Conformational Characterization of TMEM176B as a druggable immunometabolic target

• Grant number: 24/21904-0
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: August 01, 2025
• End date: January 31, 2028
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Ana Lígia Barbour Scott
• Grantee: Yolanda Maria Barros Marcello
• Host Institution: Centro de Matemática, Computação e Cognição (CMCC). Universidade Federal do ABC (UFABC). Ministério da Educação (Brasil). Santo André , SP, Brazil

Abstract

The NLRP3 inflammasome plays a critical role in the innate immune system, and thus in inflammatory and homeostatic processes. The TMEM176B channel, in turn, negatively regulates this complex by controlling caspase-1 activation and the secretion of inflammatory cytokines IL-1¿ and IL-18, as well as modulating Ca2+ and K+ fluxes. Studies have been exploring TMEM176B as a target in cancer immunotherapies. This doctoral project aims to structurally characterize TMEM176B by exploring its diverse conformational dynamics and interactions with inhibitors. The goal is to validate oligomeric models developed using AlphaFold, analyze mutations of interest such as A134T, and understand the molecular mechanisms that influence its function as an immunometabolic target. To achieve this, we propose the use of Normal Mode Analysis (ANM) and hybrid methodologies such as VMOD and MDeNM (Molecular Dynamics with excited Normal Modes), along with the application of Markov State Models, to evaluate the stability of mutants and protein-ligand complexes, including TMEM176B/BayK8644 or TMEM176B with inhibitors identified through virtual screening using the NuBBEDB library. Furthermore, the resulting potential drugs will be extensively characterized using software such as NCIPLOT and BIOVIA. Preliminary results indicate higher structural quality and more prominent potential channels for the tetramer compared to the dimer, while residues with the greatest flexibility are the same for both oligomers, according to ANM. Ultimately, the execution of this project aims to elucidate structural and biochemical mechanisms of action through in silico models, complementing experimental results obtained by our collaborators. (AU)