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

Mapping Biomolecular Interactions in 3D with AI

Mapping Biomolecular Interactions in 3D with AIMapping Biomolecular Interactions in 3D with AIMapping Biomolecular Interactions in 3D with AI




          Accelerating antiviral discovery 

          through advanced AI


Interactys-AI 

NEQ. 2281724825

What is Interactys-AI?

 Interactys-AI is an emerging biotechnology company leveraging advanced AI to map 3D virus-host protein interactions, most particularly the surface interactome. By detailing complex infection mechanisms, the platform accelerates the design of targeted antiviral molecules to combat current infections and proactively mitigate future pandemics.


 

On January 22, 2026, Interactys-AI was officially incorporated under the Registre des entreprises du Québec (REQ). Being its founder, I now serve as the company's CEO. In addition to developing advanced AI tools for modeling proteins, protein complexes, and interaction networks, Interactys-AI provides specialized expertise to researchers to accelerate scientific discovery.

The Interactys-AI Pipeline

Interactys-AI: Toward AI-Driven Structural Mapping of Virus–Host Interfaces for Antiviral Repurposing and Pandemic Preparedness

by Christian Poitras, Ali Harake, Nathalie Grandvaux, Benoit Coulombe  

Understanding how viruses engage host cell surfaces is fundamental to infection biology and therapeutic development. While vaccines remain central to prevention, recent global crises have emphasized the need for complementary antiviral strategies that can be mobilized rapidly against both known and emerging pathogens. In this context, artificial intelligence (AI) systems for biomolecular structure prediction, culminating in AlphaFold 3, are reshaping what is experimentally and conceptually achievable. Here, we present “Interactys-AI”, a framework designed to exploit AI-based structural modeling to systematically map virus–host protein–protein interactions (PPIs) and connect them to actionable drug repurposing opportunities. Beyond a technical workflow, Interactys-AI reflects a broader transformation toward predictive and anticipatory antiviral discovery. We describe the conceptual foundations of the platform, its implementation, and its application to influenza A H5N1 hemagglutinin. We further discuss how structural AI may redefine preparedness strategies, highlight current limitations, and outline future directions toward real-time therapeutic hypothesis generation.


Paper available here

https://www.mdpi.com/2218-273X/16/4/541 


BIOMOLECULES SPECIAL ISSUE 2026

The Future of Protein Research: New Paradigms and Transformative Technologies


Special Issue Information

Dear Colleagues,

Protein science is entering a transformative era. Breakthroughs in cryo-electron microscopy, single-cell and spatial proteomics, and increasingly powerful AI-driven approaches (including structure prediction and interaction modeling) are not only accelerating discovery—they are redefining how we conceptualize protein function, interaction networks, and therapeutic intervention.

This Special Issue of Biomolecules is designed to capture this moment of transition.

Rather than focusing solely on traditional reviews, we aim to assemble a collection of forward-looking, high-impact contributions that articulate emerging directions, challenge existing paradigms, and outline the next frontiers in protein research.

We particularly welcome reviews, perspectives, opinions, and commentaries that:

  • Provide new conceptual frameworks or reinterpret established fields;
  • Highlight emerging technologies shaping protein science;
  • Explore complex protein systems, including interactomes and dynamic assemblies;
  • Address translational opportunities, including drug discovery and synthetic biology;
  • Discuss the integration of AI and data-driven approaches into protein research.

We encourage contributions from leading experts, established investigators, and members of the Biomolecules editorial community, with the goal of creating a selective and authoritative issue that reflects both depth and vision.

Our ambition is not only to summarize the state of the field but to define where it is going next.

By bringing together these perspectives, this Special Issue will serve as a reference point for future research, stimulate interdisciplinary dialogue, and help shape the evolving landscape of protein science.

Prof. Dr. Benoit Coulombe
Guest Editor


Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


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.

Further information on MDPI's Special Issue policies can be found at www.mdpi.com


Our Key Publications

Colorful data streams connecting to a complex digital matrix representing data processing.

Poitras C, Harake A, Grandvaux N, Coulombe B. Interactys-AI: Toward
AI-Driven Structural Mapping of Virus–Host Interfaces for Antiviral
Repurposing and Pandemic Preparedness. 2026 Biomolecules. https://www.mdpi.com/2218-273X/16/4/541


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

Service Offering (Publication-Level Research Support)

Two views of a protein complex with distinct green and orange regions.

 

Interactys-AI provides advanced, AI-driven structural biology services designed to support high-impact scientific publications, translational research, and competitive funding applications.


Our expertise includes:


  • Identification and mapping of protein–protein interactions
    Using an advanced, customized implementation of AlphaFold 3, we model and analyze protein–protein interaction networks with a focus on biological relevance and mechanistic insight.


  • Assessment of drug interference with protein–protein interactions
    Structural characterization of how small molecules, peptides, or biologics may disrupt or modulate protein–protein interfaces, supporting drug repurposing, target validation, and mechanism-of-action studies.


  • High-confidence structural modeling of proteins and complexes
    Generation of detailed structural models for individual proteins and multi-component complexes, suitable for publication, grant proposals, and downstream experimental design.


  • Scientific collaborations and funding applications
    Active participation in collaborative research projects, including conceptual input, structural analyses, and figure generation in support of grant submissions and consortium-based funding initiatives.

Interactys-AI in the News

Modern news studio with multiple 'Breaking News' screens and a sleek anchor desk.

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


The study details the identification of human cell-surface proteins that interact with the hemagglutinin (HA) protein of the highly pathogenic H5N1 avian influenza. This research is a crucial step toward understanding how this virus may adapt to human infection and the role of AI in structural biology in preventing such transmission. 


As a result, our findings were prominently featured by several major French-language media organizations, including La Presse, L’Actualité, and TVA Nouvelles. This coverage underscores the importance of AI-driven structural biology in enhancing 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

About Benoit Coulombe

Portrait of a bald man in a gray blazer and white shirt.

 

Benoit Coulombe, PhD, spent most of his carreer as a molecular biology and biochemistry professor at the Montreal Clinical Research Institute (IRCM) affiliated to the University of Montreal. He is now retired and devotes his time to the creation of the biotechnology company Interactys-AI. 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). He is the founder and CEO of Interactys-AI.



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