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Selection of HIV-1 for Resistance to Fifth Generation Protease Inhibitors Reveals Two Independent Pathways to High-Level Resistance

https://doi.org/10.1101/837120
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Combining mutations in HIV‐1 protease to understand mechanisms of resistance
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Use of a Fluorescence Plate Reader for Measuring Kinetic Parameters with Inner Filter Effect Correction
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Large scale purification and refolding of HIV-1 protease fromEscherichia coli inclusion bodies
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Effective blocking of HIV‐1 proteinase activity by characteristic inhibitors of aspartic proteinases
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Fifteen years of HIV Protease Inhibitors: raising the barrier to resistance
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Combating Susceptibility to Drug Resistance
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Substrate Envelope-Designed Potent HIV-1 Protease Inhibitors to Avoid Drug Resistance
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Dissecting the Microscopic Steps of the Cyclophilin A Enzymatic Cycle on the Biological HIV-1 Capsid Substrate by NMR
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Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope
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HIV-1 Protease Uses Bi-Specific S2/S2′ Subsites to Optimize Cleavage of Two Classes of Target Sites
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Hydrophobic Sliding: A Possible Mechanism for Drug Resistance in Human Immunodeficiency Virus Type 1 Protease
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Co-evolution of nelfinavir-resistant HIV-1 protease and the p1–p6 substrate
inferredcites →https://doi.org/10.1016/s0021-9258(19)50290-3openalex-snapshot
Regulation of autoproteolysis of the HIV-1 and HIV-2 proteases with engineered amino acid substitutions
inferredcites →https://doi.org/10.1016/s0969-2126(02)00720-7openalex-snapshot
Substrate Shape Determines Specificity of Recognition for HIV-1 Protease
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Protease inhibitor monotherapy for long-term management of HIV infection: a randomised, controlled, open-label, non-inferiority trial
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Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond
inferredcites →https://doi.org/10.1021/acs.jctc.0c01244openalex-snapshot
Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning
inferredcites →https://doi.org/10.1021/acs.jctc.6b01262openalex-snapshot
Interdependence of Inhibitor Recognition in HIV-1 Protease
inferredcites →https://doi.org/10.1021/acs.jctc.7b00601openalex-snapshot
Elucidating the Interdependence of Drug Resistance from Combinations of Mutations
inferredcites →https://doi.org/10.1021/acschembio.9b00370openalex-snapshot
Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance
inferredcites →https://doi.org/10.1021/acsinfecdis.8b00336openalex-snapshot
Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease
inferredcites →https://doi.org/10.1021/acsmedchemlett.0c00043openalex-snapshot
Novel HIV-1 Protease Inhibitors with Morpholine as the P2 Ligand to Enhance Activity against DRV-Resistant Variants
inferredcites →https://doi.org/10.1021/bi027019uopenalex-snapshot
A Major Role for a Set of Non-Active Site Mutations in the Development of HIV-1 Protease Drug Resistance
inferredcites →https://doi.org/10.1021/bi049459mopenalex-snapshot
Comparing the Accumulation of Active- and Nonactive-Site Mutations in the HIV-1 Protease
inferredcites →https://doi.org/10.1021/ct200668aopenalex-snapshot
HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern
inferredcites →https://doi.org/10.1021/ja2095766openalex-snapshot
Hydrophobic Core Flexibility Modulates Enzyme Activity in HIV-1 Protease
inferredcites →https://doi.org/10.1021/ja504096mopenalex-snapshot
Drug Resistance Conferred by Mutations Outside the Active Site through Alterations in the Dynamic and Structural Ensemble of HIV-1 Protease
inferredcites →https://doi.org/10.1038/329654a0openalex-snapshot
Inhibition of retroviral protease activity by an aspartyl proteinase inhibitor
inferredcites →https://doi.org/10.1038/nature12162openalex-snapshot
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
inferredcites →https://doi.org/10.1038/srep11286openalex-snapshot
Fluorogenic Assay for Inhibitors of HIV-1 Protease with Sub-picomolar Affinity
inferredcites →https://doi.org/10.1056/nejm199709113371102openalex-snapshot
Treatment with Indinavir, Zidovudine, and Lamivudine in Adults with Human Immunodeficiency Virus Infection and Prior Antiretroviral Therapy
inferredcites →https://doi.org/10.1073/pnas.1414063111openalex-snapshot
Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease
inferredcites →https://doi.org/10.1073/pnas.1419945112openalex-snapshot
Structural basis of HIV-1 capsid recognition by PF74 and CPSF6
inferredcites →https://doi.org/10.1073/pnas.85.18.6612openalex-snapshot
Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A.
inferredcites →https://doi.org/10.1074/jbc.271.52.33231openalex-snapshot
Human Immunodeficiency Virus
inferredcites →https://doi.org/10.1074/jbc.m112.339374openalex-snapshot
Context Surrounding Processing Sites Is Crucial in Determining Cleavage Rate of a Subset of Processing Sites in HIV-1 Gag and Gag-Pro-Pol Polyprotein Precursors by Viral Protease
inferredcites →https://doi.org/10.1080/23744235.2019.1694696openalex-snapshot
Lack of impact of protease inhibitor resistance-associated mutations on the outcome of HIV-1-infected patients switching to darunavir-based dual therapy
inferredcites →https://doi.org/10.1080/25787489.2020.1734752openalex-snapshot
96-week results of a dual therapy with darunavir/ritonavir plus rilpivirine once a day vs triple therapy in patients with suppressed viraemia: virological success and non-HIV related morbidity evaluation
inferredcites →https://doi.org/10.1089/aid.2007.0173openalex-snapshot
Resistance Profile of Darunavir: Combined 24-Week Results from the POWER Trials
inferredcites →https://doi.org/10.1089/aid.2008.0216openalex-snapshot
Darunavir Concentrations in Cerebrospinal Fluid and Blood in HIV-1–Infected Individuals
inferredcites →https://doi.org/10.1093/jac/dkn544openalex-snapshot
Mutations associated with virological response to darunavir/ritonavir in HIV-1-infected protease inhibitor-experienced patients
inferredcites →https://doi.org/10.1093/jac/dkr504openalex-snapshot
Long-term efficacy of darunavir/ritonavir monotherapy in patients with HIV-1 viral suppression: week 96 results from the MONOI ANRS 136 study
inferredcites →https://doi.org/10.1093/nar/gkg100openalex-snapshot
Human immunodeficiency virus reverse transcriptase and protease sequence database
inferredcites →https://doi.org/10.1097/00002030-199805000-00001openalex-snapshot
The duration of viral suppression during protease inhibitor therapy for HIV-1 infection is predicted by plasma HIV-1 RNA at the nadir
inferredcites →https://doi.org/10.1097/qad.0000000000000778openalex-snapshot
Week 48 efficacy and central nervous system analysis of darunavir/ritonavir monotherapy versus darunavir/ritonavir with two nucleoside analogues
inferredcites →https://doi.org/10.1097/qad.0b013e3282effa87openalex-snapshot
The presence of the Trim5α escape mutation H87Q in the capsid of late stage HIV-1 variants is preceded by a prolonged asymptomatic infection phase
inferredcites →https://doi.org/10.1097/qad.0b013e32833dec20openalex-snapshot
Efficacy of darunavir/ritonavir maintenance monotherapy in patients with HIV-1 viral suppression: a randomized open-label, noninferiority trial, MONOI-ANRS 136
inferredcites →https://doi.org/10.1110/ps.25502openalex-snapshot
Lack of synergy for inhibitors targeting a multi‐drug‐resistant HIV‐1 protease
inferredcites →https://doi.org/10.1111/j.1468-1293.2012.00989.xopenalex-snapshot
The MONET trial: week 144 analysis of the efficacy of darunavir/ritonavir ( DRV/r ) monotherapy versus DRV/r plus two nucleoside reverse transcriptase inhibitors, for patients with viral load < 50 HIV ‐1 RNA copies/ mL at baseline
inferredcites →https://doi.org/10.1126/science.2106161openalex-snapshot
Novel Fluorogenic Substrates for Assaying Retroviral Proteases by Resonance Energy Transfer
inferredcites →https://doi.org/10.1128/aac.00870-06openalex-snapshot
Natural Polymorphisms in the Human Immunodeficiency Virus Type 2 Protease Can Accelerate Time to Development of Resistance to Protease Inhibitors
inferredcites →https://doi.org/10.1128/aac.01228-10openalex-snapshot
Three Residues in HIV-1 Matrix Contribute to Protease Inhibitor Susceptibility and Replication Capacity
inferredcites →https://doi.org/10.1128/aac.05549-11openalex-snapshot
Interplay between Single Resistance-Associated Mutations in the HIV-1 Protease and Viral Infectivity, Protease Activity, and Inhibitor Sensitivity
inferredcites →https://doi.org/10.1128/aac.47.2.759-769.2003openalex-snapshot
Selection of High-Level Resistance to Human Immunodeficiency Virus Type 1 Protease Inhibitors
inferredcites →https://doi.org/10.1128/aac.48.6.2159-2165.2004openalex-snapshot
Mutation D30N Is Not Preferentially Selected by Human Immunodeficiency Virus Type 1 Subtype C in the Development of Resistance to Nelfinavir
inferredcites →https://doi.org/10.1128/aac.49.6.2314-2321.2005openalex-snapshot
TMC114, a Novel Human Immunodeficiency Virus Type 1 Protease Inhibitor Active against Protease Inhibitor-Resistant Viruses, Including a Broad Range of Clinical Isolates
inferredcites →https://doi.org/10.1128/jvi.00003-09openalex-snapshot
Positive Selection Pressure Introduces Secondary Mutations at Gag Cleavage Sites in Human Immunodeficiency Virus Type 1 Harboring Major Protease Resistance Mutations
inferredcites →https://doi.org/10.1128/jvi.00214-14openalex-snapshot
Host and Viral Determinants of Mx2 Antiretroviral Activity
inferredcites →https://doi.org/10.1128/jvi.00266-14openalex-snapshot
HIV-1 Protease-Substrate Coevolution in Nelfinavir Resistance
inferredcites →https://doi.org/10.1128/jvi.00493-12openalex-snapshot
Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein
inferredcites →https://doi.org/10.1128/jvi.00522-15openalex-snapshot
Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations
inferredcites →https://doi.org/10.1128/jvi.00628-09openalex-snapshot
Human Immunodeficiency Virus Type 1 Protease-Correlated Cleavage Site Mutations Enhance Inhibitor Resistance
inferredcites →https://doi.org/10.1128/jvi.00967-10openalex-snapshot
In Vitro Selection of Highly Darunavir-Resistant and Replication-Competent HIV-1 Variants by Using a Mixture of Clinical HIV-1 Isolates Resistant to Multiple Conventional Protease Inhibitors
inferredcites →https://doi.org/10.1128/jvi.01411-14openalex-snapshot
Compensatory Substitutions in the HIV-1 Capsid Reduce the Fitness Cost Associated with Resistance to a Capsid-Targeting Small-Molecule Inhibitor
inferredcites →https://doi.org/10.1128/jvi.03202-15openalex-snapshot
SUN2 Overexpression Deforms Nuclear Shape and Inhibits HIV
inferredcites →https://doi.org/10.1128/jvi.03486-12openalex-snapshot
Structural and Thermodynamic Basis of Amprenavir/Darunavir and Atazanavir Resistance in HIV-1 Protease with Mutations at Residue 50
inferredcites →https://doi.org/10.1128/jvi.70.6.3763-3769.1996openalex-snapshot
Second locus involved in human immunodeficiency virus type 1 resistance to protease inhibitors
inferredcites →https://doi.org/10.1128/jvi.71.9.6662-6670.1997openalex-snapshot
Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites
inferredcites →https://doi.org/10.1128/jvi.72.9.7632-7637.1998openalex-snapshot
Resistance-Associated Loss of Viral Fitness in Human Immunodeficiency Virus Type 1: Phenotypic Analysis of Protease and gag Coevolution in Protease Inhibitor-Treated Patients
inferredcites →https://doi.org/10.1128/jvi.75.16.7230-7243.2001openalex-snapshot
Hydrophobic Amino Acids in the Human Immunodeficiency Virus Type 1 p2 and Nucleocapsid Proteins Can Contribute to the Rescue of Deleted Viral RNA Packaging Signals
inferredcites →https://doi.org/10.1128/jvi.75.2.589-594.2001openalex-snapshot
Human Immunodeficiency Virus Type 1 Protease Cleavage Site Mutations Associated with Protease Inhibitor Cross-Resistance Selected by Indinavir, Ritonavir, and/or Saquinavir
inferredcites →https://doi.org/10.1128/jvi.76.20.10226-10233.2002openalex-snapshot
Replacement of the P1 Amino Acid of Human Immunodeficiency Virus Type 1 Gag Processing Sites Can Inhibit or Enhance the Rate of Cleavage by the Viral Protease
inferredcites →https://doi.org/10.1128/jvi.78.22.12446-12454.2004openalex-snapshot
Structural Basis for Coevolution of a Human Immunodeficiency Virus Type 1 Nucleocapsid-p1 Cleavage Site with a V82A Drug-Resistant Mutation in Viral Protease
inferredcites →https://doi.org/10.1128/mbio.02425-17openalex-snapshot
Mechanism of Darunavir (DRV)’s High Genetic Barrier to HIV-1 Resistance: A Key V32I Substitution in Protease Rarely Occurs, but Once It Occurs, It Predisposes HIV-1 To Develop DRV Resistance
inferredcites →https://doi.org/10.1172/jci67399openalex-snapshot
Multi-step inhibition explains HIV-1 protease inhibitor pharmacodynamics and resistance
inferredcites →https://doi.org/10.1177/0956462419896478openalex-snapshot
Maintenance of virologic suppression and improvement in comorbidities after simplification to raltegravir plus boosted darunavir among treatment-experienced HIV-infected patients
inferredcites →https://doi.org/10.1177/135965350801300214openalex-snapshot
Virological Response to Darunavir/Ritonavir-Based Regimens in Antiretroviral-Experienced Patients (PREDIZISTA Study)
inferredcites →https://doi.org/10.1371/journal.ppat.1000345openalex-snapshot
Gag Mutations Strongly Contribute to HIV-1 Resistance to Protease Inhibitors in Highly Drug-Experienced Patients besides Compensating for Fitness Loss
inferredcites →https://doi.org/10.2147/tcrm.s1709openalex-snapshot
Combating HIV resistance – focus on darunavir
inferredcites →https://doi.org/10.3389/fphar.2019.01225openalex-snapshot
Efficacy and Safety of Raltegravir-Based Dual Therapy in AIDS Patients: A Meta-Analysis of Randomized Controlled Trials
inferredcites →https://doi.org/10.3390/v2112509openalex-snapshot
Molecular Basis for Drug Resistance in HIV-1 Protease
inferredcites →https://doi.org/10.3851/imp1710openalex-snapshot
Analysis of Drug Resistance during HIV RNA Viraemia in the Monet Trial of Darunavir/Ritonavir Monotherapy
inferredcites →https://doi.org/10.3851/imp3330openalex-snapshot
Boosted Darunavir and Dolutegravir Dual Therapy among a Cohort of Highly Treatment-Experienced Individuals

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1021/acs.jctc.0c01244openalex-snapshot
Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning
inferred← citeshttps://doi.org/10.1093/infdis/jiab305openalex-snapshot
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