The binding pose and affinity between a ligand and enzyme are very important pieces of information for computer-aided drug design. In the initial stage of a drug discovery project, this information is often obtained by using molecular docking methods. Autodock4 and Autodock Vina are two commonly used open-source and free software tools to perform this task, and each has been cited more than 6000 times in the last ten years. It is of great interest to compare the success rate of the two docking software programs for a large and diverse set of protein–ligand complexes. In this study, we selected 800 protein–ligand complexes for which both PDB structures and experimental binding affinity are available. Docking calculations were performed for these complexes using both Autodock4 and Autodock Vina with different docking options related to computing resource consumption and accuracy. Our calculation results are in good agreement with a previous study that the Vina approach converges much faster than AD4 one. However, interestingly, AD4 shows a better performance than Vina over 21 considered targets, whereas the Vina protocol is better than the AD4 package for 10 other targets. There are 16 complexes for which both the AD4 and Vina protocols fail to produce a reasonable correlation with respected experiments so both are not suitable to use to estimate binding free energies for these cases. In addition, the best docking option for performing the AD4 approach is the long option. However, the short option is the best solution for carrying out Vina docking. The obtained results probably will be useful for future docking studies in deciding which program to use.

Syringic acid (SA) is a natural phenolic acid found in vegetables, fruits, and other plant-based foods. A range of biological activities were proposed for this compound including anticancer, antimicrobial, anti-inflammation, and anti-diabetic activities, as well as antioxidant and antinitrosant properties. In this study, the focus is on the latter two. The HO • , HOO • , NO, and NO 2 scavenging activities of SA were evaluated in physiological environments by kinetic and thermodynamic calculations. The computed rate constants of the HO • radical scavenging of SA were 4.63 × 10 9 and 9.77 × 10 7 M −1 s −1 in polar and nonpolar solvents, respectively. A comparison with the experimentally determined rate constant in aqueous solution yields a k calculated /k experimental ratio of 0.3, thus the computed kinetic data are reasonably accurate. SA exhibited excellent HOO • and NO 2 scavenging activity in water (k overall (HOO • ) = 1.53 × 10 8 M −1 s −1 and k overall (NO 2 ) = 1.98 × 10 8 M −1 s −1 ), whereas it did not show NO scavenging activity in any of the studied environments. In lipid medium, SA exhibited weak activity. Thus, in polar environments, the HOO • radical scavenging of SA is 1.53 times higher than that of ascorbic acid. Consistently, SA is a promising antioxidant and antinitrosant agent in polar environments.

Oxidative stress is implicated in aging and aging-related diseases, including cancer.