Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses

Cécilia Hognon; Tom Miclot; Cristina Garcia Iriepa; Antonio Francés-Monerris; Stephanie Grandemange; Alessio Terenzi; Marco Marazzi; Giampaolo Barone; Antonio Monari

Coronaviruses inducing severe acute respiratory syndrome (SARS) gained first worldwide attention in 2003 following the outbreak of SARS disease that mainly affected different southeastern Asian countries. 1-3 By the end of 2019 and the beginning of 2020, a novel coronavirus, styled SARS-CoV-2, has emerged and caused the Covid-19 pandemic. 4-7 At the time of writing this communication, Covid-19 has spread in all continents, excluding Antarctica. In April, the 5 th 2020 a number of more than 1 million confirmed cases has been reported, as well as more than 66,000 deaths. 8 Furthermore, severe limitations and social distancing measures have been implemented by an increasing number of countries, in the attempt to limit the spreading of the pandemic. 9 Indeed, coronaviruses, and SARS-CoV-2 in particular, are characterized by high infectious and transmissibility rates, and may, in certain cases, severely attack the lungs and the respiratory system, an occurrence which can lead to the necessity of respiratory assistance and even to death, especially in presence of others comorbidities. [10] [11] [12] Since the first outbreak of the pandemic, important scientific works appeared, aiming at understanding at a molecular level the mechanisms of action of SARS-CoV-2, and corona viruses in general, that may be related to its transmissibility and mortality. Important successes have notably been achieved in both genome sequencing and structural resolution of the different viral proteins, also with the assistance of molecular modeling and simulation. [13] [14] [15] [16] [17] [18] [19] [20] [21] In fact, the possibility of finding efficient therapeutic strategies requires the elucidation of the fine mechanism that mediate the virus attack to the host cell, the resistance to the host immune system, and finally its virulence. [22] [23] [24] [25] Among the multifaced protein envelope of coronaviruses the so-called non-structural protein 3 (Nsp3) represents a large protein, localized in the cytoplasm, consisting of about 2,000 amino acids and comprising several different domains, also including a transmembrane region. Among the . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.07.029447 doi: bioRxiv preprint 4 different domains of Nsp3, 26 ,27 whose precise function of some of them has not been entirely clarified yet, the so-called SARS Unique Domain (SUD) deserves a special attention, since it is present only in SARS-type coronaviruses and hence it has been associated to the increased pathogenicity of this viral family. The structure of SUD (presumably a common domain of different SARS viruses) has been resolved experimentally, [28] [29] [30] and it has been proved that the macrodomain is indeed constituted by a dimer of two symmetric monomers. Furthermore, both experimental and molecular docking investigations have pointed out a possible favorable interaction of SUD with nucleic acids, and in particular with RNA in G-quadruplex (G4) conformation. 28 The presence of a high density of . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.07.029447 doi: bioRxiv preprint 5 lysine residues at the interface between two SUD monomers, forming a positively charged pocket, also suggests