Insights into saquinavir resistance in the G48V HIV-1 protease: quantum calculations and molecular dynamic simulations (Q40317435)

19 September 2017

Insights into saquinavir resistance in the G48V HIV-1 protease: quantum calculations and molecular dynamic simulations (English)

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19 September 2017

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Kitiyaporn Wittayanarakul

1

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19 September 2017

Ornjira Aruksakunwong

2

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19 September 2017

Suwipa Saen-oon

3

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19 September 2017

Wasun Chantratita

4

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19 September 2017

Vudhichai Parasuk

5

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19 September 2017

Pornthep Sompornpisut

6

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19 September 2017

Supot Hannongbua

7

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19 September 2017

language of work or name

English

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publication date

12 November 2004

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19 September 2017

13

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inferred from page(s)

published in

Biophysical Journal

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19 September 2017

88

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19 September 2017

2

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19 September 2017

867-879

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Peptidomimetic inhibitors of HIV protease

19 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

HIV protease inhibition: limited recent progress and advances in understanding current pitfalls

22 September 2017

1 reference

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Treatment of antiretroviral-drug-resistant HIV-1 infection

22 September 2017

1 reference

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New challenges in quantum chemistry: Quests for accurate calculations for large molecular systems

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Follow the protons: a low-barrier hydrogen bond unifies the mechanisms of the aspartic proteases

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance

22 September 2017

1 reference

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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

22 September 2017

1 reference

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Crystal structure of an in vivo HIV-1 protease mutant in complex with saquinavir: Insights into the mechanisms of drug resistance

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

The HIV type 1 protease inhibitor saquinavir can select for multiple mutations that confer increasing resistance

22 September 2017

1 reference

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Inhibitors of HIV-1 protease: a major success of structure-assisted drug design

22 September 2017

1 reference

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SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Structure of a G48H mutant of HIV-1 protease explains how glycine-48 replacements produce mutants resistant to inhibitor drugs

22 September 2017

1 reference

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AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR

22 September 2017

1 reference

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Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Human immunodeficiency virus protease expressed in Escherichia coli exhibits autoprocessing and specific maturation of the gag precursor

22 September 2017

1 reference

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Human immunodeficiency virus 1 protease expressed in Escherichia coli behaves as a dimeric aspartic protease

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Domain communication in the dynamical structure of human immunodeficiency virus 1 protease

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Rational design of peptide-based HIV proteinase inhibitors

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Structure at 2.5-A resolution of chemically synthesized human immunodeficiency virus type 1 protease complexed with a hydroxyethylene-based inhibitor

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Prediction of pH-dependent properties of proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Rational approaches to resistance: using saquinavir

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Kinetic properties of saquinavir-resistant mutants of human immunodeficiency virus type 1 protease and their implications in drug resistance in vivo

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Human immunodeficiency virus. Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Resistance of HIV Type 1 to Proteinase Inhibitor Ro 31-8959

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Structure, dynamics and solvation of HIV-1 protease/saquinavir complex in aqueous solution and their contributions to drug resistance: molecular dynamic simulations

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305161

Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.

20 August 2018

1 reference

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HIVdb: a database of the structures of human immunodeficiency virus protease

20 August 2018

1 reference

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Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site

20 August 2018

1 reference

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Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model

20 August 2018

1 reference

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Solution NMR evidence that the HIV-1 protease catalytic aspartyl groups have different ionization states in the complex formed with the asymmetric drug KNI-272.

20 August 2018

1 reference

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Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics.

20 August 2018

1 reference

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Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase

20 August 2018

1 reference

12 December 2020

Molecular dynamics of HIV-1 protease

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

12 December 2020

On the calculation of pKas in proteins

1 reference

12 December 2020

Relative binding free energies of peptide inhibitors of HIV-1 protease: the influence of the active site protonation state

1 reference

12 December 2020

Ionization states of the catalytic residues in HIV-1 protease

1 reference

12 December 2020

Quantum mechanical calculations on biological systems

1 reference

12 December 2020

10.1529/BIOPHYSJ.104.046110

Identifiers

DOI

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19 September 2017

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19 September 2017

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