Benoit Coulombe Lab

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Our goal is to discover small molecules that interfere with the function of enzymes and proteins that are essential for the growth of epidemic viruses, to ultimately develop antiviral medications.

The genome of epidemic viruses such as coronaviruses and flu viruses is made of RNA and encodes a number of proteins essential for viral replication and propagation. The biogenesis of viral protein complexes and structures, leading to infectious viral particles, proceeds according to an established scenario that requires involvement of host factors. Our strategy is aimed at developing new avenues to combat epidemic viruses by targeting essential aspects of their growth cycle. Our focus is not only on SARS-CoV-2 (COVID-19), but also on a recently discovered swine flu virus able to replicate in human cells, but that has not shown human to human transmission yet. Our antiviral discovery platform is designed to rapidly react to emerging viral threats. We combine our expertise in proteomics and biochemistry with that of our collaborators in medicinal chemistry, virology,  biophysics and clinical sciences to discover new antiviral molecules. We believe that the most significant innovations come to life at the intersection of disciplines.

Interfering with entry of the virus in target cells

The SARS-CoV-2 spike (S) glycoprotein recognizes and binds the ACE2 receptor at the surface of target cells to initiate the infection process and deliver viral materials in cells. We use various approaches including phage display to discover peptides and proteins that block this protein-protein interaction in order to impair viral entry and interfere with infection.

Interfering with genome replication to stop viral growth

A SARS-CoV-2 RNA dependent RNA polymerase (RdRp) is required to copy the viral genome and trigger the replication process in infected cells. The RdRp is a privileged target for drug discovery because its chemical inhibition can interfere with viral growth. Remdesivir, a nucleoside analogue approved by the FDA to treat COVID-19, provides a proof of concept that SARS-CoV-2 RdRp is a valuable target for antiviral development. We develop and use screening technologies to identify chemical compounds and peptides that can target the RdRp machinery. SARS-CoV-2 genome replication and transcription involves up to five viral proteins in addition to RdRp. Novel inhibitors not only serve to develop medications to combat epidemics, but also to better understand mechanisms of viral replication. Advanced biochemical studies are necessary to understand the complexity and dynamics of enzyme mechanisms, therefore providing an essential complement to structural data. This is particularly important when structural data has been obtained on partial complexes that may not adopt an adequate conformation.

Interfering with virus biogenesis?

We have been astonished to find out that subunits of the PAQosome associate with SARS-CoV-2 proteins in human cells (Krogan dataset), suggesting a role for the PAQosome in virus biogenesis. The "Particle for Arrangement of Quaternary Structure" (PAQosome) is a 12-subunit molecular chaperone required for assembly of several human complexes, including the nuclear RNA polymerase I, II and III, some sno and snRNPs , the ribosome, PIKKs and others. Validation studies are needed to confirm a role for the PAQosome in SARS-CoV-2 biogenesis and evaluate if this complex is a relevant target in the drug discovery process for COVID-19.




Systematic Analysis of the Protein Interaction Network for the Human Transcription Machinery Reveals the Identity of the 7SK Capping Enzyme.

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.

Mol Cell. 2007 Jul 20;27(2):262-74.  (404 citations)

Discovery of the 7SK methylphosphate capping enzyme and a series of chaperone-like proteins that associate with RNA polymerase to regulate its biogenesis, some being components of a chaperone complex later named “Particle for Arrangement of Quaternary structure” (PAQosome)

DNA Bending and Wrapping Around RNA Polymerase: A "Revolutionary" Model Describing Transcriptional Mechanisms.

Coulombe B, Burton ZF.

Microbiol Mol Biol Rev. 1999 Jun;63(2):457-78.  (153 citations)

A Newly Uncovered Group of Distantly Related Lysine Methyltransferases Preferentially Interact With Molecular Chaperones to Regulate Their Activity.

Cloutier P, Lavallée-Adam M, Faubert D, Blanchette M, Coulombe B.

PLoS Genet. 2013;9(1):e1003210.  (128 citations)

Wrapping of Promoter DNA Around the RNA Polymerase II Initiation Complex Induced by TFIIF.

Robert F, Douziech M, Forget D, Egly JM, Greenblatt J, Burton ZF, Coulombe B.

Mol Cell. 1998 Sep;2(3):341-51.  (125 citations)

Mechanism of Promoter Melting by the Xeroderma Pigmentosum Complementation Group B Helicase of Transcription Factor IIH Revealed by protein-DNA Photo-Cross-Linking.

Douziech M, Coin F, Chipoulet JM, Arai Y, Ohkuma Y, Egly JM, Coulombe B.

Mol Cell Biol. 2000 Nov;20(21):8168-77.  (89 citations)

High-resolution Mapping of the Protein Interaction Network for the Human Transcription Machinery and Affinity Purification of RNA Polymerase II-associated Complexes.

Cloutier P, Al-Khoury R, Lavallée-Adam M, Faubert D, Jiang H, Poitras C, Bouchard A, Forget D, Blanchette M, Coulombe B.

Methods. 2009 Aug;48(4):381-6.  (83 citations)

Composition of the R2TP/PFDL co-chaperone complex, later renamed “Particle for Arrangement of Quaternary structure” (PAQosome)

Structural Perspective on Mutations Affecting the Function of Multisubunit RNA Polymerases.

Trinh V, Langelier MF, Archambault J, Coulombe B.

Microbiol Mol Biol Rev. 2006 Mar;70(1):12-36.  (83 citations)

The Protein Interaction Network of the Human Transcription Machinery Reveals a Role for the Conserved GTPase RPAP4/GPN1 and Microtubule Assembly in Nuclear Import and Biogenesis of RNA Polymerase II.

Forget D, Lacombe AA, Cloutier P, Al-Khoury R, Bouchard A, Lavallée-Adam M, Faubert D, Jeronimo C, Blanchette M, Coulombe B.

Mol Cell Proteomics. 2010 Dec;9(12):2827-39.  (76 citations)

Photo-cross-linking of a Purified Preinitiation Complex Reveals Central Roles for the RNA Polymerase II Mobile Clamp and TFIIE in Initiation Mechanisms.

Forget D, Langelier MF, Thérien C, Trinh V, Coulombe B.

Mol Cell Biol. 2004 Feb;24(3):1122-31.  (73 citations)

Recessive Mutations in POLR1C Cause a Leukodystrophy by Impairing Biogenesis of RNA Polymerase III.

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.

Nat Commun. 2015 Jul 7;6:7623. *Co-senior authors  (71 citations)



  1. Unraveling the molecular basis of novel forms of hypomyelinating leukodystrophies (CIHR, Lead G. Bernard MUHC).

  2. A biomarker discovery pipeline for precision medicine (Government of Quebec/IRCM, Lead B. Coulombe IRCM).

  3. A patient-derived iPSC platform of disease relevant cell models for biological studies (ALS Canada and Brain Canada, Lead G. Rouleau The Neuro).

  4. A machine learning approach to decipher protein-protein interactions in human plasma (IVADO and Genome Québec, Lead B. Coulombe IRCM).

  5. Modulation of protein interactions by the Superoxide Dismutase 1 (SOD1) (supported by Atomwise Inc, Lead B. Coulombe IRCM).

  6. The soluble fragment of neuroligin-1 as a blood biomarker of prodromal Alzheimer’s disease (Weston Brain Institute, Lead J. Brouillette HSCM).

  7. Characterization of neuro-muscular junctions in ALS patients (ALS Canada, Lead R. Robitaille, U Montreal).

  8. Reducing the activity of the phosphatase STEP to improve memory performance during aging (CIHR, Lead J. Brouillette HSCM).

  9. Screening of chemical compounds that correct assembly defects of RNA polymerase III carrying a leukodystrophy-causing mutation (Leukodystrophy’s Foundation, Lead B. Coulombe IRCM).


PROTEOMIC PROCEDURES (Open to collaboration)

  • Protein Affinity Purification coupled to Mass Spectrometry (AP-MS)

  • Proximity-Dependent Protein Identification (BioID)

  • Tandem Mass Tag (TMT)-Based Discovery Proteomics

  • Protein Affinity Capture coupled to quantitative Mass Spectrometry (PAC-qMS)

  • Phage Display Peptide/Protein Library Screening (PhD)



Dr. Benoit Coulombe

Dr. Benoit Coulombe

Dr. Marie-Soleil Gauthier

Dr. Marie-Soleil Gauthier

Senior Associate Researcher

Dr. Maxime Pinard

Associate Researcher

Dr. Esen Sokullu

Postdoctoral Fellow

Dr. Samaneh Dastpeyman

Postdoctoral Fellow
Christian Poitras

Christian Poitras

Systems Analyst
Alexa Derksen

Alexa Derksen

Master Degree Student (Dr. G. Bernard)
Golden Marble

Vijaya Madhoo

Administrative Assistant
Diane Forget

Diane Forget

Honorary Lab Member

2020-06-26 :

Diane Forget prend sa retraite après 27 ans de service dévoué pour le laboratoire. Elle a eu

une contribution exceptionnelle pour nos publications, la formation de personnel, l'administration des fonds de recherche et la planification des espaces de laboratoire. Avec toute notre reconnaissance, merci et bonne continuation.




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