# Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics
## 1 The COVID-19 Pandemic
### Spike Protein  
The ability of the SARS-CoV-2 virus to infect human cells heavily depends on a surface glycoprotein known as the S/spike protein [74], named after its peculiar shape [75]. For this reason, both mRNA vaccines and mAbs are designed to target this protein and prevent the virus's entry into the cell, thereby limiting its replication [76].  
Concerning these, although different pathways for SARS-CoV-2 cell entry are possible [77; 78], the principal and better-characterized one involves binding to the human ACE2 receptor (hACE2) [79], a membrane-anchored metallopeptidase that is abundantly present in various districts of the human body, from the vascular endothelium to the epithelia of lungs and small intestine [80]. On its own, host cell receptor binding is not sufficient to ensure entrance within host cells. Priming and activating the S protein by host proteases is required to enhance its cell-cell and virus-cell fusion processes and increase viral shielding from neutralizing antibodies [79; 81]. The list of priming proteases includes, but is not limited to, TMPRSS2, a transmembrane serine protease that is often co-expressed with ACE2 in SARS-CoV-2 target cells; Furin; and cathepsin B/L [79; 82; 83]. The priming process entails the exposure of a lipophilic fusion peptide (FP), which penetrates the host cell membrane triggering the viral fusion [84] thanks to its strong membrane-perturbing capacities [85]  
From a structural perspective, the spike is a trimeric transmembrane glycoprotein composed of 1273 amino acids organized in two main subunits, S1 and S2, and several functional domains [86].  
The S1 subunit comprises two main domains, specifically the N-terminal and C-terminal domains (NTD and CTD, respectively), which are both involved in the binding to host cell receptors [86]. The CTD contains the receptor-binding domain (RBD, residues 319-541), consisting of two motifs. Firstly, a core structure is formed by a twisted five-stranded antiparallel \(\beta\) sheet (\(\beta\)1, \(\beta\)2, \(\beta\)3, \(\beta\)4, and \(\beta\)7), with three short helices (\(\alpha\)1, \(\alpha\)2, and \(\alpha\)3). Secondly, an extended loop (receptor binding motif, RBM) is formed by a two-stranded \(\beta\) sheet (\(\beta\)5 and \(\beta\)6), lying at one edge of the core and containing most of the residues involved in binding to hACE2 [87] (Figure 1).  
The S2 subdomain has significant roles in spike protein trimerization and in mediating the virion entry into the host cell once the molecular contacts have been established [88]. It is formed by relevant subdomains such as the transmembrane domain (TD) (residues 1296-1317), which exerts both the spike anchoring to the outer side of the viral membrane and the maintenance of the trimeric quaternary structure [89; 90], and a cytoplasm domain (CD) (residues 1318-1353), which mediates viral assembly and c  
Figure 1: (**A**) Crystal structure of spike RBD (teal) in complex with hACE2 (pink), deposited in the Protein Data Bank with accession code 6 MOJ. (**B**) Close-up view of interface contacts between the spike RBD and hACE2: hydrogen bonds are represented as black dashed lines.  
thermore, the previously mentioned fusion peptide, a cleavage S2\({}^{\prime}\) site (residues 815/816), and two heptad-repeat domains (HR1/HR2) (residues 984-1104/1246-1295) are also part of S2 [92].