Interference with the Assembly of SARS-CoV-2 virions Targeting E Protein by rational drug design

• Grant number: 24/03520-0
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: August 30, 2024
• End date: August 29, 2025
• Field of knowledge: Biological Sciences - Microbiology
• Principal Investigator: Carsten Wrenger
• Grantee: Lizdany Florez Alvarez
• Supervisor: Christian Betzel
• Host Institution: Instituto de Ciências Biomédicas (ICB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: Universität Hamburg (UHH), Germany
• Associated to the scholarship: 22/01812-8 - Interference with the Assembly of SARS-CoV-2 virions Targeting E Protein by rational drug design, BP.DR

Abstract

This research project aims to assess the impact of molecules identified through rational drug design that can disturb the assembly of SARS-CoV-2 virions in vitro by targeting the E protein of the virus. In this context the main goals of the proposed research project are to gain detailed structural insights into the pentameric structure of the E protein, its subcellular localization, and its role as a viroporin applying complementary structural biology methods, as modern bio-imaging methods, Cryo-EM and X-ray solution scattering. The SARS-CoV-2 E-protein oligomer functions as a membrane-channel that facilitates the transport of Na+, K+, H+, and Ca2+ ions. During SARS-CoV-2 infection this E-protein channel contributes to the induction of the inflammatory response associated with the acute respiratory distress syndrome (ARDS) observed in COVID-19. Consequently, the E-protein channel plays a significant role in viral pathogenesis. Moreover, this channel formed by the E protein is crucial for the efficient trafficking of virions, preserving their infectivity, and preventing premature proteolytic processing of the Spike protein through pH neutralization in the Golgi. By interfering effective and specific the function of the SARS-CoV-E protein viroporin it will be possible to disrupt viral pathogenesis, impair the assembly and release of new viruses, which therefore will open new routes to identify novel and effective antiviral therapeutics. In this sense I intend to evaluate the effect of specific compounds, which are capable to inhibit the ion channel function of the SARS-CoV-E protein on viral progeny production, applying latest integrative and complementary structural biology approaches, as a combination of correlative light and electron microscopy combined with conventional Cryo-EM and X-ray solution small angle scattering (SAXS). And, if it will be possible to obtain X-ray suitable crystals of the E-protein oligomer I will also apply X-ray crystallography, ideally serial diffraction methods to obtain on top time resolved insights about how compounds diffuse and bind to the E-protein oligomer. Analyzing the 3D structure of the E-protein oligomer in different spatial and time resolutions regimes, applying methods mentioned before, will allow to identify the location of the channel structure in cellulo, and will allow to characterize its interaction with selected candidate compounds. All data and results will enrich also the current available information available about this viroporin, which is highly conserved among coronaviruses, and which represents a new and valuable target for drug development and basic virology research. Furthermore, particular imaging methods and procedures applied and established can be utilized for topic related future research projects at USP/ICB.