An in silico approach to design peptide mimetics based on docking and molecular dynamics simulation of EGFR–matuzumab complex

Epidermal growth factor receptor (EGFR) plays an essential role in anticancer therapy. Matuzumab is an antibody for the treatment of colorectal, lung and stomach cancer. Matuzumab binds efficiently to EGFR and blocks its phosphorylation. The recent clinical successes have established application of peptides for cancer treatment. The present contribution introduces an in silico approach to design peptides based on molecular dynamics simulation (MDs) of the matuzumab-EGFR complex in water environment. Moreover, principal component analysis has been used to select multiple conformations of the complex in MDs for designing the peptides. The paratope and epitope in each conformation of the complex were determined, and the alanine scanning was used to identify the hot spots of EGFR conformers. The conformations of the peptides were optimized using PEP-FOLD server and MDs. The selected conformations were analyzed in a docking study to realize the binding site of the EGFR. Finally, pharmokinetics properties of the peptides were calculated. The designed oligopeptides were EWRSYYYWH, YYYWHNEWN, YYYWHNEWS and HNHSRNYGS with a higher affinity to the EGFR relative to the previously reported peptides. The newly designed peptides were investigated for their in vivo toxicities on rats, and all of them were non-toxic.     

Design of potential anti-tumor PARP-1 inhibitors by QSAR and molecular modeling studies

Molecular Diversity - Poly ADP-ribose polymerase-1 (PARP-1) inhibitors have been recognized as new agents for the treatment of patients with breast cancer type 1 (BRCA1) disorders. The quantitative...     

Adsorptive stripping voltammetric determination of copper(II) ion using phenyl pyridyl ketoneoxime (PPKO)

A sensitive and selective procedure is presented for the voltammetric determination of copper(II) ion. The procedure involves an adsorptive accumulation of Cu2+-PPKO on a hanging mercury drop electrode, followed by a stripping voltammetric measurement of reduction current of adsorbed complex at about -0.30 V (vs. SCE). The optimum conditions for the analysis of copper(II) ion include pH (5.8-7.0), 60 microgM PPKO and an accumulation potential of -0.5 V (vs. SCE). The peak current is proportional to the concentration of copper over the range 0.3-76 ng mL(-1) with a detection limit of 0.01ng mL(-1) with an accumulation time of 60 s. The speciation of different forms of complex between copper(II) ion and PPKO, using the Best (Martell program), followed pH measurement were examined. The method was applied to the determination of copper(II) ion content in real samples successfully.