Designing the macrolide-amygdalin complexes as CDK6 inhibitors: A multi-algorithm approach to develop safe and effective drugs through molecular docking, ADMET, molecular dynamic simulation and DFT studies.

The current paper presents a rational approach to design new selective and low-toxicity anti-breast cancer agents (a combination of amygdalin and mushroom-derived macrolides). This was done in order to address the effect of cyanogenic toxicity of amygdalin besides improving its ability to target tumors. The library of 142 macrolide-amygdalin complexes was prepared and assayed using a multistage workflow of computations of field-based 3D-QSAR, molecular docking, state-of-the-art MM-GBSA calculations of free energies, computations of DFT/NBO, molecular dynamics (MD) simulations, and in-silico toxicity and hemolytic analyses. The 3D-QSAR models, which proved statistically strong (R2 = 0.86–0.99; Q2 = 0.70–0.73) showed that the steric and hydrophobic interactions were the most important determinants of the anticancer activity. The structure-activity analysis found B45, B46, B47, and B102 as the most active with large predicted pIC₅₀ values (5.05.8). A further molecular docking of the Cyclin D1-CDK4 (2W96), CDK6-V-cyclin (4TTH) showed higher binding affinities of the two complexes as compared to the FDA approved inhibitor Palbociclib, which established strong hydrogen bonds and hydrophobic interactions with key residues ASP129, HIS132, VAL234 and ASP233. MM-GBSA analysis obtained positive ΔG bind values (-55 to -65 kcal/mol), which validates stable binding energetics. The results of DFT and NBO suggested a high level of electronic delocalization, low HOMO-LUMO gaps, and high reactivity stability, whereas MD simulations showed no significant changes in RMSD and Rg during 100 ns, which confirmed the stability of conformations. Their non-toxic and biocompatible properties were confirmed by toxicity prediction of the ProTox-III server and hemolytic docking of oxy- and deoxyhemoglobin. Overall, the findings imply that the macrolide-amygdalin hybridization can be used to stabilize the cyanogenic group, increase the pharmacological selectivity, and serve as an excellent starting point towards the development of the next-generation CDK4/6-inhibitors against breast cancer.