Mechanisms of activation and inhibition of Zika virus NS2B-NS3 protease

Chen, Xia; Yang, Kailin; Wu, Chunlei; Chen, Cheng; Hu, Chengping; Buzovetsky, Olga; Wang, Zefang; Ji, Xiaoyun; Xiong, Yong; Yang, Haitao

doi:10.1038/cr.2016.116

Cited by 81 publications

(90 citation statements)

References 15 publications

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“…In contrast, the catalytically inactive NS2B-NS3pro S135A mutant exhibited <5% of the activity of the WT construct. Our results correlate well with the data by Chen et al (2016) who also reported the cleavage of the Arg/Lys-rich substrate by ZIKV protease.…”

Section: Resultssupporting

confidence: 93%

Characterization of the Zika virus two-component NS2B-NS3 protease and structure-assisted identification of allosteric small-molecule antagonists

et al. 2017

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The recent re-emergence of Zika virus (ZIKV)1, a member of the Flaviviridae family, has become a global emergency. Currently, there are no effective methods of preventing or treating ZIKV infection, which causes severe neuroimmunopathology and is particularly harmful to the developing fetuses of infected pregnant women. However, the pathology induced by ZIKV is unique among flaviviruses, and knowledge of the biology of other family members cannot easily be extrapolated to ZIKV. Thus, structure-function studies of ZIKV proteins are urgently needed to facilitate the development of effective preventative and therapeutic agents. Like other flaviviruses, ZIKV expresses an NS2B-NS3 protease, which consists of the NS2B cofactor and the NS3 protease domain and is essential for cleavage of the ZIKV polyprotein precursor and generation of fully functional viral proteins. Here, we report the enzymatic characterization of ZIKV protease, and we identify structural scaffolds for allosteric small-molecule inhibitors of this protease. Molecular modeling of the protease-inhibitor complexes suggests that these compounds bind to the druggable cavity in the NS2B-NS3 protease interface and affect productive interactions of the protease domain with its cofactor. The most potent compound demonstrated efficient inhibition of ZIKV propagation in vitro in human fetal neural progenitor cells and in vivo in SJL mice. The inhibitory scaffolds could be further developed into valuable research reagents and, ultimately, provide a roadmap for the selection of efficient inhibitors of ZIKV infection.

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Section: Resultssupporting

confidence: 93%

Characterization of the Zika virus two-component NS2B-NS3 protease and structure-assisted identification of allosteric small-molecule antagonists

et al. 2017

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“…Recent structural studies on ZIKV protease have demonstrated that free bZiPro exists in the closed conformation . Interestingly, the crystal structures of free gZiPro adopt a similar open conformation as reported for the proteases of DENV and WNV. The difference between bZiPro and gZiPro is that the latter contains an artificial Gly 4 ‐Ser‐Gly 4 linker.…”

mentioning

confidence: 61%

Structural characterization of the linked NS2B‐NS3 protease of Zika virus

Phoo

Loh

et al. 2017

FEBS Letters

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The Zika virus (ZIKV) NS2B-NS3 protease is an important drug target. The conventional flaviviral protease constructs used for structural studies contain the NS2B cofactor region linked to the NS3 protease domain via a glycine-rich flexible linker. Here, we examined the structural dynamics of this conventional Zika protease (gZiPro) using NMR spectroscopy. Although the glycine-rich linker in gZiPro does not alter the overall folding of the protease in solution, gZiPro is not homogenous in ion exchange chromatography. Compared to the unlinked protease construct, the artificial linker affects the chemical environment of many residues including H51 in the catalytic triad. Our study provides a direct comparison of ZIKV protease constructs with and without an artificial linker.

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“…It is also surprised to find that although the dimeric SARS-CoV 3C-like protease has a very large dimeric interface area of over 1000 Å 2 , one single interfacial mutation such as Gl1A within the chymotrypsin fold (Chen et al, 2016;Hu et al, 2009), and R298A within the extra domain is sufficient to eliminate the dimerization. Most amazingly, it has been also shown that the residues for controlling dimerization are not just limited to the interfacial ones, because residues located away from the dimerization interface was also identified to be crucial for dimerization (Barrila et al, 2006(Barrila et al, , 2010.…”

Section: Inactivation Of the Catalytic Machinery By Structurally-drivmentioning

confidence: 99%

Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses

Lim

Gupta

Roy

et al. 2019

Progress in Biophysics and Molecular Biology

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Coronavirus 3C-like and Flavivirus NS2B-NS3 proteases utilize the chymotrypsin fold to harbor their catalytic machineries but also contain additional domains/co-factors. Over the past decade, we aimed to decipher how the extra domains/co-factors mediate the catalytic machineries of SARS 3C-like, Dengue and Zika NS2B-NS3 proteases by characterizing their folding, structures, dynamics and inhibition with NMR, X-ray crystallography and MD simulations, and the results revealed: 1) the chymotrypsin fold of the SARS 3C-like protease can independently fold, while, by contrast, those of Dengue and Zika proteases lack the intrinsic capacity to fold without co-factors. 2) Mutations on the extra domain of SARS 3C-like protease can transform the active catalytic machinery into the inactive collapsed state by structurally-driven allostery. 3) Amazingly, even without detectable structural changes, mutations on the extra domain are sufficient to either inactivate or enhance the catalytic machinery of SARS 3C-like protease by dynamically-driven allostery. 4) Global networks of correlated motions have been identified: for SARS 3C-like protease, N214A inactivates the catalytic machinery by decoupling the network, while STI/A and STIF/A enhance by altering the patterns of the network. The global networks of Dengue and Zika proteases are coordinated by their NS2B-cofactors. 5) Natural products were identified to allosterically inhibit Zika and Dengue proteases through binding a pocket on the back of the active site. Therefore, by introducing extra domains/cofactors, nature develops diverse strategies to regulate the catalytic machinery embedded on the chymotrypsin fold through folding, structurally- and dynamically-driven allostery, all of which might be exploited to develop antiviral drugs.

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Mechanisms of activation and inhibition of Zika virus NS2B-NS3 protease

Cited by 81 publications

References 15 publications

Characterization of the Zika virus two-component NS2B-NS3 protease and structure-assisted identification of allosteric small-molecule antagonists

Characterization of the Zika virus two-component NS2B-NS3 protease and structure-assisted identification of allosteric small-molecule antagonists

Structural characterization of the linked NS2B‐NS3 protease of Zika virus

Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses

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