Computational protocol: Dual-targeting anti-angiogenic cyclic peptides as potential drug leads for cancer therapy

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Protocol publication

[…] Samples were dissolved in 90% H2O/10% D2O (D2O; 99.9% purity; Cambridge Isotope Laboratories, Woburn, MA) with a final concentration of 1 mM at pH 5.5. 4,4-Dimethyl-4-silapentane-1-sulfonic acid (DSS) was used as a chemical shift reference for spectral calibration. One-dimensional (1H) and two-dimensional (TOCSY and NOESY) spectra were recorded for all native and grafted peptides at 298 K on a Bruker Avance 600 MHz spectrometer, with mixing times of 200–300 ms for NOESY experiments. All spectra were assigned using CCPNMR. All amino acid spin systems were specifically assigned based on Wuthrich et al.. For the αH secondary shifts, these were analyzed based on subtracting the random coil 1H NMR chemical shifts of Wishart et al. from experimental αH chemical shifts. The three-dimensional molecular structure of SFTI-1 and MCoTI-II were illustrated using MOLMOL. […]

Pipeline specifications

Software tools CcpNmr, MOLMOL
Applications NMR-based proteomics analysis, Protein structure analysis
Diseases Neoplasms, Drug-Related Side Effects and Adverse Reactions
Chemicals Somatostatin