Peptides as Therapeutic Agents for Dengue Virus

Chew, Miaw-Fang; Poh, Keat-Seong; Poh, Chit-Laa

On the other hand, the N-benzoyl capped tetrapeptide sequence (Nle-Lys-Arg-Arg) was previously shown to be the favoured amino acid residues for the S1-S4 subsites of the NS2B-NS3 protease binding cavity [165, 166] . Yusof et al. (2000) showed that the Arg-Arg residues in the P1 and P2 positions located next to the cleavage site were responsible for the high binding affinity against the protease, while Li et al. (2005) found that Lys and Nle (norleucine) in the P3 and P4 positions were essential for high binding affinity [165, 166] . Interestingly, Nitsche et al. (2012) showed that the removal of an arginine resulted in better inhibitory activity [167] . Nitsche et al. (2012) showed that a retro-peptide based on the sequence R-Arg-Lys-Nle-NH2 with an arylcyano-acrylamide group as N-terminal cap possessed the best inhibition activity at Ki value of 4.9 µM [167] . It is hypothesized that the arylcyanoacrylamide moiety mimic the first Arg in the P1 position while the Arg-Lys-Nle tripeptide bound to other protein pockets of NS2B-NS3 protease. Unfortunately, even though the drug candidate possessed good binding ability, it did not have significant antiviral activity in the cell culture against DENV. Therefore, Nitsche et al. (2013) further optimized the lead candidate via structure activity relationship assays in a subsequent study and successfully developed a thiazolidinedione-based peptide hybrid (hybrid 24b) containing a hydrophobic group with a better Ki value of 1.5 µM [168] . Nonetheless, drugs designed via structure-based activity faced the limitation due to the differences in protease structures derived from crystallization versus the in vivo protease structures, thereby the antiviral candidate which has high binding affinity against the crystallized protease structure might not have the same binding affinity against the protease in vivo. To overcome this challenge, Nitsche et al. (2013) further modified the N-terminal cap moieties and incorporated membrane-permeable peptide to increase the potential antiviral activities [168] . The peptide hybrid which possessed the best antiviral activity in the cell culture was found to be the rhodanine-based peptide hybrid 10a with an EC50 value of 16.7 µM and Ki value of 9.3 µM. From the study, the Arg-Lys residues were found to be sufficient to create high target affinity with Ki values below 2 µM.