Molecular modeling study of the induced-fit effect on kinase inhibition: the case of fibroblast growth factor receptor 3 (FGFR3).

Tyrosine kinases are a wide family of targets with strong pharmacological relevance. These proteins undergo large-scale conformational motions able to inactivate them. By the end of one of these structural processes, a new cavity is opened allowing the access to a specific type of inhibitors, called type II.

Targeted molecular dynamics (TMD) of the full-length KcsA potassium channel: on the role of the cytoplasmic domain in the opening process.

Some recent papers clearly indicate that the cytoplasmic domain of KcsA plays a role in pH sensing. We have performed, for the first time, a targeted molecular dynamics (TMD) simulation of the opening of full-length KcsA at pH 4 and pH 7, with a special interest for the cytoplasmic domain. Association energy calculations show a stabilization at pH 7 confirming that the protonation of some amino-acids at pH 4 in this domain plays a role in the opening process.

Molecular dynamics simulations of 2-amino-6-arylsulphonylbenzonitriles analogues as HIV inhibitors: interaction modes and binding free energies.

Molecular dynamics (MD) simulations in water environment were carried out on the HIV-1 reverse transcriptase (RT), and its complexes with one representative of each of three series of inhibitors: 2-amino-6-arylsulphonylbenzonitriles and their thio and sulphinyl congeners. Molecular Mechanics Generalized Born Surface Area (MM-GBSA) was used to calculate the binding free energy based on the obtained MD trajectories. Calculated energies are correlated to activity.

Hairy carbon nanotube@nano-Pd heterostructures: design, characterization, and application in Suzuki C-C coupling reaction.

Poly(glycidyl methacrylate), PGMA, was prepared via ATRP in bulk solution, and its epoxy groups were further acid-hydrolyzed in order to obtain a polymer with glycerol moieties (noted POH). The POH chain end C-Br bonds were subjected to a nucleophilic attack by NaN(3), resulting in azide-terminated POH (POH-N(3)). The CNTs were modified by in-situ-generated alkynylated diazonium cations from the para-alkynylated aniline of the formulas H(2)N-C(6)H(4)-C≡C-H, yielding CNT-C(6)H(4)-C≡C-H nanotubes.

Receptor- and ligand-based 3D-QSAR study for a series of non-nucleoside HIV-1 reverse transcriptase inhibitors.

Molecular modeling of a series of HIV reverse transcriptase (RT) non-nucleoside inhibitors (2-amino-6-arylsulfonylbenzonitriles and their thio and sulfinyl congeners) was carried out by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches. Docking simulations were employed to position the inhibitors into RT active site to determine the most probable binding mode and most reliable conformations. The study was conducted using a complex receptor-based and ligand-based alignment procedure and different alignment modes were studied to obtain highly reliable and predictive CoMFA and CoMSIA models with cross-validated q(2) value of 0.