(Q85037178)

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Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations

scientific article published on 04 October 2011

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scholarly article

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21969102%20AND%20SRC:MED&resulttype=core&format=json

14 February 2020

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21969102%20AND%20SRC:MED&resulttype=core&format=json

14 February 2020

3

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14 February 2020

Thomas Mavromoustakos

5

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14 February 2020

author name string

Haralambos Tzoupis

1

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14 February 2020

Georgios Leonis

2

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14 February 2020

Varnavas Mouchlis

4

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14 February 2020

Manthos G Papadopoulos

6

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14 February 2020

publication date

4 October 2011

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Europe PubMed Central

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14 February 2020

Journal of Computer - Aided Molecular Design

1 reference

Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21969102%20AND%20SRC:MED&resulttype=core&format=json

14 February 2020

25

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Europe PubMed Central

PubMed publication ID

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14 February 2020

10

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Europe PubMed Central

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14 February 2020

959-976

1 reference

Europe PubMed Central

PubMed publication ID

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14 February 2020

https://scigraph.springernature.com/pub.10.1007/s10822-011-9475-4

0 references

HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ADMET in silico modelling: towards prediction paradise?

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Linear and nonlinear optical properties of [60]fullerene derivatives.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparison of multiple Amber force fields and development of improved protein backbone parameters

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Optimizing the binding of fullerene inhibitors of the HIV-1 protease through predicted increases in hydrophobic desolvation

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Overcoming drug resistance in HIV-1 chemotherapy: the binding thermodynamics of Amprenavir and TMC-126 to wild-type and drug-resistant mutants of the HIV-1 protease

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Development and testing of a general amber force field

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Development and biological evaluation of C(60) fulleropyrrolidine-thalidomide dyad as a new anti-inflammation agent

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Fifteen years of HIV Protease Inhibitors: raising the barrier to resistance

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A Bioactive Fullerene Peptide

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Linear and nonlinear optical properties of triphenylamine-functionalized C60: insights from theory and experiment.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluating the potency of HIV-1 protease drugs to combat resistance

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Buckminsterfullerene's (C60) octanol-water partition coefficient (Kow) and aqueous solubility

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Correlating partitioning and caco-2 cell permeability of structurally diverse small molecular weight compounds

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Preparation of C60-based active esters and coupling of C60 moiety to amines or alcohols

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Anti-HIV properties of cationic fullerene derivatives

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleoside reverse transcriptase inhibitors and HIV mutagenesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Designing libraries with CNS activity

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Relating sequence evolution of HIV1-protease to its underlying molecular mechanics

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Constant pH molecular dynamics in generalized Born implicit solvent

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Amber biomolecular simulation programs

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Targeting SVCT for enhanced drug absorption: synthesis and in vitro evaluation of a novel vitamin C conjugated prodrug of saquinavir.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Strategy in drug design. Cluster anlysis as an aid in the selection of substituents

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

3D QSAR CoMFA/CoMSIA, molecular docking and molecular dynamics studies of fullerene-based HIV-1 PR inhibitors.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Insights into the molecular mechanism of hERG1 channel activation and blockade by drugs.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Synthesis and evaluation of 3'-azido-2',3'-dideoxypurine nucleosides as inhibitors of human immunodeficiency virus

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Polymer-fullerene composite solar cells

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Chlorofullerene C60Cl6: a precursor for straightforward preparation of highly water-soluble polycarboxylic fullerene derivatives active against HIV.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Human immunodeficiency virus-1 protease. 1. Initial velocity studies and kinetic characterization of reaction intermediates by 18O isotope exchange

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

In silico drug screening approach for the design of magic bullets: a successful example with anti-HIV fullerene derivatized amino acids

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural analysis of lead fullerene-based inhibitor bound to human immunodeficiency virus type 1 protease in solution from molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

MDCK (Madin-Darby canine kidney) cells: A tool for membrane permeability screening

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Blockade of HERG channels by HIV protease inhibitors.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Unique Thermodynamic Response of Tipranavir to Human Immunodeficiency Virus Type 1 Protease Drug Resistance Mutations

1 reference

https://pubmed.ncbi.nlm.nih.gov/21969102

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1007/S10822-011-9475-4

1 reference

Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21969102%20AND%20SRC:MED&resulttype=core&format=json

14 February 2020

DBLP publication ID

journals/jcamd/TzoupisLDMMP11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21969102%20AND%20SRC:MED&resulttype=core&format=json

14 February 2020

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