A multiplex method for rapidly identifying viral protease inhibitors

Seo Jung Hong; Samuel J. Resnick; Sho Iketani; Ji Won Cha; Benjamin Alexander Albert; Christopher T. Fazekas; Ching Wen Chang; Hengrui Liu; Shlomi Dagan; Michael R. Abagyan; Pavla Fajtová; Bruce Culbertson; Brooklyn Brace; Eswar R. Reddem; Farhad Forouhar; J. Fraser Glickman; James M. Balkovec; Brent R. Stockwell; Lawrence Shapiro; Anthony J. O’Donoghue; Yosef Sabo; Joel S. Freundlich; David D. Ho; Alejandro Chavez

doi:10.1038/s44320-024-00082-1

A multiplex method for rapidly identifying viral protease inhibitors

Seo Jung Hong
, Samuel J. Resnick
, Sho Iketani
, Ji Won Cha
, Benjamin Alexander Albert
, Christopher T. Fazekas
, Ching Wen Chang
, Hengrui Liu
, Shlomi Dagan
, Michael R. Abagyan
, Pavla Fajtová
, Bruce Culbertson
, Brooklyn Brace
, Eswar R. Reddem
, Farhad Forouhar
, J. Fraser Glickman
, James M. Balkovec
, Brent R. Stockwell
, Lawrence Shapiro
, Anthony J. O’Donoghue

Yosef Sabo, Joel S. Freundlich, David D. Ho, Alejandro Chavez

Center for Discovery and Innovation

Hackensack Meridian School of Medicine

Research output: Contribution to journal › Article › peer-review

Abstract

With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor’s potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.

Original language	English
Article number	2016
Pages (from-to)	158-172
Number of pages	15
Journal	Molecular Systems Biology
Volume	21
Issue number	2
DOIs	https://doi.org/10.1038/s44320-024-00082-1
State	Published - Feb 3 2025

ASJC Scopus subject areas

Information Systems
General Immunology and Microbiology
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences
Computational Theory and Mathematics
Applied Mathematics

Keywords

Antiviral
Biosensors
Drug Screening
High-Throughput
Multiplex

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10.1038/s44320-024-00082-1

Cite this

Hong, S. J., Resnick, S. J., Iketani, S., Cha, J. W., Albert, B. A., Fazekas, C. T., Chang, C. W., Liu, H., Dagan, S., Abagyan, M. R., Fajtová, P., Culbertson, B., Brace, B., Reddem, E. R., Forouhar, F., Glickman, J. F., Balkovec, J. M., Stockwell, B. R., Shapiro, L., ... Chavez, A. (2025). A multiplex method for rapidly identifying viral protease inhibitors. Molecular Systems Biology, 21(2), 158-172. Article 2016. https://doi.org/10.1038/s44320-024-00082-1

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abstract = "With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor{\textquoteright}s potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.",

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author = "Hong, \{Seo Jung\} and Resnick, \{Samuel J.\} and Sho Iketani and Cha, \{Ji Won\} and Albert, \{Benjamin Alexander\} and Fazekas, \{Christopher T.\} and Chang, \{Ching Wen\} and Hengrui Liu and Shlomi Dagan and Abagyan, \{Michael R.\} and Pavla Fajtov{\'a} and Bruce Culbertson and Brooklyn Brace and Reddem, \{Eswar R.\} and Farhad Forouhar and Glickman, \{J. Fraser\} and Balkovec, \{James M.\} and Stockwell, \{Brent R.\} and Lawrence Shapiro and O{\textquoteright}Donoghue, \{Anthony J.\} and Yosef Sabo and Freundlich, \{Joel S.\} and Ho, \{David D.\} and Alejandro Chavez",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

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doi = "10.1038/s44320-024-00082-1",

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Hong, SJ, Resnick, SJ, Iketani, S, Cha, JW, Albert, BA, Fazekas, CT, Chang, CW, Liu, H, Dagan, S, Abagyan, MR, Fajtová, P, Culbertson, B, Brace, B, Reddem, ER, Forouhar, F, Glickman, JF, Balkovec, JM, Stockwell, BR, Shapiro, L, O’Donoghue, AJ, Sabo, Y, Freundlich, JS, Ho, DD & Chavez, A 2025, 'A multiplex method for rapidly identifying viral protease inhibitors', Molecular Systems Biology, vol. 21, no. 2, 2016, pp. 158-172. https://doi.org/10.1038/s44320-024-00082-1

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AU - Hong, Seo Jung

AU - Resnick, Samuel J.

AU - Iketani, Sho

AU - Cha, Ji Won

AU - Albert, Benjamin Alexander

AU - Fazekas, Christopher T.

AU - Chang, Ching Wen

AU - Liu, Hengrui

AU - Dagan, Shlomi

AU - Abagyan, Michael R.

AU - Fajtová, Pavla

AU - Culbertson, Bruce

AU - Brace, Brooklyn

AU - Reddem, Eswar R.

AU - Forouhar, Farhad

AU - Glickman, J. Fraser

AU - Balkovec, James M.

AU - Stockwell, Brent R.

AU - Shapiro, Lawrence

AU - O’Donoghue, Anthony J.

AU - Sabo, Yosef

AU - Freundlich, Joel S.

AU - Ho, David D.

AU - Chavez, Alejandro

PY - 2025/2/3

Y1 - 2025/2/3

N2 - With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor’s potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.

AB - With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor’s potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.

KW - Antiviral

KW - Biosensors

KW - Drug Screening

KW - High-Throughput

KW - Multiplex

UR - https://www.scopus.com/pages/publications/85214255898

U2 - 10.1038/s44320-024-00082-1

DO - 10.1038/s44320-024-00082-1

M3 - Article

C2 - 39762652

SN - 1744-4292

VL - 21

SP - 158

EP - 172

JO - Molecular Systems Biology

JF - Molecular Systems Biology

IS - 2

M1 - 2016

ER -

A multiplex method for rapidly identifying viral protease inhibitors

Abstract

ASJC Scopus subject areas

Keywords

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