Insights into SARS-CoV-2: Exploring Protein Dynamics and RNA Functionality for future Therapeutic Strategies

The main goal of this thesis is to thoroughly understand the structural and dynamic properties of key biomolecular components of SARS-CoV-2 with the aim of developing pan- coronavirus methods. For this reason, the thesis divided into two parts: a protein-oriented exploration and a genetic-material-focused analysis. The protein-oriented approach delves deep into the immunoreactive, dynamic, and structural characteristics of SARS-CoV-2 Spike protein and its variants. By investigating these intricate details, we aim to unravel pivotal insights that transcend individual variants, ultimately leading us to identify fundamental patterns applicable to a broader range of viral agents. This understanding serves as a basis to devising adaptable strategies capable of addressing both present and future pandemics. On the other hand, the genetic approach deepens the possibility of targeting secondary structures of the virus RNA other than the classical ones, the G-quadruplexes (G4). Through the synergy of these two distinct yet interlinked approaches, this thesis aims to construct a comprehensive framework for addressing the challenges posed by viral mechanisms. By combining knowledge from the world of proteins and genetics, we aspire to build a general computational strategy for the study of the fine mechanisms regulating viral-host interactions and viral life regulation.