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Please use this identifier to cite or link to this item: http://dspace.utalca.cl/handle/1950/8761

Title: Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-Based De Novo Design: Study of Binding Mode of Diastereomer Compounds
Authors: Caballero, J.
Alzate-Morales, J.H.
Vergara-Jaque, A.
Keywords: 2 d autocorrelation
in-silico
conformational stability
guanine derivatives
CDK2
inhibitors
drug discovery
COMFA
prediction
onion
Issue Date: Dec-2011
Publisher: AMER CHEMICAL SOC
Citation: JOURNAL OF CHEMICAL INFORMATION AND MODELING Volume: 51 Issue: 11 Pages: 2920-2931 DOI: 10.1021/ci200306w
Abstract: N1 substituted pyrazole derivatives show diverse B-Raf kinase inhibitory activities when different hydroxy-substituted cycloalkyl groups are placed at this position. Docking, molecular dynamics (MD) simulations, and hybrid calculation methods (Quantum Mechanics/Molecular Mechanics (QM/MM)) were performed on the complexes, in order to explain these differences. Docking of the inhibitors showed the same orientation that X-ray crystal structure of the analogous (1E)-5-[1-(4-piperidinyl)-3-(4-pyridinyl)-1H-pyrazol-4-yl]-2,3-dihydro-1H-inden-1-one oxirne. MD simulations of the most active diastereomer compounds containing cis- and trans-3-hydroxycyclohexyl substituents showed stable interactions with residue Ile463 at the entrance of the B-Raf active site. On the other hand, the less active diastereomer compounds containing cis- and trans-2-hydroxycyclopentyl substituents showed interactions with inner residues Asn580 and Ser465. We found that the differences in activity can be explained by considering the dynamic interactions between the inhibitors and their surrounding residues within the B-Raf binding site. We also explained the activity trend by using a testing scoring function derived from more reliable QM/MM calculations. In addition, we search for new inhibitors from a virtual screening carried out by fragment-based de novo design. We generated a set of approximately 200 virtual compounds, which interact with Ile463 and fulfill druglikeness properties according to Lipinski, Veber, and Chose rules.
Description: Caballero, J (Caballero, Julio)1; Alzate-Morales, JH (Alzate-Morales, Jans H.)1; Vergara-Jaque, A (Vergara-Jaque, Ariela)1. Addresses: 1. Univ Talca, Ctr Bioinformat & Simulac Mol, Talca, Chile
URI: http://dspace.utalca.cl/handle/1950/8761
ISSN: 1549-9596
Appears in Collections:Artículos en publicaciones ISI - Universidad de Talca

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