gms | German Medical Science

The main proteinase (M^pro, also called 3CL^pro) is responsible for the majority of cleavages of the SARS coronavirus polyproteins. It is therefore a very attractive target for therapeutic intervention. The first inhibitor suggested to be a useful starting point for the design of anti-SARS drugs, and shown to exhibit antiviral activity in vitro, is in fact directed against the main proteinase [Ref. 1].

We have determined a number of crystal structures of M^pros from different coronaviruses, including transmissible gastroenteritis virus (TGEV) [Ref. 2], human coronavirus 229E [Ref. 1], and SARS coronavirus [Ref. 3]. These were the first crystal structures of any coronavirus protein. At present, we use crystals of the SARS-CoV M^pro to screen for low-molecular-weight compounds that bind to the enzyme, and could function as potential inhibitors. Naturally, these studies yield a relatively large number of crystal structures of the free enzyme, i.e. with no inhibitor bound. We use this large body of structural information to gain insight into the structural flexibility of the M^pro.

All coronavirus main proteinases analyzed so far form dimers at slightly elevated concentrations in solution and in the crystal. In the case of the SARS-CoV, one of the subunits in the dimer is in a catalytically competent conformation, while the other is not, when the enzyme has been crystallized at pH 6.0 [Ref. 3]. At higher pH values, however, both monomers are in the active conformation. This earlier observation of ours [Ref. 3] has been confirmed in the present structures. The pH-dependent conformational transition and its possible biological significance will be discussed. Furthermore, through a detailed comparison of a large number of crystal structures of the SARS-CoV main proteinase, as well as comparisons to the homologous enzymes of TGEV and HCoV 229E, regions of higher flexibility of the protein have been identified. It is found that at least two regions near the substrate-binding site of the proteinase exhibit much-above-average flexibilty. Such data will therefore be useful in rational drug design efforts.