De Novo Discovery of Nonstandard Macrocyclic Peptides as Noncompetitive Inhibitors of the Zika Virus NS2B-NS3 Protease

Abstract

The Zika virus presents a major public health concern due to severe fetal neurological disorders associated with infections in pregnant women. In addition to vaccine development, the discovery of selective antiviral drugs is essential to combat future epidemic Zika virus outbreaks. The Zika virus NS2B-NS3 protease, which performs replication-critical cleavages of the viral polyprotein, is a promising drug target. We report the first macrocyclic peptide-based inhibitors of the NS2B-NS3 protease, discovered de novo through in vitro display screening of a genetically reprogrammed library including noncanonical residues. Six compounds were selected, resynthesized, and isolated, all of which displayed affinities in the low nanomolar concentration range. Five compounds showed significant protease inhibition. Two of these were validated as hits with submicromolar inhibition constants and selectivity toward Zika over the related proteases from dengue and West Nile viruses. The compounds were characterized as noncompetitive inhibitors, suggesting allosteric inhibition.

Structure‐guided screening of chemical database to identify NS3‐NS2B inhibitors for effective therapeutic application in dengue infection

“…Hence, to overcome such situation presently, available more resources, much faster, and advance scientific techniques need to be adopted and explored. Earlier, a number of studies have proposed various traditional and specific methods for the identification of different chemical entities and demonstrated their selective inhibition mechanism and inhibitory efficacy against NS3‐NS2B protease complex at different levels …”

Experimental and computational studies on molecular mechanism by which Curcumin allosterically inhibits Dengue protease

“…The unique NS2B-NS3 serine proteases are highly conserved in Flaviviruses and have been established as a key target for discovery/design of inhibitors to treat Flavivirus infections (40)(41)(42)(43). Currently, most campaigns targeted their active sites for the discovery/design of competitive inhibitors (22,23).…”

“…In this context, one promising solution is to discover/design of their allosteric inhibitors which bind to the cavities other than the active sites. Nevertheless, due to the general challenge in understanding the mechanisms for allosteric processes, only a few attempts were devoted to developing allosteric inhibitors of the Flaviviral proteases (18,19,21,22,(40)(41)(42)(43). In particular, so far no complete mechanism has been elucidated for the allosteric inhibition on any Flaviviral NS2B-NS3 proteases.…”

Structural basis for binding mechanism of human serum albumin complexed with cyclic peptide dalbavancin

“…6,7 Of note, the screening of cyclic peptides containing natural as well as non-natural amino acids from a large number of combinations enabled the identification of peptides showing a high binding capacity to various target proteins. [8][9][10][11] While conventional linear peptides are highly unstable against gastric acid pH, cyclization allows the overcoming of this problem suggesting that cyclic peptides may be orally 4 administered for therapeutic purposes. Furthermore, although conventional peptide pharmaceuticals are challenged by proteolytic degradation, the main chain structure modifications and unnatural amino acids contained in cyclic peptides render them less susceptible to degradation.…”