Multitarget directed ligands as a modern approach for drug design has gained increasing attention in the recent decades as a more effective therapeutic strategy, especially in the framework of multifactorial diseases including cancer, leading to synergistic anti-tumor effects and reduced drug-drug interactions.

The systematic development of CK2/HDAC dual inhibitors held by Drug Design and Synthesis Research Group at San Pablo CEU University led to novel dual-target ligands construction through the pharmacophores combining of Tucidinostat as zinc-binding group (ZBG) chelating Zn²⁺ cation at the catalytic domain of HDAC1, and CX-4945 as the competitive CK2 inhibitor, which also acts as Surface Recognition Domain (Cap group) in HDACs. Alkyl linear chains of varying length and alkyl chains incorporating phenyl or/and triazole motifs were introduced as the Linkers to connect the Cap structure to the ZBG.  

The objective was to discover the impact of the linkers` composition on the conformational behavior of the dual inhibitors in explicit water and chloroform environments. The workflow included geometry optimization with Gaussian16 followed by 100 ns MD simulations using Amber 16 suite [4]. Trajectory analysis with cpptraj allowed to retrieve the molecular descriptors which are essential to predict cell permeability and characterize conformers’ shape (radius of gyration), polarity (Polar surface area) and the ability to fold (the number of intramolecular hydrogen bonds and ZBG-Cap mass-centered distance). Clustering analysis of generated conformers resulted in 10 clusters which represent the most probable and stable conformations.