Combined crystallographic fragment screening and deep mutational scanning enable discovery of Zika virus NS2B-NS3 protease inhibitors
Abstract
Abstract The Zika viral protease NS2B-NS3 is essential for the cleavage of viral polyprotein precursor into individual structural and non-structural (NS) proteins and is therefore an attractive drug target. Generation of a robust crystal system of co-expressed NS2B-NS3 protease has enabled us to perform a crystallographic fragment screening campaign with 1076 fragments. 46 fragments with diverse scaffolds are identified to bind in the active site of the protease, with another 6 fragments observed in a potential allosteric site. To identify binding sites that are intolerant to mutation and thus suppress the outgrowth of viruses resistant to inhibitors developed from bound fragments, we perform deep mutational scanning of the NS2B-NS3 protease. Merging fragment hits yields an extensive set of ‘mergers’, defined as synthetically accessible compounds that recapitulate constellations of observed fragment-protein interactions. In addition, the highly sociable fragment hits enable rapid exploration of chemical space via algorithmic calculation and thus yield diverse possible starting points. In this work, we maximally explore the binding opportunities to NS2B-NS3 protease, facilitating its resistance-resilient antiviral development.
Article Details
Authors (36)
Xiaomin Ni
Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
R. Blake Richardson
Andre Schutzer Godoy
Matteo P. Ferla
Caroline Kikawa
Human Biology Division, Fred Hutchinson Cancer Center
Jenke Scheen
William W. Hannon
Eda Capkin
Noa Lahav
Blake H. Balcomb
Peter G. Marples
Michael Fairhead
Siyi Wang
State Key Laboratory of Advanced Fiber Materials, Key Laboratory of Science and Technology of Eco-Textile, Ministry of Education, College of Chemistry and Chemical Engineering
Eleanor P. Williams
Charles W. E. Tomlinson
Department of Biology, University of York
Jasmin C. Aschenbrenner
Ryan M. Lithgo
Max Winokan
Charline Giroud
Isabela Dolci
Rafaela Sachetto Fernandes
Glaucius Oliva
Anu V. Chandran
Mary-Ann Xavier
Martin A. Walsh
Warren Thompson
Jesse D. Bloom
Nathaniel T. Kenton
Alpha A. Lee
Annette von Delft
Haim Barr
Karla Kirkegaard
Violetta L. Horton Professor, Departments of Genetics and of Microbiology and Immunology, Stanford University School of Medicine
Lizbé Koekemoer
Daren Fearon
Matthew J. Evans
School of Chemistry, Monash University, P.O. Box 23, Melbourne, Victoria 3800, Australia
Frank von Delft