Both were subsequently found to be precursors of more potent inhibitors, analogues with various substituents on the triazole or imidazole rings, some with Ki values in the nM range, reviewed, amongst others, by Zien et al. and Battistutta et al.. Notwithstanding the high structural similarity between TBBt and TBBz, they differ significantly in their mode of binding to CK2a, with a root mean square deviation of over 2.5 A ° between corresponding locations of the Br atoms within the binding pocket. The complex with TBBz is stabilized by two welldefined halogen bonds, and an analogous pattern of two halogen bonds involving the same aminoacid residues, but making short contacts with other bromine atoms of the ligand, observed in complex with 3,4,5,6,7-pentabromo-1H-indazole. No such bonds were observed in the structure of the complex with TBBt. The foregoing stimulated development of many other, structurally unrelated, potent selective inhibitors, culminating in the appearance of Cylene’s oral CX-4945, the first low-molecular weight CK2 inhibitor to reach the clinic in phase I and phase II clinical trials, in patients with solid tumors, multiple myeloma, and Castleman’s disease. The biological importance of the company website halogeno benzotriazoles and benzimidazoles is further underlined by the fact that they are selective inhibitors of various protein kinases. Moreover, some of them efficiently inhibit the NTPase/helicase activities of hepatitis C and related viruses. In addition, Townsend and coworkers have demonstrated that a number of halogeno benzimidazole nucleosides are potent inhibitors of some herpesviruses, one of which is presently in clinical trials for HCMV infections. The foregoing reflects the current widespread interest in elucidating the role of halogenated ligands in biological systems, extensively reviewed, amongst others, by Aufinger et al., Voth & Ho, Parisini et al., Grant & Lunney, Lu et al. and Rendine et al.. We have previously demonstrated that replacement of one of the bromines of TBBt, that at C, by a variety of other substituents, differing in size, electronegativity and hydrophobicity, resulted in significant changes in ionic equilibrium, protomeric preference for the neutral form, and inhibitory activity against CK2a. In general, the hydrophobicity of the anionic form of the ligand was found the principle factor influencing its inhibitory activity. To further define the role of the individual Br atoms of TBBt, as regards potency and selectivity as inhibitors of CK2a, we have synthesized all the possible two mono-, four di-, and two tribromobenzotriazoles, and herein we model the structure of their complexes with CK2a and examine the relation between their physico-chemical properties and inhibitory activities vs. CK2a. Binding of all analogues to CK2a was analyzed by mining the free energy of binding, estimated by ligand docking to the protein, the location of which was restricted to the region proximal to the TBBt binding site. Estimated values of free energy of binding are well correlated with inhibitory activities, including the parent Bt. For 5-BrBt and 5,6-Br2Bt, binding was underestimated by approximately 0.8 kcal/mol. However, the docking procedure was performed in the absence of explicit water molecules, to avoid the almost insurmountable problem of simultaneous docking of three independent molecules, namely – a given ligand and the two water molecules located in the binding pocket in the complex of CK2a with TBBt. But the absence of explicit water molecules, directly involved in ligand binding, causes systematic displacement of ligands toward Lys68 and Glu81. To further clarify this problem, an additional 5 ns molecular dynamics was performed for each ligand in the presence of explicit water molecules. Analysis of the last 3 ns of each MD trace indicated that, for all ligands, their flexibility inside the CK2a binding pocket is comparable, and the root mean square fluctuation values, which are a measure of differences in ligand locations in snapshots of the MD trajectory, vary over a narrow range of 0.4-0.6 A °. It follows that the binding pocket may readily adapt to the smaller ligands, and, consequently, the entropic contribution arising from ligand translational degrees of freedom is almost the same for all the ligands. For all nine brominated Bt derivatives the average location was found almost the same, and identical to that of TBBt in the crystal structure with CK2a. The only significant deviation was noted for the parent Bt, which was found inactive. The foregoing shows that all the halogenated Bt derivatives bind in the same orientation to CK2a. The correlation between experimental IC50 values and the energy terms, estimated both from the docking procedure, and directly from ab initio QM calculations for solvation, further demonstrate that the putative contribution of halogen bonding is significantly smaller than the other energy terms used in the calculations, if at all.