1.  Introduction
Pandemics involving pathogenic human coronaviruses have wreaked havoc on the human populace. During the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic in 2002–2003, a high fatality rate of 10% was observed in the approximately 8,000 individuals infected (Marra et al., 2003; Peiris et al., 2003; Rota et al., 2003; SARS Working Group, 2003). In 2012, the middle east respiratory syndrome coronavirus (MERS-CoV) had a much higher fatality rate of 36% and infected more than 1,700 individuals (de Groot et al., 2013; Zaki et al., 2012). However, the recent SARS-CoV outbreak of 2019, also referred to as SARS-CoV-2 or COVID-19 (Chen et al., 2020), began in Wuhan in China and spread rapidly due to close human-to-human proximity (Li et al., 2020). The SARS-CoV-2 has caused significant devastation globally due to the sheer number of people infected. According to statistics published by the World Health Organization (WHO), there were 4,334,451 known cases of Covid-19 worldwide, out of which 19,737,794 cases alone are reported from America, while Europe attributes 9,664,042 cases, causing death casualties of over 1,157,509 globally as of Oct 27, 2020.
Similar to SARS-CoV and MERS-CoV, SARS-CoV-2 (exhibiting 80% and 50% homology, respectively) (Kim et al., 2020; Zhu et al., 2020) belongs to the genera beta coronavirus (family Coronaviridae in the order Nidovirales) (Enjuanes et al., 2006; Perlman & Netland, 2009), which is known to infect mammals (Li, 2016) and has manifested an illustrious capability of cross-species transmission, including humans (Menachery et al., 2017). The SARS-CoV-2 is an enveloped virus characterized by a positive-sense, single-stranded RNA genome of almost 30 kb, surrounded by a helical capsid comprised of nucleo capsid protein (N). The viral envelope is associated with three primary structural proteins viz. membrane proteins (M) and envelope proteins (E), which perform virus assembly; and spike proteins (S), which facilitate the viral attachment and thus, the virus entrance into the host cells. The large protrusions formed by spikes on the surface of the virus give it the appearance of having crowns, which, in Latin, translates to corona (Li, 2016). These shorter, sgRNA-encoded structural proteins and several accessory proteins are known to be conserved (Kim et al., 2020). The large ectodomain of the spike consists of receptor binding S1 and membrane fusion S2 subunits. For many CoVs, the S1 and S2 domains remain non-covalently linked. In β coronaviruses, the cleavage between the S1 and S2 regions is not obligatory. However, the host proteases have been observed to cause cleavage within the fusion domain (S2), which leads to irreversible conformational changes, activating the protein for membrane fusion (Zhou et al., 2020). The S2 subunit contains two regions with 4, 3 hydrophobic heptad repeats (HR), HR1 and HR2, which are conserved in sequence and position. The HR2 is located adjacent to the trans-membrane domain, while the HR1 occurs ∼170 residues upstream of HR2. The HR region has been observed to be a common motif in several viral fusion proteins. Structurally, the HR1 domain exists as a homo-trimeric coil, packing the HR2 domain (in an anti-parallel manner) in its hydrophobic grooves, thereby bringing the N-terminal fusion peptide closer to the trans-membrane anchor, further facilitating fusion due to proximity (Bosch et al., 2003). Various host receptors viz. angiotensin-converting enzyme 2 (ACE2), amino peptidase N (APN), dipeptidyl peptidase 4 (DPP4), carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), and sugar recognize S1 domain of the spike protein to render virus entry into cells (Li, 2016). Several reports have been published recently discovering inhibitors against the target via a computational methodologies, which involve the usage of FDA approved compounds and natural compounds (Wei et al., 2020), spice molecules (Rout et al., 2020), small-molecule compounds of ZINC Drug Database (Kadioglu, 2020; Wu et al., 2020) along with traditional Chinese medicine and natural products and derivatives (Wu et al., 2020) and medicinal compounds (Salman et al., 2020).
Apart from structural proteins which play a crucial role in the lifecycle of the virus, remarkable number of functional proteins categorized as non-structural proteins (Nsp’s), involved in viral replication, transcription, translation and protein modifications, and host infection are equally important (Wu et al., 2020). Among many such proteins, a well characterized distinguished drug target for SARS-Cov-2 is the 33.8 kDa, 3 C-like main protease, also called as the main protease or Nsp5 (3CLpro or Mpro or Nsp5) (Wu et al., 2020; Zhang et al., 2020). Together with the papain like proteases (Plpro), the enzyme is responsible for the processing of polyproteins produced by the viral RNA (Zhang et al., 2020). The Mpro along with Plpro cleaves the 790 kDa polyprotein1ab to generate 15 Nsp’s. The Mpro processes the polyprotein1ab at 11 sites to produce mature Nsp4-Nsp16 (Wu et al., 2020). Recently, the crystal structure of Mpro has also been reported at a resolution of 1.75 Å. The Mpro structure consists of three domains, domains I and II comprising of six-stranded anti-parallel β barrels spanning from residues 10 to 99 and 100 to 182, respectively forming the substrate-binding site between them and the domain III which is responsible for modulating the Mpro dimerization is a cluster of five helices ranging from residues 198 to 303 (Zhang et al., 2020). Due to the availability of the crystal structure and the absence of any human homologue, the Mpro is a lucrative drug target to work upon for the discovery of novel antiviral agents (Jin et al., 2020; Wu et al., 2020; Zhang et al., 2020). Recently, numerous studies have emerged against this target, discovering novel inhibitors by utilizing computational approaches which include the use of natural molecules (Aanouz et al., 2020; Das et al., 2020), commercially available drugs and zinc library (Das et al., 2020; Elmezayen, 2020; Ton et al., 2020), antiviral compounds (Khan, 2020; Kumar et al., 2020; Muralidharan, 2020), peptide molecules (Pant, 2020), generative chemistry approaches for drug design (Alex, 2020), combinatorial strategy of using anti-virals, natural products, anti-fungals, anti-protozoals and anti-nematodes (Das et al., 2020), and spice molecules (Rout et al., 2020).
Many pharmacological agents such as antiviral agent’s viz. remdesvir, ribavirin, favipiravir, chloroquine, hydroxychloroquine, oseltamivir and umifenovir; immunomodulatory agents including toclizumab, inteferons; adjunctive agents like azithromycin, corticosteroids have been repurposed for treating COVID-19. However, so far no therapy has been (Lam et al., 2020) recognized as an effective treatment against the deadly disease. It has, therefore, become the need of the hour to adopt computational approaches for drug discovery and repurpose other existing marketed drugs for its treatment. Drug repurposing via high-throughput screening of various databases is a cost-effective and time-saving approach. The present report pertains to the above-described drug discovery effort using a repurposing screening strategy to target the SARS-CoV-2 spike protein and main protease. Together, these proteins play a key role in binding to host cell receptors and causing fusion to render viral entry, determining the host range and tissue tropism, eliciting an immune response by the host, viral replication, transcription and protein processing (Li, 2016).