Virus-Host Protein Interactions - Benoit Coulombe PhD

Virus-Host Protein Interactions - Benoit Coulombe PhDVirus-Host Protein Interactions - Benoit Coulombe PhDVirus-Host Protein Interactions - Benoit Coulombe PhD

Virus-Host Protein Interactions - Benoit Coulombe PhD

Virus-Host Protein Interactions - Benoit Coulombe PhDVirus-Host Protein Interactions - Benoit Coulombe PhDVirus-Host Protein Interactions - Benoit Coulombe PhD

Targeting virus-host protein interactions using AI for antiviral discovery

Targeting virus-host protein interactions using AI for antiviral discoveryTargeting virus-host protein interactions using AI for antiviral discoveryTargeting virus-host protein interactions using AI for antiviral discovery



Interactys-AI

Interactys-AI in the News

Following the publication of our article in Viruses
“AI-Powered Identification of Human Cell Surface Protein Interactors of the Hemagglutinin Glycoprotein of High-Pandemic-Risk H5N1 Influenza Virus”,
our work attracted significant attention from Québec’s major news outlets.

The study reports the identification of human cell-surface proteins that can interact with the hemagglutinin (HA) protein of highly pathogenic H5N1 avian influenza — a key step toward understanding how this virus could potentially adapt to human infection and how such transmission might be prevented.

As a result, our findings were featured by several major media organizations in French language, including La Presse, L’Actualité, and TVA Nouvelles, highlighting the importance of AI-driven structural biology for pandemic preparedness.

Featured TV report (TVA Nouvelles)

“Grippe aviaire : une percée majeure pour freiner une possible transmission humaine”
TVA Nouvelles, January 9, 2026

🔗 https://www.tvanouvelles.ca/2026/01/09/grippe-aviaire-une-percee-majeure-pour-freiner-une-possible-transmission-humaine

What is Interactys-AI?

INTERACTYS-AI is a technology platform dedicated to the characterization of protein-protein interactions in three dimensions using advanced artificial intelligence. Our ultimate goal is to create an open, high-resolution atlas of interaction networks involved in the infection process of human cells by pathogenic viruses. This platform aims at accelerating the discovery of novel therapeutic strategies, foster collaboration across disciplines, and advance the global knowledge base in structural biology and biomedical research. A main focus of Interactys-AI is the combat against emerging viruses at high-risk to cause pandemics.

Our Key Publications

Fernandes MGF, Pinard M, Sokullu E, Gagnon JF, Calon F, Coulombe B, Consortium pour l’identification précoce de la maladie d’Alzheimer (CIMA-Q), Brouillette J. Differences in blood levels of neuroligin-derived peptides in a cohort for early detection of Alzheimer's disease. 2026 Journal of Gerontology: Biological Sciences. 


Poitras C, Coulombe B. AI-Powered Identification of Human Cell Surface Protein Interactors of the Hemagglutinin Glycoprotein of High-Pandemic-Risk H5N1 Influenza Virus. 2025 Viruses. In press - https://www.mdpi.com/1999-4915/17/12/1638 


Moursli Y, Faubert D, Grou C, Coulombe B. Discovery and characterization of a pancreatic β cell subpopulation expressing an unknown surface epitope through single cell proteomics. 2025 bioRxiv. https://lnkd.in/e8GDAs5i 


Moursli Y, Poitras C, Coulombe B. Investigating pancreatic β cell membrane epitopes using unbiased cell-based Fab-phage display. bioRxiv, 2025.03.29.645157; doi: https://doi.org/10.1101/2025.03.29.645157. 


Hashimoto-Roth E, Forget D, Gaspar VP, Bennett SAL, Gauthier MS, Coulombe B, Lavallée-Adam M. MAGPIE: A Machine Learning Approach to Decipher Protein-Protein Interactions in Human Plasma. J Proteome Res. 2025 Jan 7. doi: 10.1021/acs.jproteome.4c00160. Epub ahead of print. PMID: 39772751.


Pinard M, Dastpeyman S, Poitras C, Bernard G, Gauthier MS, Coulombe B. Riluzole partially restores RNA polymerase III complex assembly in cells expressing the leukodystrophy-causative variant POLR3B R103H. Mol Brain. 2022 Nov 30;15(1):98. doi: 10.1186/s13041-022-00974-z


Sokullu E, Pinard M, Gauthier MS, Coulombe B. Analysis of the SARS-CoV-2-host protein interaction network reveals new biology and drug candidates: focus on the spike surface glycoprotein and RNA polymerase. Expert Opin Drug Discov. 2021 Aug;16(8):881-895. doi: 10.1080/17460441.2021.1909566.


Sokullu E, Gauthier MS, Coulombe B. Discovery of Antivirals Using Phage Display. Viruses. 2021 Jun 10;13(6):1120. doi: 10.3390/v13061120. 


Cloutier P, Poitras C, Durand M, Hekmat O, Fiola-Masson É, Bouchard A, Faubert D, Chabot B, Coulombe B. R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein Nat Commun. 2017 May 31;8:15615. doi: 10.1038/ncomms15615. PMID: 28561026


Houry WA, Bertrand E, Coulombe B. The PAQosome, an R2TP-Based Chaperone for Quaternary Structure Formation Trends Biochem Sci. 2018 Jan;43(1):4-9. doi: 10.1016/j.tibs.2017.11.001. Epub 2017 Dec 5. Review. PMID: 29203338


Thiffault I, Wolf NI, Forget D, Guerrero K, Tran LT, Choquet K, Lavallée-Adam M, Poitras C, Brais B, Yoon G, Sztriha L, Webster RI, Timmann D, van de Warrenburg BP, Seeger J, Zimmermann A, Máté A, Goizet C, Fung E, van der Knaap MS, Fribourg S, Vanderver A, Simons C, Taft RJ, Yates JR 3rd, Coulombe B, Bernard G. Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III Nat Commun. 2015 Jul 7;6:7623. doi: 10.1038/ncomms8623. PMID: 26151409


Jeronimo C, Forget D, Bouchard A, Li Q, Chua G, Poitras C, Thérien C, Bergeron D, Bourassa S, Greenblatt J, Chabot B, Poirier GG, Hughes TR, Blanchette M, Price DH, Coulombe B. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme Mol Cell. 2007 Jul 20;27(2):262-74. PMID: 17643375

Invitation To Contribute a Paper

FINAL DEADLINE: FEBRUARY 28th, 2026


VIRUS-HOST PROTEIN INTERACTIONS


Joint Special Issue of the Journals Biomolecules (IF 4.8) and Viruses (IF 3.5)


Guest Editor

Prof. Benoit Coulombe
1. Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
2. Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada

Special Issue Information

Dear Colleagues,

Protein–protein interactions play essential roles in viral infections. Some viral proteins join together to form protein complexes that exert key roles in the virus life cycle. The RNA polymerase complex is an example. Additionally, some viral proteins interact with host factors during the infection process, usurping the function of these factors in favor of viral functions. Together, these protein–protein interactions are central in the pathophysiology of viral infection. As a consequence, perturbation of these key interactions has the potential to impair virus replication and propagation. Over recent years, a number of molecules, including small chemicals, peptides and antibodies, have been reported to interfere with viral functions by perturbating protein–protein interactions. The molecules showing virus specificity can serve as antiviral agents en route to the discovery of new drugs. This joint Special Issue of the open access journals Viruses (Impact Factor 3,5) and Biomolecules (Impact Factor 4,8) is dedicated to experimental studies or reviews dealing with the use of protein–protein interactions as targets for antiviral drug discovery. This Special Issue also represents a powerful tool in the combat against threatening human viruses.


Manuscript Submission Information on the MDPI Website - https://www.mdpi.com 

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

High Pandemic Risk Virus: H5N1

H5N1 is a highly pathogenic avian influenza. It is tightly monitored since 2023-2025 because there has been intense circulation among wild and farmed birds, with occasional spillover into humans as cases were reported in Chile, the UK, and the USA. The pandemic risk is HIGH because it is already transmitted to mammals (minks, seals, cattle) and continues to acquire mutations that could facilitate human-to-human transmission. The emergence of a variant that can spread efficiently between humans could be catastrophic. We currently develop and use AI procedures to identify host factors that are targeted by H5N1 proteins as they can lead to antiviral discovery.


Poitras C, Coulombe B. AI-Powered Identification of Human Cell Surface Protein Interactors of the Hemagglutinin Glycoprotein of High-Pandemic-Risk H5N1 Influenza Virus. 2025 Viruses. In press (https://www.mdpi.com/1999-4915/17/12/1638)


Published Version:


https://www.mdpi.com/1999-4915/17/12/1638



About Benoit Coulombe

Benoit Coulombe, PhD, is a molecular biologist and biochemist at the Montreal Clinical Research Institute (IRCM) affiliated to the University of Montreal. Pr. Coulombe has published 109 scientific articles so far (totalling nearly 9000 citations) and was among the pioneers in applying AI to protein interactomes (see Jeronimo et al 2007). Several of his publications are dealing with viral mechanisms.


LINKEDIN ACCOUNT: 

www.linkedin.com/in/benoit-coulombe-31a22a132


X ACCOUNT:

@BenCoulombePhD 

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