Molecular Advances in Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV)

Chow, Ken Yan Ching; Hon, Chung Chau; Hui, Raymond Kin Hi; Wong, Raymond Tsz Yeung; Yip, Chi Wai; Zeng, Fanya; Leung, Frederick Chi Ching

Concerning the candidate target for vaccine development, the S1 unit of the spike proteins has been identified as the host protective antigen and used as a vaccine candidate in other coronaviruses (110 ) . An extensive structural analysis of the corresponding pro- The branch length shows the genetic distance with reference to the horizontal scale bar. All sample names were hidden for the convenience of display, except the index case isolate HKU-33 (gray) and subcluster transition isolates (dark). The locations of these isolates on the tree were pinpointed by dots besides their names. The hypothetical common ancestors of the subclusters were highlighted as described in the right bottom of the figure. tein in SARS is thus desirable. With the identification of the SARS-CoV functional receptor (30 ) and the mapping of the receptor-binding domain on the spike protein (31 ) , subunit vaccine targeting the receptorbinding domain and the preparation of killed or attenuated vaccine using ACE2 expression cell line may be promising (30 ) . Antiviral drugs represent an alternative anti-SARS strategy to vaccination. Inhibiting chemicals targeting the SARS-CoV replication-related proteins were considered as anti-SARS-CoV drug candidates, e.g. inhibition the enzymatic activity of 3CL PRO . An extensive structural analysis of 3CL PRO encoded from nsp5 on ORF 1a was performed (28 , 111 ) . The 3CL PRO structure showed a considerable degree of conservation of the substrate-binding sites, with the evidence that it could retain its proteolytic activity upon TGEV (transmissible gastroenteritis virus) main proteinase (111 ) , though another group mentioned that the inactive property of the enzyme might exist in vitro (112 ) . From this result, these authors suggested that the use of rhinovirus 3C PRO inhibitor might be useful in anti-SARS therapy. Two months later, a research group from the US conducted a study on the interaction of two chemicals (KZ7088 and the AVLQSGFR octapeptide) with 3CL PRO (113 ), further highlighting the importance of the main proteinase as a target for anti-viral drug design. Fan et al (114 ) provided valuable additional information, and concluded that only the dimeric form of the 3CL PRO is active and that the proteinase-substrate interaction can be speeded up if more beta-sheet-like structure is involved in the substrate. Recently the crystal structure of 3CL PRO was reported by Yang et al (115 ) . The 3CL PRO crystal underwent conformational changes under different pH conditions while complexing with the specific inhibitor at the same time. A serine-protease fold with a Cys-His at the active site was recognized. On the other hand, the modeling of the structure of 20-O-MT domain located at nsp16 was proposed by von Grotthuss et al (116 ) using the 3D jury system with high reliability (3D jury score >100). The conservation of the unique tetrad residues K-D-K-E of the domain assigned a proposed mRNA cap methylation function of this domain, suggesting an alternative target for anti-viral drug design. In addition to main proteases, blocking the virus entry should be considered as well. Structural analysis of the S2 domain of the SARS-CoV S protein, which plays a role in fusion of the virus with host cell, revealed a conservation of sequence motifs with the wellstudied gp41 protein of HIV-1 and other viruses with class I transmembrane domain (27 ) . Such a structure may be another target for drug design.