Mapping biomolecular interactions in 3D with AI

• Moursli Y, Poitras C, Coulombe B, (2025). 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

 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.

Special Issue: Virus-Host Protein Interactions

Journals Biomolecules (IF 4,8) and Viruses (IF 3,5) Joint Special Issue

Special Issue Editor

Prof. Dr. Benoit Coulombe

Guest Editor
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

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.

Prof. Dr. Benoit Coulombe
Guest Editor

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