A QM/MM study of the binding of RAPTA ligands to cathepsin B (Q62112721)

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5 February 2020

title

A QM/MM study of the binding of RAPTA ligands to cathepsin B (English)

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5 February 2020

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1

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5 February 2020

Samuel Genheden

2

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5 February 2020

Ulf Ryde

3

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5 February 2020

author name string

Antonella Ciancetta

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Samuel Genheden

2

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Ulf Ryde

3

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publication date

24 June 2011

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21701919%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computer - Aided Molecular Design

5 February 2020

published in

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5 February 2020

volume

25

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issue

8

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5 February 2020

page(s)

729-742

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From bench to bedside--preclinical and early clinical development of the anticancer agent indazolium trans-[tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019 or FFC14A).

5 February 2020

cites work

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12 December 2020

Rationalization of the inhibition activity of structurally related organometallic compounds against the drug target cathepsin B by DFT.

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12 December 2020

On the Convergence of QM/MM Energies

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Exploring metallodrug-protein interactions by mass spectrometry: comparisons between platinum coordination complexes and an organometallic ruthenium compound.

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

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Emerging protein targets for anticancer metallodrugs: inhibition of thioredoxin reductase and cathepsin B by antitumor ruthenium(II)-arene compounds

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Modulation of the metastatic progression of breast cancer with an organometallic ruthenium compound.

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QM/MM approaches in medicinal chemistry research

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A categorization of metal anticancer compounds based on their mode of action

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In vitro and in vivo evaluation of ruthenium(II)-arene PTA complexes

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The role of quantum mechanics in structure-based drug design

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Rank-ordering protein-ligand binding affinity by a quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area model

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Hydrolysis study of the bifunctional antitumour compound RAPTA-C, [Ru(η6-p-cymene)Cl2(pta)]

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Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy.

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A Phase I and pharmacological study with imidazolium-trans-DMSO-imidazole-tetrachlororuthenate, a novel ruthenium anticancer agent.

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Climbing the Density Functional Ladder: Nonempirical Meta–Generalized Gradient Approximation Designed for Molecules and Solids

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A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands

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Estimates of ligand-binding affinities supported by quantum mechanical methods.

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Gold compounds as anticancer agents: chemistry, cellular pharmacology, and preclinical studies

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Organometallic chemistry, biology and medicine: ruthenium arene anticancer complexes

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Exploring the binding of inhibitors derived from tetrabromobenzimidazole to the CK2 protein using a QM/MM-PB/SA approach.

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Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

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Down-regulation of tumour gelatinase/inhibitor balance and preservation of tumour endothelium by an anti-metastatic ruthenium complex

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Elucidation of the interactions of an anticancer ruthenium complex in clinical trials with biomolecules utilizing capillary electrophoresis hyphenated to inductively coupled plasma-mass spectrometry. Short communication

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Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models

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Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics

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Redox behavior of tumor-inhibiting ruthenium(iii) complexes and effects of physiological reductants on their binding to GMP

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Unraveling the role of proteases in cancer

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12 December 2020

Down-regulation of cathepsin B expression impairs the invasive and tumorigenic potential of human glioblastoma cells

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12 December 2020

Non-platinum chemotherapeutic metallopharmaceuticals

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12 December 2020

QM/MM methods for biomolecular systems

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

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Very fast empirical prediction and rationalization of protein pKa values

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Kinetics and mechanism of the reduction of (ImH)[trans-RuCl4(dmso)(Im)] by ascorbic acid in acidic aqueous solution

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12 December 2020

The coordination of the catalytic zinc in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations

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QM/MM linear response method distinguishes ligand affinities for closely related metalloproteins

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12 December 2020

Influence of chemical stability on the activity of the antimetastasis ruthenium compound NAMI-A.

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12 December 2020

QM/MM-PBSA method to estimate free energies for reactions in proteins.

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12 December 2020

Exploring protein native states and large-scale conformational changes with a modified generalized born model

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12 December 2020

Bioorganometallic chemistry--from teaching paradigms to medicinal applications

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12 December 2020

10.1007/S10822-011-9448-7

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21701919%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/CiancettaGR11

5 February 2020

DBLP publication ID

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DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1004037539

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