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.
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 oxime. 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 Ghose rules.
Centro de Bioinformática y Simulación Molecular, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile. jcaballero@utalca.cl
Julio
J
Caballero
Jans H
JH
Alzate-Morales
Ariela
A
Vergara-Jaque
D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D015195:Drug Design; D055808:Drug Discovery / Q000379:methods*; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009369:Neoplasms / Q000188:drug therapy / Q000201:enzymology; D011485:Protein Binding; D047428:Protein Kinase Inhibitors / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D048493:Proto-Oncogene Proteins B-raf / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D011720:Pyrazoles / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D021281:Quantitative Structure-Activity Relationship; D011789:Quantum Theory; D012984:Software; D013237:Stereoisomerism; D013329:Structure-Activity Relationship
D000596:Amino Acids; D008024:Ligands; D047428:Protein Kinase Inhibitors; D011720:Pyrazoles; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf