About
I’m a programmer. I’m a drug designer. I fucking love drugs. 1st love of my life, but still looking for my fairy tale.
I’m on a quest to understand the thermodynamics of molecules and how they cooperate altogether to form the basis of Life.
Activity
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Guy Rocher a 100 ans aujourd’hui. Je rends hommage à cette grande figure de l’Université de Montréal qui a tant fait pour la construction du Québec…
Guy Rocher a 100 ans aujourd’hui. Je rends hommage à cette grande figure de l’Université de Montréal qui a tant fait pour la construction du Québec…
Liked by Louis-Philippe Morency
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#PALMARÈS | 🤖 ✨ Le professeur Yoshua Bengio fait partie des 💯 personnes les plus influentes au monde selon le magazine TIME, notamment en raison de…
#PALMARÈS | 🤖 ✨ Le professeur Yoshua Bengio fait partie des 💯 personnes les plus influentes au monde selon le magazine TIME, notamment en raison de…
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C'est avec grand plaisir que j'animerai un panel sur les défis en cosméceutique au Québec jeudi 28 mars prochain. Vous vous questionnez sur la…
C'est avec grand plaisir que j'animerai un panel sur les défis en cosméceutique au Québec jeudi 28 mars prochain. Vous vous questionnez sur la…
Liked by Louis-Philippe Morency
Experience
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Le Bonhomme Pharma
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Education
Licenses & Certifications
Publications
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Identification of an alternative translation initiation site in the sequence of the commonly used Glutathione S-Transferase tag
Journal of Biotechnology
A large number of proteins are expressed in fusion with a tag to perform their purification. Glutathione-S-Transferase (GST) is a widely used tag to achieve passenger protein purification. Accordingly, commonly used commercial expression vectors contain the coding sequence of GST in order to express fusion proteins. However, fusion proteins are sometimes expressed in a truncated form that may result from an incomplete synthesis, proteolytic cleavage or the presence of a functional alternative…
A large number of proteins are expressed in fusion with a tag to perform their purification. Glutathione-S-Transferase (GST) is a widely used tag to achieve passenger protein purification. Accordingly, commonly used commercial expression vectors contain the coding sequence of GST in order to express fusion proteins. However, fusion proteins are sometimes expressed in a truncated form that may result from an incomplete synthesis, proteolytic cleavage or the presence of a functional alternative translation initiation site. In particular, a truncated as well as a full-length fusion protein were observed when expressing RGS9-1 Anchor Protein without its C-terminal segment (bR9AP) in fusion with GST. Moreover, this truncated protein was found to be purified together with the full-length fusion protein. Here, we identified for the first time an alternative translation initiation site within the sequence of GST that likely becomes accessible for translation only when it is fused with a passenger protein. Indeed, bioinformatics analyses suggest that the secondary structure of the mRNA of the GST-bR9AP fusion protein is different from that of GST alone, which likely allows accessibility of an alternative Shine-Dalgarno sequence coupled with an additional initiation codon within the sequence of GST. The functionality of this alternative translation initiation site was confirmed by site-directed mutagenesis, which resulted in the absence of a truncated fusion protein and, consequently, only a purified full-length fusion protein. This is an extremely important finding in view of the wide use of GST as a purification and solubility-enhancing tag.
Other authorsSee publication -
Functional diversity of TMPRSS6 isoforms and variants expressed in hepatocellular carcinoma cell lines
Scientific Reports / Nature
TMPRSS6, also known as matriptase-2, is a type II transmembrane serine protease that plays a major role in iron homeostasis by acting as a negative regulator of hepcidin production through cleavage of the BMP co-receptor haemojuvelin. Iron-refractory iron deficiency anaemia (IRIDA), an iron metabolism disorder, is associated with mutations in the TMPRSS6 gene. By analysing RNA-seq data encoding TMPRSS6 isoforms and other proteins involved in hepcidin production, we uncovered significant…
TMPRSS6, also known as matriptase-2, is a type II transmembrane serine protease that plays a major role in iron homeostasis by acting as a negative regulator of hepcidin production through cleavage of the BMP co-receptor haemojuvelin. Iron-refractory iron deficiency anaemia (IRIDA), an iron metabolism disorder, is associated with mutations in the TMPRSS6 gene. By analysing RNA-seq data encoding TMPRSS6 isoforms and other proteins involved in hepcidin production, we uncovered significant differences in expression levels between hepatocellular carcinoma (HCC) cell lines and normal human liver samples. Most notably, TMPRSS6 and HAMP expression was found to be much lower in HepG2 and Huh7 cells when compared to human liver samples. Furthermore, we characterized the common TMPRSS6 polymorphism V736A identified in Hep3B cells, the V795I mutation found in HepG2 cells, also associated with IRIDA, and the G603R substitution recently detected in two IRIDA patients. While variant V736A is as active as wild-type TMPRSS6, mutants V795I and G603R displayed significantly reduced proteolytic activity. Our results provide important information about commonly used liver cell models and shed light on the impact of two TMPRSS6 mutations associated with IRIDA.
Other authorsSee publication -
Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design
Methods in Molecular Biology / Springer
Docking simulations help us understand molecular interactions. Here we present a hands-on tutorial to utilize FlexAID (Flexible Artificial Intelligence Docking), an open source molecular docking software between ligands such as small molecules or peptides and macromolecules such as proteins and nucleic acids. The tutorial uses the NRGsuite PyMOL plugin graphical user interface to set up and visualize docking simulations in real time as well as detect and refine target cavities. The ease of use…
Docking simulations help us understand molecular interactions. Here we present a hands-on tutorial to utilize FlexAID (Flexible Artificial Intelligence Docking), an open source molecular docking software between ligands such as small molecules or peptides and macromolecules such as proteins and nucleic acids. The tutorial uses the NRGsuite PyMOL plugin graphical user interface to set up and visualize docking simulations in real time as well as detect and refine target cavities. The ease of use of FlexAID and the NRGsuite combined with its superior performance relative to widely used docking software provides nonexperts with an important tool to understand molecular interactions with direct applications in structure-based drug design and virtual high-throughput screening.
Other authorsSee publication -
Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects
BMC Pharmacology and Toxicology / BioMed Central
Promiscuity in molecular interactions between small-molecules, including drugs, and proteins is widespread. Such unintended interactions can be exploited to suggest drug repurposing possibilities as well as to identify potential molecular mechanisms responsible for observed side-effects. We perform a large-scale analysis to detect binding-site molecular interaction field similarities between the binding-sites of the primary target of 400 drugs against a dataset of 14082 cavities within 7895…
Promiscuity in molecular interactions between small-molecules, including drugs, and proteins is widespread. Such unintended interactions can be exploited to suggest drug repurposing possibilities as well as to identify potential molecular mechanisms responsible for observed side-effects. We perform a large-scale analysis to detect binding-site molecular interaction field similarities between the binding-sites of the primary target of 400 drugs against a dataset of 14082 cavities within 7895 different proteins representing a non-redundant dataset of all proteins with known structure. Statistically-significant cases with high levels of similarities represent potential cases where the drugs that bind the original target may in principle bind the suggested off-target.
Other authorsSee publication -
NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID
Bioinformatics / Oxford University Press
Ligand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chains…
Ligand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chains and definition of geometric constraints. Furthermore, the NRGsuite permits the visualization of the docking simulation in real time. The NRGsuite give access to powerful docking simulations that can be used in structure-guided drug design as well as an educational tool. The NRGsuite is implemented in Python and C/C++ with an easy to use package installer. The NRGsuite is available for Windows, Linux and MacOS.
Availability and implementation: http://biophys.umontreal.ca/nrgOther authorsSee publication -
Structure and pH‐induced alterations of recombinant and natural spider silk proteins in solution
Biopolymers
The spinning process of spiders can modulate the mechanical properties of their silk fibers. It is therefore of primary importance to understand what are the key elements of the spider spinning process to develop efficient industrial spinning processes. We have exhaustively investigated the native conformation of major ampullate silk (MaS) proteins by comparing the content of the major ampullate gland of Nephila clavipes, solubilized MaS (SolMaS) fibers and the recombinant proteins rMaSpI and…
The spinning process of spiders can modulate the mechanical properties of their silk fibers. It is therefore of primary importance to understand what are the key elements of the spider spinning process to develop efficient industrial spinning processes. We have exhaustively investigated the native conformation of major ampullate silk (MaS) proteins by comparing the content of the major ampullate gland of Nephila clavipes, solubilized MaS (SolMaS) fibers and the recombinant proteins rMaSpI and rMaSpII using 1H solution NMR spectroscopy
Honors & Awards
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1st annual hackathon of the BDC
Bank of Development Canada (BDC)
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Médaille du Lieutenant-gouverneur pour la jeunesse (bronze)
Lieutenant-gouverneur du Québec
Languages
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English
Native or bilingual proficiency
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French
Native or bilingual proficiency
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Spanish
Limited working proficiency
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C++
Full professional proficiency
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Perl
Native or bilingual proficiency
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Python
Native or bilingual proficiency
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C
Native or bilingual proficiency
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R
Full professional proficiency
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Java
Professional working proficiency
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Bash
Native or bilingual proficiency
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Swift
Full professional proficiency
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Assembly
Limited working proficiency
More activity by Louis-Philippe
C’est avec fierté et audace que j’ai accepté de m’impliquer à titre de bénévole de la campagne L’heure est brave de l’Université de Montréal sur le…
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La Faculté de pharmacie - UdeM est fière de développer ce nouveau programme de formation en entrepreneuriat en sciences de la vie et technologie de…
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L'équipe du professeur Nicolas Doucet a réalisé une avancée importante dans le domaine de la conservation évolutive de la dynamique moléculaire chez…
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Très fier des succès bien mérités de mon ex-doctorant Pierre-Luc Boudreault! Un nom à surveiller! Bravo Pierre-Luc!
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« 🎶Les Débrouillards🎶+Découverte, mais pour les ados ». Si j’avais eu à décrire mon projet de rêve, c’est pas mal les mots que j’aurais utilisés…
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Normand Voyer, professeur au Département de chimie, fait partie des 14 actrices et acteurs de changement au Canada qui ont été sélectionnés pour…
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Tous sont les bienvenus à ce Colloque organisé par des professeurs de la Faculté de pharmacie - UdeM. Venez participer à la discussion avec nos…
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Reposting for visibility. My former colleagues are looking for a medical imaging software developer. #imeka #softwaredeveloper #medical #dmri
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