# Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics
## 1 The COVID-19 Pandemic
### Potential Targets of Interest  
Although targeting the SARS-CoV-2 main protease was successful in individuating several clinical candidate drugs, even leading to the first approval of a COVID-19 specifically designed drug, other drug discovery campaigns aimed at different viral targets are needed for therapy diversification, potentially combined and synergic treatment, and resistance prevention [202, 203, 204]. Altogether, the SARS-CoV-2 genome encodes four major structural proteins, including nucleocapsid (N), membrane (M), envelope (E), and the spike as mentioned earlier (S), plus 16 nonstructural proteins, encompassing the previously mentioned main protease [205]. Although M\({}^{\text{pro}}\) plays a pivotal role in processing the SARS-CoV-2 viral polyproteins, it is not the only component of the functional replicase complex that is required for the viral spread process [206]. Alongside this, a secondary but still relevant enzyme operates, namely the papain-like protease (PL\({}^{\text{pro}}\), the catalytic domain of protein nsp3) [207]. Despite being a cysteine protease similar to M\({}^{\text{pro}}\), PL\({}^{\text{pro}}\) exerts its enzymatic functions through a catalytic triad composed of Cys111, His272, and Asp286 [208]. Further, PL\({}^{\text{pro}}\) processes peptide bonds located at the C-terminal end of LXGG motifs [209]. Functionally speaking, this 343-residue segment, which is part of the multidomain nsp3 protein, is responsible for cleaving the SARS-CoV-2 polyproteins at three different sites, resulting in the liberation of nsp1, nsp2, and nsp3 proteins [210]. Moreover, PL\({}^{\text{pro}}\) is also responsible for cleaving post-translational modifications on known regulators of host innate immune response [211]. As demonstrated by the approval of Remdesivir by regulatory agencies, another valuable target for the development of COVID-19 drugs is represented by the RNA-dependent RNA polymerase (RdRp) [49]. This complex machinery comprises four subunits, including one nsp12, responsible for the catalytic activity of the assembly; one nsp7; and two nsp8, with the latest two acting as cofactors [212]. The assembled holoenzyme presides RNA replication, a process that results in the formation of nine subgenomic RNAs [213]. The active site of nsp12 resides in its C-terminal RdRp domain and includes residues spanning from Thr611 to Met626, which are involved in binding one turn of double-stranded RNA, while residues D760 and D761 are required for recognition of the 3\({}^{\prime}\) end and are essential for RNA synthesis [214, 215]. Remdesivir binds within the active site, forming direct contact with residues K545, R553, D623, S682, T687, N691, S759, D760, and D761 and blocking the catalytic machinery by delaying the chain termination process [216, 217]. During the RNA synthesis process, the RdRp also interoperates with nsp13 (helical case) [218], an enzyme involved in unwinding the RNA secondary structure of the 5\({}^{\prime}\) untranslated section of the viral genome [219] to increase the efficiency of the copy process [220, 221]. From a structural perspective, the nsp13 is a 596 residue, triangular pyramid-shaped helicase, which exploits its function thanks to the energy provided by its NTPase domain composed of six conserved residues (K288, S289, D374, E375, Q404, and R567) [222]. Adding to its helicase activity, the nsp13 active site also exerts RNA 5\({}^{\prime}\) triphosphatase activity, further highlighting its importance in the maturation process of the viral mRNA [223]. The 5\({}^{\prime}\) end of the newly synthetized mRNA is then subjected to post-translational modifications to boost both its stability (preventing cleavage from exonucleases), protein translation, and viral immune escape [224]. This activity is sequentially carried out by two S-adenosyl-L-methionine-dependent methyltransferases, namely nsp14 and nsp16 [225]. Specifically, the 527 residues' nsp14 encompass both a proofreading exoribonuclease (ExoN) and an N7-methyltransferaseenzymatic enzymatic activity [226].