About Coronavirus Proteins
The Coronavirus Spike protein (S Protein) is one of four major structural proteins covering the surface of each virion. The Spike protein is a highly glycosylated, type I transmembrane protein responsible for host cell entry. Structurally, there are two domains, S1 and S2, that play major roles in receptor binding and membrane fusion. Within the N-terminal S1 domain is the receptor binding domain (Spike RBD protein). The Spike RBD binds to the host cell and initiates viral infection. The SARS-CoV-2 Spike RBD tightly associates with human ACE-2. Once the Spike S1 domain binds to its host receptor, conformational changes occur in the Spike S2 domain allowing for membrane attachment and eventually transfer of the nucleocapsid into the cell. Because of its essential role during Coronavirus infection, the Spike protein is major therapeutic target.
The Coronavirus Nucleocapsid protein (N Protein) is a multifunctional RNA-binding protein required for viral RNA transcription, replication, and packaging. The Nucleocapsid protein consists of three domains, an N-terminal RNA-binding domain, a central intrinsically disordered region, followed by a C-terminal dimerization domain. The RNA-binding domain contains multiple positively charged binding surfaces that form charged interactions with RNA promoting its helical arrangement. The Nucleocapsid protein is highly antigenic making it an attractive target for vaccine development and serological assays.
The Coronavirus Papain-like protease (PLPro) is one of several nonstructural proteins (nsps) and along with 3CL Protease, is responsible for processing of viral proteins into functional, mature subunits during maturation. For example, PLPro cleaves a site at the amino-terminal end of the viral replicase region. In addition to its role in viral protein maturation, Papain-like protease exhibits both a deubiquitinating and deISG15ylating activity. In vivo, this protease antagonizes innate immunity by acting on IFN beta and NF- kappa B signaling pathways. Purified PLPro is used in vitro with polyubiquitin substrates demonstrating a strong preference for K48 linkages.
The Coronavirus 3CL protease (3CLpro) is the other main protease in addition to the Papain-like protease and is required for processing of viral polypeptides into distinct, functional proteins. The SARS-CoV-2 3CL Protease is a C30-type cysteine protease located within the non-structural proteins 3 (NS3) region of the viral polypeptide. Analysis of the Coronavirus genome reveals at least 11 sites of cleavage for the 3CL Protease, many containing the amino acid sequence LQ[S/A/G]. In addition to the Papain-Like Protease, 3CLpro presents a promising therapeutic target for COVID-19. One attractive advantage of 3CLpro is that no human proteases are known to have a similar cleavage specificity making inhibitors of 3CLpro unlikely to cause mechanism-based toxicity.