Tag Archives: molecular docking

Designing, docking and heterologous expression of an anti-HER2 affibody molecule

N. Salmanian Tabasi1, A. Gholizadeh1, B. Baghban Kohnehrouz2

1Research Institute for Fundamental Sciences, University of Tabriz, Iran;
2Department of Plant Breeding and Biotechnology, University of Tabriz, Iran;
e-mail: aghz_bioch@yahoo.co.in

Affibody molecules are small protein scaffolds mostly based on triple-helical bundle protein domains. Many triple helix-based affibody proteins have shown prominent properties for tumor imaging and therapy. In our opinion, the structural organizations and the sizes of affibody molecules could be modified to increase their recognition abilities and binding affinities to human epidermal growth factor receptor type 2 (HER2). Thereby, the purpose of this study was to design and characterize a novel platform of affibody molecule consisting of five separate helixes (encoding 99 amino acids with a duplicate of helixes 1 and 2 at N-terminus plus GGGC chelator peptide sequence at C-terminus) enable of binding to HER2 with higher avidity. Using in silico screening methods, the structure and the interactive potential of designed affibody was comparatively investigated. The molecular expression and production of the designed affibody in Escherichia coli cells was successfully examined and reported.


Design of transcription inhibitors on the basis of N-arylamides of 9-methyl- and 9-methoxyphenazine-1-carboxylic acids

L. G. Palchykovska, О. V. Vasylchenko, M. O. Platonov, V. G. Kostina,
N. A. Lysenko, I. V. Alexeeva, D. M. Hovorun, A. D. Shved

Institute of Molecular Biology and Genetics, National Academy
of Sciences of Ukraine, Kyiv,
e-mail: L.Palchykovska@imbg.org.ua

A convenient method of synthesis was develo­ped and two series of N-arylamides of 9-methyl- and 9-methoxyphenazine-1-carboxylic acids were obtained. By the molecular docking method the mode оf the synthesized compounds interaction with catalytic pocket of the RNA polymerase Т7 transcription complex was simulated. Key ligand-receptor intermolecular contacts were identified. They are realized by various types of non-covalent interactions with line of conservative amino acid residues involved in recognition of incoming nucleotide, catalytic act of RNA synthesis as well as in stabilizing the RNA–DNA hybrid at early steps of transcription. In silico data indicate sufficient affinity of ligands for the receptor and allow to predict their ability to inhibit the functioning­ of RNA poly­merase T7 transcription complex that is consistent with preliminary experimental results. Initial testing in a model RNA polymerase T7 transcription system demonstrates significant inhibition of in vitro RNA synthesis by investigated compounds at a concentration of 25 µg/ml (~80 µM).

Effect of fullerene C(60) on ATPase activity and superprecipitation of skeletal muscle actomyosin

K. S. Andreichenko1, S. V. Prylutska1, K. O. Medynska1, K. I. Bogutska1,
N. E. Nurishchenko1, Yu. I. Prylutskyy1, U. Ritter2, P. Scharff2

Joint Ukrainian-German Center on Nanobiotechnology
1Taras Shevchenko National University of Kyiv, Ukraine;
e-mail: prylut@ukr.net;
2Technical University of Ilmenau, Institute of Chemistry
and Biotechnology, Germany

Creation of new biocompatible nanomaterials, which can exhibit the specific biological effects, is an important complex problem that requires the use of last accomplishments of biotechnology. The effect of pristine water-soluble fullerene C60 on ATPase activity and superprecipitation reaction of rabbit skeletal muscle natural actomyosin has been revealed, namely an increase of actomyosin superprecipitation and Мg2+, Са2+– and K+-ATPase activity by fullerene was investigated. We conclude that this finding offers a real possibility for the regulation of contraction-relaxation of skeletal muscle with fullerene C60.