Impact of SNPs, off-targets, and passive permeability on efficacy of BCL6 degrading drugs assigned by virtual screening and 3D-QSAR approach

by Selleckchem | May 15 2023

B-cell lymphoma 6 (BCL6) regulates various genes and is reported to be overexpressed in lymphomas and other malignancies. Thus, BCL6 inhibition or its tagging for degradation would be an amenable therapeutic approach. A library of 2500 approved drugs was employed to find BCL6 inhibitory molecules via virtual screening. Moreover, the 3D core structure of 170 BCL6 inhibitors was used to build a 3D QSAR model and predict the biological activity. The SNP database was analyzed to study the impact on the destabilization of BCL6/drug interactions. Structural similarity search and molecular docking analyses were used to assess the interaction between possible off-targets and BCL6 inhibitors. The tendency of drugs for passive membrane permeability was also analyzed. Lifitegrast (DB11611) had favorable binding properties and biological activity compared to the BI-3802. Missense SNPs were located at the essential interaction sites of the BCL6. Structural similarity search resulted in five BTB-domain containing off-target proteins. BI-3802 and Lifitegrast had similar chemical behavior and binding properties against off-target candidates. More interestingly, the binding affinity of BI-3802 (against off-targets) was higher than Lifitegrast. Energetically, Lifitegrast was less favorable for passive membrane permeability. The interaction between BCL6 and BI-3802 is more prone to SNP-derived variations. On the other hand, higher nonspecific binding of BI-3802 to off-target proteins could bring about higher undesirable properties. It should also be noted that energetically less desirable passive membrane translocation of Lifitegrast would demand drug delivery vehicles. However, further empirical evaluation of Lifitegrast would unveil its true potential.

Comments：

It seems that the authors of this study employed a variety of computational methods to identify potential BCL6 inhibitors from a library of approved drugs. They used virtual screening to identify molecules that could bind to BCL6 and then used 3D QSAR modeling to predict their biological activity. They also analyzed the SNP database to understand how genetic variations could impact the interaction between BCL6 and potential inhibitors.

One interesting finding was that Lifitegrast (DB11611) had favorable binding properties and biological activity compared to BI-3802, another potential inhibitor. However, Lifitegrast was less favorable for passive membrane permeability, meaning it may require drug delivery vehicles for effective use. Additionally, the authors identified several off-target proteins that could potentially interact with the inhibitors and used molecular docking analyses to assess their interactions.

Overall, this study provides a promising starting point for further empirical evaluation of Lifitegrast as a potential BCL6 inhibitor. However, it also highlights the importance of considering off-target effects and membrane permeability when designing and evaluating potential drugs.