Evasion of apoptosis is a promising hallmark of cancer cells owing to aberrant expression of Bcl-2 pro-survival proteins. Targeting such pro-survival Bcl-2 family members has significant appeal and also a vital directive in achieving desired clinical outcomes. Focusing on the inadequacies of current Bcl-2 targeted therapy, we predicted the contributors of differential activity of small molecules implementing QSAR analysis for a large data set of small molecules including Bcl-2 and Bcl-xL (1650 compounds) reported in the literature. We developed QSAR models for diverse scaffolds (7 cores) to gain insights into vital functional groups contributing to anti-apoptotic activity [1]. The vital descriptors and moieties accounting for the biological activity were identified and benchmarked against experimentally determined binding patterns. Further, we have developed a user-friendly web server for predicting a specific/dual inhibitor of Bcl-2 and Bcl-xL [http://www.iitm.ac.in/bioinfo/APPLE/]. Among all designing tactics, scaffold hopping and hierarchical virtual screening methods are fruitful and persist as an utmost priority in the drug discovery process. Despite the potentiality, both were not employed in a radical manner for PPI (protein-protein interaction) targets [2] which prompted us to develop a novel method uniting both the methodologies for a key PPI involving anti-apoptotic Bcl-2 and its counter pro-apoptotic partners, reported in various cancers[3]. In this study, after a fine refinement of existing scaffolds, we generated a focused library of 8270 novel compounds considering seven scaffolds. We enumerated the libraries using clustering, PAINS filtering, physicochemical characterization and SAR (Structure-Activity Relationship) matching. The results motivated the generation of a focused library of 50 active lead compounds towards the Bcl-2 interface [4]. Based on the binding energy, predicted IC50 and similarity, we found 29 compounds from a commercial library and selected for validation using in vitro and in vivo assays and found three highly active lead compounds SM216, SM396 and SM949. Further, the binding analysis using SPR and LC/MS/MS revealed the covalent binding of SM396 to the BH4 domain of Bcl-2. The mechanistic studies validate the selective killing effect of the three compounds on cancerous cells sparing the normal cells by inducing Bcl-2 dependent apoptotic pathway. The compounds exhibited efficacious in vivo activity as single agents in MDA-MB-231 xenograft model (at nanomolar dosage). Overall, these findings depict SM216, SM396 and SM949 as promising leads, pointing to the clinical translation of these compounds as a targeted therapy to circumvent the clinical conundrum of triple-negative breast cancer [5].

Publications:
[1]. V. Kanakaveti, R. Sakthivel, Suresh K. Rayala and M. Michael Gromiha (2017). Importance of functional groups in predicting the activity of small molecule inhibitors of Bcl-2 and BCL-xL. Chem Biol Drug Des. 90, 308-316.
[2]. V. Kanakaveti, P. Anoosha, R. Sakthivel, S. K. Rayala and M. Michael Gromiha (2019). Influence of amino acid mutations and small molecules for targeted inhibition of proteins involved in cancer. Curr Top Med Chem. 19, 457-466.
[3]. V. Kanakaveti, A. Shanmugam, C. Ramakrishnan, P. Anoosha, R. Sakthivel, S. K. Rayala and M. Michael Gromiha (2020). Computational Approaches for Identifying Potential Inhibitors on Targeting Protein Interactions in Drug Discovery. Adv Prot Chem Str Biol 121, 25-47.
[4]. V. Kanakaveti, R. Sakthivel, S. K. Rayala and M. Michael Gromiha (2019). Forging new scaffolds from old: Combining Scaffold hopping and Hierarchical virtual screening for identifying novel Bcl-2 inhibitors. Curr Top Med Chem. 19, 1162-1172.
[5]. V. Kanakaveti, R. Sakthivel, Rahul Kanumuri, Vaishnavi B, Roshni S, Ravishankar Pitani, G. Venkataraman, S. K. Rayala and M. Michael Gromiha (2020) Targeting BH4 domain with novel covalent and non-covalent small molecule inhibitors in triple-negative breast cancer. Cell Death Dis (under consideration)