question of when protease is activated and suggests that only a modest acceleration of protease activation kinetics may be required to induce potent and specific elimination of HIV-infected cells.</p>
Simulation and analysis data set for apo-conformational kinetics and gated ligand binding to HIV-1 protease
<p>The data set provided here accompanies a study described in the manuscript:</p> <p>S. Kashif Sadiq, Abraham Muñiz Chicharro, Patrick Friedrich, Rebecca Wade, A multiscale approach for computing gated ligand binding from molecular dynamics and Brownian dynamics simulations. (2021) Preprint available: https://doi.org/10.1101/2021.06.22.449380</p> <p>This study combines molecular dynamics MD simulations and associated conformational analyses and Markov state models (MSMs) with Brownian dynamics (BD) simulations to compute conformation gated ligand association kinetics to HIV-1 protease.</p> <p>To download the data, go to a directory where you would like to download the files. Then for each of the provided tar files enter the following command:</p> <p>tar xvf $X.tar</p> <p>where $X is the name prefix of the corresponding tar file.</p> <p>The unpacked data set creates a ./data sub-directory which itself contains two further sub-directories: MD and BD. Please see README.txt files within these sub directories for further instructions on the software tools and scripts that have been provided therein for using and reproducing the data set. The MD README.txt is found within: data_MD_MSM_analysis.tar, the BD README.txt is found within: data_BD_examples.tar.</p> <p>Please note, the python Jupyter notebook and associated module for further analysis of the MSM from the pre-defined feature set calculated in the study as well as other analyses can also be found at:</p> <p>https://github.com/kashifsadiq/hiv1pr-msm/</p> <p>MD trajectory files are provided for further analysis but are not required to reproduce the MSM and conformational analyses reported in the study. To facilitate overview, MSM analysis has been stored in several object files. To exactly reproduce the reported MD/MSM analyses, untar only the 1) data_MD_MSM_analysis.tar and 2) data_MD_MSMobj.tar files and work through the python Jupyter notebook.</p> <p> </p>
HIV-1 Infection Study of Once a Day Versus Twice a Day Protease Inhibitor in Antiretroviral Treatment Naive Adults
ClinicalTrials.gov study NCT00450580. IPD Sharing: Not stated. Countries: 9. Publications: 2.
Genetics and HIV-1 Protease Inhibitors
ClinicalTrials.gov study NCT01388543. IPD Sharing: NO. Countries: 1. Publications: 3.
Datasets for: The HIV-1 viral protease is activated during assembly and budding prior to particle release
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Premature Activation of the HIV-1 Protease is influenced by Polymorphisms in the Hinge Region
<p><strong>Abstract: </strong>HIV-1 protease inhibitors are an essential component of antiretroviral therapy. However, drug resistance is a pervasive issue motivating the persistent search for novel therapies. Recent reports found that when protease activates within the host cell cytosol, it facilitates the pyroptotic killing of infected cells. This has led to speculation that promoting protease activation, rather than inhibiting it, could help to eradicate infected cells and potentially cure HIV-1 infection. Here, we used a nanoscale flow cytometry-based assay to characterize protease resistance mutations and polymorphisms. We quantified protease activity, viral concentration, and premature protease activation and confirmed previous findings that major resistance mutations generally destabilize the protease structure. Intriguingly, we found evidence that common polymorphisms in the hinge domain of protease can influence its susceptibility to premature activation. This suggests that viral heterogeneity could pose a considerable challenge for therapeutic strategies aimed at inducing premature protease activation in the future.</p> <p> </p> <p>Attached is the raw .fcs flow virometry data files and western blot images.</p> <p>In addition, the MIFlowCyt-EV information is attached.</p>
The Pharmacokinetics of Double Boosted Protease Inhibitors in Antiretroviral-naive HIV-1 Infected Patients
ClinicalTrials.gov study NCT00400738. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Switching From Protease Inhibitor (PI) to Etravirine in HIV-1 Infected Subjects With Viremia Suppression
ClinicalTrials.gov study NCT01034917. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Dual Boosted Protease Inhibitor Regimens Without Any Additional Antiretroviral Therapy in HIV-1 Infected Patients (ANRS127)
ClinicalTrials.gov study NCT00122603. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Italian Registry of HIV-1 Infected Patients With Drug-RESistant Virus to Reverse Transcriptase Inhibitors, InteGrasE and Viral Protease.
ClinicalTrials.gov study NCT04098315. IPD Sharing: YES. Countries: 1. Publications: 3.
TMC114-C211: Trial of an Investigational Protease Inhibitor TMC114 With Ritonavir ("TMC114/r") in HIV-1 Infected Patients Who Have Never Been Treated With Antiretroviral Medications.
ClinicalTrials.gov study NCT00258557. IPD Sharing: Not stated. Countries: 25. Publications: 2.
Impact of Raltegravir Intensification on HIV-1-infected Subjects With Complete Viral Suppression Under Monotherapy With Protease Inhibitors
ClinicalTrials.gov study NCT01480713. IPD Sharing: Not stated. Countries: 1. Publications: 1.
BLQ Study: A Study of a Protease Inhibitor With Fuzeon (Enfuvirtide) in Treatment-Experienced Patients With HIV-1.
ClinicalTrials.gov study NCT00326963. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Study of Protease Inhibitor Regimen Switch in HIV-1 Infected Patients With Undetectable Viral Load to Prove the Non-inferiority of Once Daily Dose Regimen Versus the Current Twice Daily Regimen to Mai
ClinicalTrials.gov study NCT00849160. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study Switching HIV-1 Infected Patients With an Undetectable Viral Load on a First Protease Inhibitor-Based Regimen to an Efavirenz-Based Regimen
ClinicalTrials.gov study NCT00135382. IPD Sharing: Not stated. Countries: 2. Publications: 0.
A Dose Ranging Study Of GW640385 Boosted With Ritonavir (Rtv) In Comparison To A RTV-Boosted Protease Inhibitor (PI) In HIV-1 Infected PI-Experienced Adults
ClinicalTrials.gov study NCT00242879. IPD Sharing: Not stated. Countries: 11. Publications: 0.
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