Interaction of two peptide drugs with biomacromolecules analyzed by molecular docking and multi-spectroscopic methods

Spectroscopic studies on noncovalent binding of nicotinamide-modified BRCA1 (856-871) analogs to calf thymus DNA

Various peptide drugs have entered the market with the development of molecular biology. Peptide drugs are used for treat diseases such as diabetes, breast cancer, and HIV infection. In this study, three nicotinamide-modified peptides were synthesized by modifying the N-terminus of BRCA1 (856-871, Y856R, K862Y, R866W) peptide with three nicotinic acid derivatives using solid-phase peptide synthesis. The results of calf thymus DNA (ctDNA) binding activity indicated that binding constants of BRCA1 (856-871, Y856R, K862Y, R866W) (P0) and three nicotinamide-modified peptides (P1, P2, and P3) to ctDNA were 1.89 × 10³, 2.97 × 10⁴, 7.61 × 10⁴, and 8.09 × 10⁴ L·mol^-1, respectively. The binding affinity of the modified peptides was superior to that of BRCA1 (856-871, Y856R, K862Y, R866W). ΔH^θ < 0 and ΔS^θ < 0 indicated that van der Waals force and hydrogen bond contributed most to peptide-ctDNA binding. Results obtained by Circular dichroism (CD) indicated that peptide binding interaction led to conformational changes in ctDNA. Ultraviolet-visible (UV) spectroscopy, ethidium bromide (EB) competition experiments, DNA melting experiments, and viscosity measurements verified that peptides interacted with ctDNA via groove binding. Ionic strength experiments manifested that electrostatic binding was also involved in peptide-ctDNA binding.

Exploration of binding mechanism of apigenin to pepsin: Spectroscopic analysis, molecular docking, enzyme activity and antioxidant assays

Pepsin plays an important role in nutrient metabolism. Apigenin (AP) is a beneficial polyphenol to human health. To enhance the bioavailability of AP and elucidate the inhibitory effect of AP on pepsin, the interaction mechanism of AP with pepsin was investigated using spectroscopic analysis and molecular docking, and the activity of pepsin and antioxidant activity of AP was also evaluated. Specifically, AP performed static quenching of pepsin and had only one binding site on pepsin. More interestingly, the interaction between AP and pepsin was spontaneous, while hydrogen bonds and van der Waals forces were the main binding forces. Generally, synchronous and three-dimensional fluorescence confirmed that AP induced the conformational changes of pepsin, and molecular docking proved the above results and illustrated the specific binding patterns. Specifically, AP inhibited the activity of pepsin, while pepsin decreased the antioxidant activity of AP. These results provided useful information for elucidating the interactions between AP and pepsin.

Interaction of bifunctional peptide-carbazole complexes with DNA and antimicrobial activity

Two peptide-carbazole conjugates, CTAT and CNLS, were designed and synthesized using carbazole Schiff base to modify the cell membrane penetrating peptide TAT (47-57) and the nuclear localization peptide NLS at the N terminus. The interaction with ctDNA was investigated by multispectral and agarose gel electrophoresis. And the effects of CNLS and CTAT on the G-quadruplex structure were explored by circular dichroism titration experiments. The results show that both CTAT and CNLS interact with ctDNA in a minor groove binding manner. Both conjugates bind more tightly to DNA than the individual substances CIBA, TAT and NLS. In addition, CTAT and CNLS are capable of unfolding parallel G-quadruplex structures and are potential G-quadruplex unfolding agents. Finally, broth microdilution was performed to test the antimicrobial activity of the peptides. The results showed that CTAT and CNLS had a 4-fold increase in antimicrobial activity compared with the parent peptides TAT and NLS. They could exert antimicrobial activity by disrupting the integrity of cell membrane bilayer and binding to DNA, and could be used as novel antimicrobial peptides for the development of novel antimicrobial antibiotics.

Novel Method for Extracting the Spectrum of a Supramolecular Complex via a Comprehensive Approach Involving Two-Dimensional Correlation Spectroscopy, Genetic Algorithm, and Grid Searching

A supramolecular complex may be formed by two solutes via a weak intermolecular interaction in a solution. The spectrum of the complex is often inundated by the spectra of the solutes that are not involved in the intermolecular interaction. Herein, a novel spectral analysis approach is proposed to retrieve the spectrum of the supramolecular complex. First, a two-dimensional (2D) asynchronous spectrum is constructed. Then, a genetic algorithm is used to obtain a heuristic spectrum of the supramolecular complex. The heuristic spectrum is a linear combination of the spectrum of the complex and the spectrum of a solute. The coefficients of the linear combination are then obtained, according to which the equilibrium constants are invariant among the sample solutions used to construct the 2D asynchronous spectrum. We have applied the approach to a supramolecular system formed by benzene and I₂. In the analysis, several binding models are evaluated, and a benzene molecule interacting with two iodine molecules via halogen bonding turns out to be the only possible model. Hence, the characteristic band of the benzene/I₂ supramolecular complex around 1819 cm^-1 in the Fourier transform infrared (FTIR) spectrum and the corresponding equilibrium constant are obtained. The above results indicate that the novel approach provides a chance to get new insight into various intermolecular interactions studied by spectroscopy.