4c and d), obviously the propane side chain in promazine is too long. based on experimentally derived parameters, and as a theoretical reference value only when performing the docking algorithm. Thus we do not expect these values are the genuine representations of inhibitory constants and we use them primarily for qualitative comparison among the drugs/inhibitors studied here. Because the lower the em K /em i is, the greater the binding affinity is, hence HIV drug ritonavir is the compound that bind to the substrate binding site of SARS-CoV proteinase with the highest binding affinity, followed by HIV inhibitor PNU and anti-parasite drug niclosamide, and UC2 is the compound with the lowest binding affinity. Moreover, the inhibitory constants of ritonavir, PNU, niclosamide, promazine and UC2 are about 10?5, 10?3, 10?2, 10?1 and 10-fold inhibitory constant of lopinavir, respectively, if we assume that a value of 10?7 ?mol for lopinavir’s inhibitory constant is correct, the inhibitory constants of ritonavir, PNU, niclosamide, promazine and UC2 could be estimated as 10?12, 10?10, 10?9, 10?8 and 10?6 ?mol, BIBR 1532 respectively. The close views of the interactions between SARS-CoV main proteinase and these drugs/inhibitors are exhibited in Figure 4 . The results show that half of lopinavir is left outside the catalytic site Rabbit Polyclonal to Ezrin (phospho-Tyr146) (Fig. 4a), for ritonavir, the thiazole group (P1) and a benzene group (P2) are inserted into S1 and S2 specificity pockets, respectively, while another benzene side chain (P3) might be too long to fit the substrate binding pocket perfectly (Fig. 4b), there is similar situation in the inhibitor AG7088,11 which has been experimentally shown to not bind with high affinity to the SARS-CoV proteinase (http://www.nature.com/nsu/030512/030512-11.html). Thus the efficacy of lopinavir/ritonavir could be poor. Indeed, consistent with our predictions, experimental observation data indicated that both lopinavir and ritonavir individually have only a weak in vitro activity against SARS-CoV. However, the addition of lopinavir/ritonavir to ribavirin and corticosteroid treatment regimens appears to reduce incubation and mortality rates, especially when administered early.12 Similarly, the half of niclosamide or promazine is left outside the active site (Fig. 4c and d), obviously the propane side chain in promazine is too long. For PNU inhibitor, seems it can basically fit into the active cleft, except the dihydrofuran side chain is a little bit long (Fig. 4e). Finally, the inhibitor UC2 binds to a position that is slightly away from the active centre (Fig. 4f), its neopentane or methylfuran side chain is a little long and makes it unable to insert into the BIBR 1532 active pocket properly. Indeed UC2 is the compound with BIBR 1532 lowest binding affinity as mentioned above. Taken together, our study illustrates that existing drugs/inhibitors may be used as starting points for the discovery of rationally designed anti-SARS proteinase drugs. Open in a separate window Figure 4 A close view of the interactions between SARS-associated coronavirus main proteinase (white cartoon) with drugs and inhibitors (yellow ball-stick): (a) lopinavir, (b) ritonavir, (c) niclosamide, (d) promazine, (e) PNU and (f) UC2..