A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
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Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption 1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Recent proteomics studies have focused on SARS-CoV-2, uncovering additional potential therapeutic targets.
“Building on this knowledge of coronavirus infection, recent proteomics studies have focused on SARS-CoV-2, uncovering additional potential therapeutic targets154,155.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [155]
Affinity-MS interactome studies examined 26 of 29 total SARS-CoV-2 proteins expressed within HEK293T human cells, suggesting 69 existing drugs merit further investigation.
“Additionally, affinity-MS interactome studies examined 26 of 29 total SARS-CoV-2 proteins expressed within HEK293T human cells155, suggesting 69 existing drugs merit further investigation.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [155]
A main evasion strategy seems to be blocking type I interferon responses at several steps, such as viral RNA recognition, nuclear translocation of inflammatory transcription factors, and STAT1/STAT2 phosphorylation.
“A predominant strategy appears to be the inhibition of the type I interferon response58–60 at multiple points, including impaired recognition of viral RNA61,62, decreased nuclear translocation of pro-inflammatory transcription factors (such as IRF3, IRF7 and STAT1)61,63 and suppression of STAT1 and STAT2 phosphorylation64,65.”
From Immunological mechanisms of vaccine-induced protection against COVID-19 in humans (2021) · cites this paper as [62]
Interaction mapping suggested that NSP13 interacts with TBK1, NSP15 with NRDP1, ORF9b with TOMM70, and ORF6 with KPNA2 or the IFN-induced NUP98-RAE1 nuclear export complex, all antagonizing IFN signaling.
“Interaction mapping further suggested that NSP13 interacts with TBK1, NSP15 with NRDP1 (an E3 ubiquitin ligase controlling the balance between JAK2-associated cytokine receptor degradation and ectodomain shedding), ORF9b with TOMM70 (an important receptor of the outer mitochondrial membrane), and ORF6 with either KPNA2 or the IFN-induced NUP98-RAE1 nuclear export complex, which are both involved”
From COVID-19 and the human innate immune system (2021) · cites this paper as Gordon et al., 2020
NSP16 suppresses global mRNA splicing and diminishes recognition of viral RNA by intracellular helicase receptors; NSP1 inhibits mRNA translation by binding 18S ribosomal RNA; NSP8 and NSP9 interfere with protein trafficking to the cell membrane; all three mechanisms independently reduce type I IFN production.
“SARS-CoV-2-derived non-structural protein 16 (NSP16) suppresses global mRNA splicing and diminishes recognition of viral RNA by intracellular helicase receptors, NSP1 leads to global inhibition of mRNA translation by binding to the 18S ribosomal RNA in the mRNA entry channel, and NSP8 and NSP9 interfere with protein trafficking to the cell membrane; all three mechanisms independently leading to”
From COVID-19 and the human innate immune system (2021) · cites this paper as Gordon et al., 2020
S1R agonism might prevent the cytokine storm seen in severe COVID-19.
“Second, numerous antidepressants are S1R agonists [13], which might prevent the cytokine storm observed in severe COVID-19 [3].”
A large PPI study in SARS-CoV-2-infected cells revealed several potential druggable pathways and proteins that may be exploited by repurposing inhibitors and that could potentially be addressed by SARS-CoV-2-targeting PROTAC molecules.
“A large PPI study in SARS-CoV-2-infected cells revealed several potential druggable pathways and proteins that may be exploited by repurposing inhibitors199, and that could potentially be addressed by SARS-CoV-2-targeting PROTAC molecules.”
From PROTAC targeted protein degraders: the past is prologue (2022) · cites this paper as [199]
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Self-citationScoring Large‐Scale Affinity Purification Mass Spectrometry Datasets with MiST
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Self-citationHuman sigma-1 receptor bound to (+)-pentazocine
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TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes
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Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19
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A high-stringency blueprint of the human proteome
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Self-citationA critical overview of computational approaches employed for COVID-19 drug discovery
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“While haloperidol carries theoretical risk of EPS, it is worth noting that the IV form is rarely associated with EPS, add haloperidol is now on the list of medications being studied as a treatment for SARS-CoV-2 because of its effects on sigma receptors [33].”
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Self-citationProfiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs
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Infectious agents and Alzheimer's disease
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Network analysis reveals rare disease signatures across multiple levels of biological organization
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SARS-CoV-2 membrane protein causes the mitochondrial apoptosis and pulmonary edema via targeting BOK
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Host mitochondrial transcriptome response to SARS-CoV-2 in multiple cell models and clinical samples
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Self-citationInvestigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections
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Mapping the multiscale structure of biological systems
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Self-citationCell deaths: Involvement in the pathogenesis and intervention therapy of COVID-19
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Expert-Augmented computational drug repurposing identified baricitinib as a treatment for COVID-19
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Genetic interaction mapping informs integrative structure determination of protein complexes
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Self-citationCOVID-19 research risks ignoring important host genes due to pre-established research patterns
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Post-COVID-19 Parkinsonism and Parkinson’s Disease Pathogenesis: The Exosomal Cargo Hypothesis
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Attenuation of SARS-CoV-2 infection by losartan in human kidney organoids
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Baricitinib attenuates the proinflammatory phase of COVID-19 driven by lung-infiltrating monocytes
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Beyond dexamethasone, emerging immuno‐thrombotic therapies for COVID‐19
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Fighting COVID-19 with Artificial Intelligence
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- Authors
- Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., Tummino, T. A., Hüttenhain, R., Kaake, R. M., Richards, A. L., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., Kim, M., Haas, P., Polacco, B. J., Braberg, H., Fabius, J. M., Eckhardt, M., Soucheray, M., Bennett, M. J., Cakir, M., McGregor, M. J., Li, Q., Meyer, B., Roesch, F., Vallet, T., Mac Kain, A., Miorin, L., Moreno, E., Naing, Z. Z. C., Zhou, Y., Peng, S., Shi, Y., Zhang, Z., Shen, W., Kirby, I. T., Melnyk, J. E., Chorba, J. S., Lou, K., Dai, S. A., Barrio-Hernandez, I., Memon, D., Hernandez-Armenta, C., Lyu, J., Mathy, C. J. P., Perica, T., Pilla, K. B., Ganesan, S. J., Saltzberg, D. J., Rakesh, R., Liu, X., Rosenthal, S. B., Calviello, L., Venkataramanan, S., Liboy-Lugo, J., Lin, Y., Huang, X.-P., Liu, Y., Wankowicz, S. A., Bohn, M., Safari, M., Ugur, F. S., Koh, C., Savar, N. S., Tran, Q. D., Shengjuler, D., Fletcher, S. J., O’Neal, M. C., Cai, Y., Chang, J. C. J., Broadhurst, D. J., Klippsten, S., Sharp, P. P., Wenzell, N. A., Kuzuoglu-Ozturk, D., Wang, H.-Y., Trenker, R., Young, J. M., Cavero, D. A., Hiatt, J., Roth, T. L., Rathore, U., Subramanian, A., Noack, J., Hubert, M., Stroud, R. M., Frankel, A. D., Rosenberg, O. S., Verba, K. A., Agard, D. A., Ott, M., Emerman, M., Jura, N., von Zastrow, M., Verdin, E., Ashworth, A., Schwartz, O., d’Enfert, C., Mukherjee, S., Jacobson, M., Malik, H. S., Fujimori, D. G., Ideker, T., Craik, C. S., Floor, S. N., Fraser, J. S., Gross, J. D., Sali, A., Roth, B. L., Ruggero, D., Taunton, J., Kortemme, T., Beltrao, P., Vignuzzi, M., García-Sastre, A., Shokat, K. M., Shoichet, B. K., & Krogan, N. J.
- Affiliations
- Gladstone Institutes (US)
- Icahn School of Medicine at Mount Sinai (US)
- University of Michigan (US)
- Centre National de la Recherche Scientifique (FR)
- University of California, San Francisco (US)
- Howard Hughes Medical Institute (US)
- European Bioinformatics Institute (GB)
- University of California San Diego (US)
- University of North Carolina at Chapel Hill (US)
- Fred Hutch Cancer Center (US)
- Institut Pasteur (FR)
- Buck Institute for Research on Aging (US)
- Corresponding author
- Vignuzzi, Marco
- Shokat, Kevan M.
- Shoichet, Brian K.
- Krogan, Nevan J.
- ORCID
- Gordon, David E.
- Bouhaddou, Mehdi
- Xu, Jiewei
- Obernier, Kirsten
- White, Kris M.
- O’Meara, Matthew J.
- Rezelj, Veronica V.
- Guo, Jeffrey Z.
- Swaney, Danielle L.
- Tummino, Tia A.
- Hüttenhain, Ruth
- Kaake, Robyn M.
- Richards, Alicia L.
- Tutuncuoglu, Beril
- Foussard, Helene
- Batra, Jyoti
- Haas, Kelsey
- Modak, Maya
- Kim, Minkyu
- Haas, Paige
- Polacco, Benjamin J.
- Braberg, Hannes
- Eckhardt, Manon
- Soucheray, Margaret
- Bennett, Melanie J.
- Cakir, Merve
- McGregor, Michael J.
- Li, Qiongyu
- Meyer, Bjoern
- Roesch, Ferdinand
- Vallet, Thomas
- Mac Kain, Alice
- Miorin, Lisa
- Moreno, Elena
- Naing, Zun Zar Chi
- Zhou, Yuan
- Peng, Shiming
- Shi, Ying
- Zhang, Ziyang
- Shen, Wenqi
- Kirby, Ilsa T.
- Melnyk, James E.
- Chorba, John S.
- Lou, Kevin
- Dai, Shizhong A.
- Barrio-Hernandez, Inigo
- Memon, Danish
- Lyu, Jiankun
- Mathy, Christopher J. P.
- Perica, Tina
- Pilla, Kala Bharath
- Ganesan, Sai J.
- Saltzberg, Daniel J.
- Rakesh, Ramachandran
- Rosenthal, Sara B.
- Calviello, Lorenzo
- Venkataramanan, Srivats
- Liboy-Lugo, Jose
- Lin, Yizhu
- Huang, Xi-Ping
- Liu, YongFeng
- Wankowicz, Stephanie A.
- Bohn, Markus
- Safari, Maliheh
- Ugur, Fatima S.
- Koh, Cassandra
- Savar, Nastaran Sadat
- Tran, Quang Dinh
- Shengjuler, Djoshkun
- Fletcher, Sabrina J.
- O’Neal, Michael C.
- Cai, Yiming
- Chang, Jason C. J.
- Broadhurst, David J.
- Klippsten, Saker
- Sharp, Phillip P.
- Wenzell, Nicole A.
- Wang, Hao-Yuan
- Trenker, Raphael
- Young, Janet M.
- Cavero, Devin A.
- Hiatt, Joseph
- Roth, Theodore L.
- Rathore, Ujjwal
- Subramanian, Advait
- Noack, Julia
- Hubert, Mathieu
- Stroud, Robert M.
- Frankel, Alan D.
- Rosenberg, Oren S.
- Verba, Kliment A.
- Agard, David A.
- Emerman, Michael
- Jura, Natalia
- von Zastrow, Mark
- Verdin, Eric
- Ashworth, Alan
- Schwartz, Olivier
- d’Enfert, Christophe
- Mukherjee, Shaeri
- Jacobson, Matt
- Malik, Harmit S.
- Fujimori, Danica G.
- Ideker, Trey
- Craik, Charles S.
- Floor, Stephen N.
- Fraser, James S.
- Gross, John D.
- Roth, Bryan L.
- Ruggero, Davide
- Taunton, Jack
- Kortemme, Tanja
- Beltrao, Pedro
- Vignuzzi, Marco
- García-Sastre, Adolfo
- Shokat, Kevan M.
- Shoichet, Brian K.
- Krogan, Nevan J.
- Venue
- Nature
- Published
- 2020-04-30
- Volume
- 583
- Issue
- 7816
- Pages
- 459-468
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC7431030
- OpenAlex
- W3022285953
- Cited by
- 4,405
- References
- 84
- Citations by year
- 2026: 147 · 2025: 279 · 2024: 391 · 2023: 547 · 2022: 841 · 2021: 1352 · 2020: 837 · 2019: 3 · 2018: 2 · 2014: 1 · 2012: 1
- FWCI
- 117.80
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion)
- Funders
- U.S. Department of Defense (HR00111920020, W81XWH)
- Howard Hughes Medical Institute
- F. Hoffmann-La Roche
- Agence Nationale de la Recherche (10-LABX-62-IBEID, ANR‐10‐LABX‐62‐IBEID, ANR-10, ANR-10-LABX-0062, grant ANR-10-LABX-62-IBEID, ANR-10-LABX-62)
- National Institutes of Health (1f32ca236347-01, W81XWH, HHSN272201400008C)
- National Heart, Lung, and Blood Institute (K08HL124068)
- National Institute of Mental Health
- National Human Genome Research Institute (R01HG009979)
- National Cancer Institute (F32CA239333, R01CA221969, F30CA239476, F32 CA236347, R01CA244550, P30CA023100, T32CA108462)
- National Institute of General Medical Sciences (R01GM140440, F32GM133144, R35GM118099, T32GM008284, R01GM117189, T32GM064337, T32GM067547, R01GM024485, R35GM122481)
- National Institute of Allergy and Infectious Diseases (HHSN272201400008C), R01AI120694, R01AI143292, R01AI122747, P50AI150476, ANR-10-LABX-62-IBEID, R01AI118974, T32AI060537, U19AI135990, P01AI063302, P01AI120943, U19AI135972, P30AI027763)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, COVID-19 pandemic, protein-protein interaction, host factors, drug repurposing, antiviral drug targets, sigma-1 receptor, sigma-2 receptor, host-virus interaction, affinity purification mass spectrometry
- MeSH terms
- Protein Domains, Betacoronavirus, COVID-19, SARS-CoV-2, COVID-19 Drug Treatment, Animals, Antiviral Agents, Chlorocebus aethiops, Cloning, Molecular, Drug Evaluation, Preclinical, Humans, Immunity, Innate, Pneumonia, Viral, Protein Binding, Mass Spectrometry, Protein Biosynthesis, Vero Cells, Viral Proteins, Receptors, sigma, Coronavirus Infections, Protein Interaction Mapping, SKP Cullin F-Box Protein Ligases, Host-Pathogen Interactions, HEK293 Cells, Drug Repositioning, Pandemics, Molecular Targeted Therapy, Protein Interaction Maps
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