title: Design and Validation of Novel Chikungunya Virus Protease Inhibitors.
abstract: Chikungunya virus (CHIKV; genus Alphavirus) is the causative agent of chikungunya fever. CHIKV replication can be inhibited by some broad-spectrum antiviral compounds; in contrast, there is very little information about compounds specifically inhibiting the enzymatic activities of CHIKV replication proteins. These proteins are translated in the form of a nonstructural (ns) P1234 polyprotein precursor from the CHIKV positive-strand RNA genome. Active forms of replicase enzymes are generated using the autoproteolytic activity of nsP2. The available three-dimensional (3D) structure of nsP2 protease has made it a target for in silico drug design; however, there is thus far little evidence that the designed compounds indeed inhibit the protease activity of nsP2 and/or suppress CHIKV replication. In this study, a set of 12 compounds, predicted to interact with the active center of nsP2 protease, was designed using target-based modeling. The majority of these compounds were shown to inhibit the ability of nsP2 to process recombinant protein and synthetic peptide substrates. Furthermore, all compounds found to be active in these cell-free assays also suppressed CHIKV replication in cell culture, the 50% effective concentration (EC50) of the most potent inhibitor being ∼1.5 μM. Analysis of stereoisomers of one compound revealed that inhibition of both the nsP2 protease activity and CHIKV replication depended on the conformation of the inhibitor. Combining the data obtained from different assays also indicates that some of the analyzed compounds may suppress CHIKV replication using more than one mechanism.
authors.affiliation: Institute of Technology, University of Tartu, Tartu, Estonia.
authors.forename: Pratyush Kumar
authors.initials: PK
authors.lastname: Das
authors.affiliation: Institute of Chemistry, University of Tartu, Tartu, Estonia.
authors.forename: Laura
authors.initials: L
authors.lastname: Puusepp
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Finny S
authors.initials: FS
authors.lastname: Varghese
authors.affiliation: Institute of Technology, University of Tartu, Tartu, Estonia.
authors.forename: Age
authors.initials: A
authors.lastname: Utt
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Tero
authors.initials: T
authors.lastname: Ahola
authors.affiliation: Department of Chemistry, Tallinn University of Technology, Tallinn, Estonia.
authors.forename: Dzmitry G
authors.initials: DG
authors.lastname: Kananovich
authors.affiliation: Department of Chemistry, Tallinn University of Technology, Tallinn, Estonia.
authors.forename: Margus
authors.initials: M
authors.lastname: Lopp
authors.affiliation: Institute of Technology, University of Tartu, Tartu, Estonia andres.merits@ut.ee mati.karelson@ut.ee.
authors.forename: Andres
authors.initials: A
authors.lastname: Merits
authors.affiliation: Institute of Chemistry, University of Tartu, Tartu, Estonia andres.merits@ut.ee mati.karelson@ut.ee.
authors.forename: Mati
authors.initials: M
authors.lastname: Karelson
mesh_terms: D000818:Animals; D000998:Antiviral Agents / Q000138:chemical synthesis*; D002264:Carboxylic Acids / Q000138:chemical synthesis / Q000494:pharmacology; D020134:Catalytic Domain; D002460:Cell Line; D002646:Chikungunya virus / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics / Q000254:growth & development; D006224:Cricetinae; D018360:Crystallography, X-Ray; D003521:Cyclopropanes / Q000138:chemical synthesis / Q000494:pharmacology; D003546:Cysteine Endopeptidases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015195:Drug Design; D004847:Epithelial Cells / Q000187:drug effects / Q000821:virology; D016679:Genome, Viral; D020128:Inhibitory Concentration 50; D062105:Molecular Docking Simulation; D020815:Polyproteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011480:Protease Inhibitors / Q000138:chemical synthesis* / Q000494:pharmacology; D020365:RNA Helicases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013237:Stereoisomerism; D013329:Structure-Activity Relationship; D014779:Virus Replication / Q000187:drug effects
chemical_list: D000998:Antiviral Agents; D002264:Carboxylic Acids; D003521:Cyclopropanes; D020815:Polyproteins; D011480:Protease Inhibitors; D003546:Cysteine Endopeptidases; C078306:nsP2 proteinase; D020365:RNA Helicases