Cancers 2022, 14, 5241. https://doi.org/10.3390/cancers14215241 www.mdpi.com/journal/cancers Article Novel BH4-BCL-2 Domain Antagonists Induce BCL-2-Mediated Apoptosis in Triple-Negative Breast Cancer Vishnupriya Kanakaveti 1,2 , Sakthivel Ramasamy 1 , Rahul Kanumuri 3 , Vaishnavi Balasubramanian 3 , Roshni Saravanan 3 , Inemai Ezhil 1 , Ravishankar Pitani 4 , Ganesh Venkatraman 3 , Suresh Kumar Rayala 1, * and M. Michael Gromiha 1, * 1 Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India 2 Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA 3 Department of Human Genetics, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education & Research, Porur, Chennai 600116, Tamil Nadu, India 4 Department of Community Medicine, Sri Ramachandra Medical College, Sri Ramachandra Institute of Higher Education & Research, Porur, Chennai 600116, Tamil Nadu, India * Correspondence: rayala@iitm.ac.in (S.K.R.); gromiha@iitm.ac.in (M.M.G.); Tel.: +91-2257-4137 (S.K.R.); +91-2257-4138 (M.M.G.) Simple Summary: Our work has led to the identification of three novel BH4 mimetics, SM216, SM396, and SM949, with nanomolar activities both in vitro and in vivo assays. SM396 binds covalently to the BH4 domain of BCL-2 while the compounds SM216 and SM949 are non-covalent BH4 binders. Our results illustrate that these compounds are highly specific to the triple-negative breast cancer cells with no effect on normal cells. Elevated levels of Cyt-c induced by these compounds suggest significant inhibition of BCL-2 leading to apoptosis. Further investigations of these potent lead compounds will lead to clinical translations in targeting challenging tumor types. Abstract: Targeting the challenging tumors lacking explicit markers and predictors for chemosensitivity is one of the major impediments of the current cancer armamentarium. Triple- negative breast cancer (TNBC) is an aggressive and challenging molecular subtype of breast cancer, which needs astute strategies to achieve clinical success. The pro-survival B-cell lymphoma 2 (BCL- 2) overexpression reported in TNBC plays a central role in deterring apoptosis and is a promising target. Here, we propose three novel BH4 mimetic small molecules, SM396, a covalent binder, and two non-covalent binders, i.e., SM216 and SM949, which show high binding affinity (nM) and selectivity, designed by remodeling the existing BCL-2 chemical space. Our mechanistic studies validate the selectivity of the compounds towards cancerous cells and not on normal cells. A series of functional assays illustrated BCL-2-mediated apoptosis in the tumor cells as a potent anti- cancerous mechanism. Moreover, the compounds exhibited efficacious in vivo activity as single agents in the 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 in targeting triple-negative breast cancer. Keywords: triple-negative breast cancer; BH4 domain; covalent BH4 inhibitors; targeted therapy Citation: Kanakaveti, V.; Ramasamy S.; Kanumuri, R.; Balasubramanian., V.; Saravanan, R.; Ezhil, I.; Pitani, R.; Venkatraman, G.; Rayala, S.K.; Gromiha, M.M. Novel BH4-BCL-2 Domain Antagonists Induce BCL-2-Mediated Apoptosis in Triple-Negative Breast Cancer. Cancers 2022, 14, 5241. https:// doi.org/10.3390/cancers14215241 Academic Editors: Reiner Strick and Ramona Erber Received: 27 August 2022 Accepted: 17 October 2022 Published: 26 October 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/license s/by/4.0/).