Design and evaluation of substrate-based octapeptide and non substrate-based tetrapeptide inhibitors of dengue virus NS2B–NS3 proteases

Abstract

A series of 45 peptide inhibitors was designed, synthesized, and evaluated against the NS2B-NS3 proteases of the four subtypes of dengue virus, DEN-1-4. The design was based on proteochemometric models for Michaelis (Km) and cleavage rate constants (kcat) of protease substrates. This led first to octapeptides showing submicromolar or low micromolar inhibitory activities on the four proteases. Stepwise removal of cationic substrate non-prime side residues and variations in the prime side sequence resulted finally in an uncharged tetrapeptide, WYCW-NH2, with inhibitory Ki values of 4.2, 4.8, 24.4, and 11.2 μM for the DEN-1-4 proteases, respectively. Analysis of the inhibition data by proteochemometric modeling suggested the possibility for different binding poses of the shortened peptides compared to the octapeptides, which was supported by results of docking of WYCW-NH2 into the X-ray structure of DEN-3 protease.

Proteochemometric modeling in a Bayesian framework

“…In the case of the dengue virus dataset, GP models show better predictive ability than those reported by Prusis et al , [41] as $Q_{\text{italicext}}^2$ value of 0.92 is obtained here (Additional file 1: Table S3) for the best GP model based on the Bessel kernel. The optimization of the noise variance, ${\sigma }_d^2$, as an hyperparameter during the training process led to a value of 0.27 log units, similar to the values of about 0.3 log units reported by Prusis et al [61] in a recent study with similar experimental setup.…”

Inhibitors compounds of the flavivirus replication process

“…A set of 45 inhibitor peptides was designed, synthesized, and evaluated against the dengue virus NS2B-NS3 protease, finding that the uncharged WCW-NH2 tetrapeptide inhibits protease in the four serotypes [50]. …”

“…Further work is required to determine the interaction mechanism.Compound 32 (keto amides)DENVSteuer et al, 2011 [49]An inhibitory effect on DENV replication was determined in a dose-dependent manner. Cytotoxicity in cell culture is unknown.Peptide WCW-NH2DENVPrusis et al, 2013 [50]Peptide WCW-NH2 inhibited protease in the four serotypes.ARDP0006 and ARDP0009DENVTonlimson and Watowich, 2011 [51]ARDP0006 and ARDP0009 inhibited DENV-2 virus replication in cell culture. Promising compounds for future research.AprotininDENVNoble et al, 2010 [53]Aprotinin envelops the enzyme and prevents the substrate from accessing the protease active site.NS3- HelicasEHalogenated benztriolesWNVSampath and Padmanabhan 2009 [3]Halogenated benztrioles were good, and selective inhibitor of the West Nile virus.IvermectinDENV, JEV, YFVMastrangelo et al, 2012 [55]; Sweeney et al, 2015 [57]Promising compound as the first specific therapy against flaviviruses (patent application EP2010/065880).ST-610DENVLim et al, 2013a [38]; Sweeney et al, 2015 [57]ST610 potently and selectively inhibited all four DENV serotypes in cell culture.…”

Targeting Host Factors to Treat West Nile and Dengue Viral Infections

“…The cyclohexenyl chalcone derivatives of natural flavonoids were also found to inhibit dengue NS3 protease [75]. Recently an uncharged tetrapeptide, WYCW-NH2, has been shown to potently inhibit DENV1-4 proteases [76] and functionalized 1,2-benzisothiazol-3(2H)-one-1,3,4-oxadiazole hybrid derivatives were shown to inhibit DENV2 and WNV proteases [77]. Hepatitis C virus (HCV) (not a flavivirus but a member of the Flaviviridae family) helicase has been inhibited with quinolone derivatives, which also inhibit the HCV RdRp activity [78] and some of these derivatives could potentially inhibit DENV helicases [79].…”