Resources

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Scientific publications

Explore publications from MFI and our collaborators spanning computational chemistry, drug discovery and molecular modelling.

Software Development:

Labarre, A., Stille, J., Burai-Patrascu, M., Martins, A., Pottel, J., Moitessier, N. Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds – Challenges and Opportunities. Journal of Chemical Information and Modeling (2022), 62, 1061-1077

Burai-Patrascu, M., Pottel, J., Pinus, S., Bezanson, M., Norrby, P-O., Moitessier, N. From Desktop to Benchtop with automated computational workflows for computer-aided design in asymmetric catalysis Nature Catalysis (2020), 3, 574-584

Usage Report:

Burai-Patrascu M., Nivedha A., Rostaing O., Chukka P., Moitessier N., Pottel J. The First CACHE Challenge – Identifying Binders of the WD-Repeat Domain of Leucine-Rich Repeat Kinase 2 ChemRxiv (2022)

Gagnon, C., et al. Biocatalytic Synthesis of Planar Chiral Macrocycles Science (2020), 367 (6480), 917-921

Comparative Study:

Scarpino, A., et al. Comparative Evaluation of Covalent Docking Tools Journal of Chemical Information and Modeling (2018), 58, 7, 1441-1458

Xu, W., Lucke, A. J., Fairlie, D. P. Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets Journal of Molecular Graphics and Modelling (2015), 57, 76-88

Other Publications

Our Science:

Weiser B., Genzling J., Burai-Patrascu M., Rostaing O., Moitessier, N. Machine Learning-Augmented Docking. 1. CYP inhibition prediction. Drug Discovery (2023), Advance Article

Wei, W., Luo, J., Waldispühl, J., Moitessier, N. Predicting Positions of Bridging Water Molecules in Nucleic Acid–Ligand Complexes. Journal of Chemical Information and Modeling (2019), 59 (6), 2941-2951

Pottel, J., Moitessier, N. Customizable Generation of Synthetically Accessible, Local Chemical Subspaces. Journal of Chemical Information and Modeling (2017), 57, 454-467

Moitessier N., Pottel J., Therrien E., Englebienne P., Liu Z., Tomberg A., Corbeil C.R. Medicinal Chemistry Projects Requiring Imaginative Structure-Based Drug Design Methods. Accounts of Chemical Research (2016), 49 (9), 1646-1657

Pottel J., Moitessier N. Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering. Journal of Chemical Information and Modeling (2015), 55, 12, 2657-2671

Pottel J., Therrien E., Gleason J.L., Moitessier N. Docking Ligands into Flexible and Solvated Macromolecules. 6. Development and Application to the Docking of HDACs and other Zinc Metalloenzymes Inhibitors. Journal of Chemical Information and Modeling (2014), 54, 254-265

Campagna-Slater V., Pottel J., Therrien E., Cantin L.-D., Moitessier N.  Development of a computational tool to rival experts in the prediction of sites of metabolism of xenobiotics by P450s. Journal of Chemical Information and Modeling (2012), 52, 2471-2483

Therrien E., Englebienne P., Arrowsmith A.G., Mendoza-Sanchez R., Corbeil C.R., Weill N., Campagna-Slater V., Moitessier N. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with FORECASTER, a novel platform for drug discovery. Journal of Chemical Information and Modeling (2012), 52, 210-224

Weill N., Corbeil C.R., De Schutter J.W., Moitessier N. Toward a computational tool predicting the stereochemical outcome of asymmetric reactions: Development of the molecular mechanics-based program ACE and application to asymmetric epoxidation reactions. Journal of Computational Chemistry  (2011), 32, 2878-2889

Englebienne P., Moitessier N. Docking ligands into flexible and solvated macromolecules. 5. Force-field-based prediction of binding affinities of ligands to proteins. Journal of Chemical Information and Modeling (2009), 49, 2564-2571

Englebienne P., Moitessier N.  Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins? Journal of Chemical Information and Modeling (2009), 49, 1568-1580

Corbeil C.R., Moitessier N.  Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs.  Journal of Chemical Information and Modeling (2009), 49, 997-1009

Fay A.-M.L., Corbeil C.R., Brown P., Moitessier N., Bowie D.  Functional characterization and in silico docking of full and partial GluK2 kainate receptor agonists.  Molecular Pharmacology (2009), 75, 1096-1107

Corbeil C.R., Englebienne P., Yannopoulos C.G., Chan L., Das S.K., Bilimoria D., L'Heureux L., Moitessier N.  Docking ligands into flexible and solvated macromolecules. 2. Development and application of FITTED 1.5 to the virtual screening of potential HCV polymerase inhibitors.  Journal of Chemical Information and Modeling (2008), 48, 902-909

Corbeil C.R., Thielges S., Schwartzentruber J.A., Moitessier N.  Toward a computational tool predicting the stereochemical outcome of asymmetric reactions: Development and application of a rapid and accurate program based on organic principles.  JAngewandte Chemie - International Edition (2008), 47, 2635-2638

Corbeil C.R., Englebienne P., Moitessier N.  Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0.  Journal of Chemical Information and Modeling (2007), 47, 435-449

User reports, reviews, and comparative studies:

Mesmar, F., et al. The herbicide acetochlor causes lipid peroxidation by inhibition of glutathione peroxidase activity. Toxicological Sciences, Volume 202, Issue 2 (2024).

Lungu, I-A., et al. In Silico Study of the Potential Inhibitory Effects on Escherichia coli DNA Gyrase of Some Hypothetical Fluoroquinolone–Tetracycline Hybrids. Pharmaceuticals (2024).

Guerrero-Morales, J., et al. Chemoenzymatic synthesis of macrocycles via dynamic kinetic resolution of secondary alcohols. Nature Synthesis (2024).

Ramos, A., et al. Discovery of Small Molecule Interleukin 17A Inhibitors with Novel Binding Mode and Stoichiometry: Optimization of DNA-Encoded Chemical Library Hits to In Vivo Active Compounds. Journal of Medicinal Chemistry (2024), 67, 8, 6456-6494.

Breinlinger, E., et al. Targeting the Tyrosine Kinase 2 (TYK2) Pseudokinase Domain: Discovery of the Selective TYK2 Inhibitor ABBV-712 Journal of Medicinal Chemistry (2023), 66, 20, 14335-14356.

Nemes, B., et al. Elucidation of the binding mode of organic polysulfides on the human TRPA1 receptor Frontiers in Physiology (2023)

Mesmar, F., et al. The herbicide acetochlor causes lipid peroxidation by inhibition of glutathione peroxidase 4 BioRxiv (2023)

Ferguson, T. E. G., et al. Novel inhibitiors and activity-based probes targeting serine proteases Frontiers in Chemistry (2022)

Alhayek, A., et al. Inhibition of Collagenase Q1 of Bacillus cereus as a Novel Antivirulence Strategy for the Treatment of Skin-Wound Infections. Advanced Therapeutics (2022)

Refaay, D.A., Ahmed, D.M., Mowafy, M.A., Shaaban, S. Evaluation of novel multifunctional organoselenium compounds as potential cholinesterase inhibitors against Alzheimer’s disease. Medicinal Chemistry Research (2022)

Zoltán Zsidó, B., et al. Prerequisite Binding Modes Determine the Dynamics of Action of Covalent Agonists of Ion Channel TRPA1. Pharmaceuticals (2021).

Zhou, Y., Jiang, Y., Chen, S-J. RNA–ligand molecular docking: Advances and challenges. WIREs Computational Molecular Science (2021), e1571

Bailey, J. J., Wuest, M., Bojovic, T., Kronemann, T., Wängler, C., Wängler, B., Wuest, F., Schirrmacher, R. On the Viability of Tadalafil-Based 18F-Radiotracers for In Vivo Phosphodiesterase 5 (PDE5) PET Imaging. ACS Omega (2021), ASAP

Souza, A.L.P.F., Cardoso, F.J.B., Martins, L.S., Alves, C.N., Silva, J.R.A., Molfetta, F.A. Molecular Modelling Study of Heteroarylamide/Sulfonamide Compounds with Antitrypanosomal Activity. Journal of Brazilian Chemical Society (2021), 32, 1, 83-97

Scarpino, A., Ferenczy, G.G., Keserü, G.M. Covalent Docking in Drug Discovery: Scope and Limitations. Current Pharmaceutical Design (2020), 26, 44, 5684-5699

Caballero, J. The latest automated docking technologies for novel drug discovery. Expert Opinion on Drug Discovery (2020)

Majewski, M.W., et al. Synthesis and Initial Pharmacology of Dual-Targeting Ligands for Putative Complexes of Integrin αVβ3 and PAR2. RSC Medicinal Chemistry (2020), 11, 940-949

Stille, J., Tjutrins, J., Wang, G., Venegas, F.A., Hennecker, C., Rueda, A.M., Miron, C.E., Labarre, A., Plescia, J., Burai Patrascu, M., Vlaho, D., Huot, M., Mittermaier, A.K., Moitessier, N. Design, Synthesis and Biological Evaluation of Novel SARS-CoV-2 3CLpro Covalent Inhibitors. European Journal of Medicinal Chemistry (2020)

Foscato, M., Jensen, V.R. Automated in Silico Design of Homogeneous Catalysts. ACS Catalysis (2020), 10, 3, 2354-2377

Plescia, J., Dufresne, C., Janmamode, N., Wahba, A.S., Mittermaier, A.K., Moitessier, N. Discovery of covalent prolyl oligopeptidase boronic ester inhibitors. European Journal of Medicinal Chemistry (2020), 185, 111783

Bernard-Gauthier, V., Mossine, A.V., Knight, A., Patnaik, D., Zhao, W-N., Cheng, C., Krishnan, H., Xuan, L.L., Chindavong, P.S., Reis, S.A., Chen, J.M., Shao, X., Stauff, J., Artaega, J., Sherman, P., Salem, N., Bonsall, D., Amaral, B., Varlow, C., Well, L., Martarello, L., Patel, S., Liang, S.H., Kurumbail, R.G., Haggarty, S.J., Scott, P.J.H., Vasdev, N. Structural Basis for Achieving GSK-3β Inhibition with High Potency, Selectivity, and Brain Exposure for Positron Emission Tomography Imaging and Drug Discovery. Journal of Medicinal Chemistry (2019), 62, 21, 9600-9617

Reinecke, M., Ruprecht, B., Poser, S., Wiechmann, S., Wilhelm, M., Heinzlmeir, S., Kuster, B., Médard, G. Chemoproteomic Selectivity Profiling of PIKK and PI3K Kinase Inhibitors. ACS Chemical Biology (2019), 14, 4, 655-664

Plescia, J., De Cesco, S., Burai Patrascu, M., Kurian, J., Di Trani, J. M., Dufresne, C., Wahba, A., Janmamode, N., Mittermaier, A. K., Moitessier, N., Integrated synthetic, biophysical and computational investigations of covalent inhibitors of prolyl oligopeptidase and fibroblast activation protein α .Journal of Medicinal Chemistry (2019), 62, 7874-7884

Burkett, D. J., Wyatt, B. N., Mews, M., Bautista, A., Engel, R., Dockendorff, C., Donaldson, W. A., St. Maurice, M. Evaluation of α-hydroxycinnamic acids as pyruvate carboxylase inhibitors. Bioorganic & Medicinal Chemistry (2019), 27, 4041-4047

Yang, Z., Shen, M., Tang, M., Zhang, W., Cui, X., Zhang, Z., Pei, H., Li, Y., Hu, M., Bai, P., Chen, L. Discovery of 1,2,4-oxadiazole-containing hydroxamic acid derivatives as histone deacetylase inhibitors potential application in cancer therapy. European Journal of Medicinal Chemistry (2019), 178, 116-130

Scarpino, A., Ferenczy, G.G., Keserü, G.M. Comparative Evaluation of Covalent Docking Tools. Journal of Chemical Information and Modeling (2018), 58, 7, 1441-1458

Sotriffer, C. Docking of Covalent Ligands: Challenges and Approaches. Molecular Informatics (2018), 37, 1800062

Wu, Y., Dockendorff, C. Synthesis of a novel bicyclic scaffold inspired by the antifungal natural product sordarin. Tetrahedron Letters (2018), 59, 3373-3376

Chen, Y., Wang, X., Xiang, W., He, L., Tang, M., Wang, F., Wang, T., Yang, Z., Yi, Y., Wang, H., Niu, T., Zheng, L., Lei, L., Li, X., Song, H., Chen, L. Development of Purine-Based Hydroxamic Acid Derivatives: Potent Histone Deacetylase Inhibitors with Marked in Vitro and in Vivo Antitumor Activities. Journal of Medicinal Chemistry (2016), 59, 5488-5504

Bernard-Gauthier, V., Aliaga, A., Boudjemeline, M., Hopewell, R., Kostikov, A., Rosa-Neto, P., Thiel, A., Schirrmacher, R. Syntheses and Evaluation of Carbon-11- and Fluorine-18-Radiolabeled pan-Tropomyosin Receptor Kinase (Trk) Inhibitors: Exploration of the 4-Aza-2-oxindole Scaffold as Trk PET Imaging Agents. ACS Chemical Neuroscience (2015), 6, 260-276

Schiavini, P., Cheong K.J., Moitessier N., Auclair K. Active site crowding of P450 3A4 as a strategy to alter its selectivity. ChemBioChem (2017), 18, 248-252

McCracken et al. Phosphorylation of a constrained azacyclic FTY720 analog enhances anti-leukemic activity without inducing S1P receptor activation. Leukemia (2017),

Mariaule G., De Cesco S., Airaghi F., Kurian J., Schiavini P., Rocheleau S., Huskić I., Auclair K., Mittermaier A., Moitessier N. 3-Oxo-hexahydro-1H-isoindole-4-carboxylic acid as a Drug Chiral Bicyclic Scaffold: Structure-based Design and Preparation of Conformationally Constrained Covalent and Non-Covalent Prolyl Oligopeptidase Inhibitors. Journal of Medicinal Chemistry (2016), 59 (9), 4221-4234

Schiavini P., Pottel J., Moitessier N., Auclair K. Metabolic Instability of Cyanothiazolidine-Based Prolyl Oligopeptidase Inhibitors: a Structural Assignment Challenge and Potential Medicinal Chemistry Implications. ChemMedChem (2015), 10, 1174-1183

Schiavini P., Dawe B., Bowie D., Moitessier N. Discovery of novel small-molecule antagonists for GluK2. Bioorganic & Medicinal Chemistry Letters (2015), 25, 2416-2420

Mendoza-Sanchez R., Cotnoir-White D., Kulpa J., Jutras I., Pottel J., Moitessier N., Mader S., Gleason J. L.  Design, synthesis and evaluation of antiestrogen and histone deacetylase inhibitor molecular hybrids. Bioorganic & Medicinal Chemistry Letters (2015), 23, 7597-7606

Agostino, M., Gandhi, N. S., Mancera, R. L.  Development and application of site mapping methods for the design of glycosaminoglycans. Bioorganic & Glycobiology (2014), 24, 840-851

Therrien E., Weill N., Tomberg A., Corbeil C.R., Lee D., Moitessier N.  Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy. Journal of Chemical Information and Modeling (2014), 54, 3198-3210

De Cesco S., Deslandes S., Therrien E., Levan D., Cueto M., Schmidt R., Cantin L.-D., Mittermaier A., Juillerat-Jeanneret L., Moitessier N.  Virtual screening and computational optimization for the discovery of covalent prolyl oligopeptidase inhibitors with activity in human cells. Journal of Medicinal Chemistry (2012), 55, 6306-6315

Castor K.J., Mancini J., Fakhoury J., Weill N., Kieltyka R., Englebienne P., Avakyan N., Mittermaier A., Autexier C., Moitessier N., Sleiman H.F.  Platinum(II) phenanthroimidazoles for targeting telomeric G-quadruplexes. ChemMedChem (2012), 7, 85-94

Lamblin M., Spingarn R., Wang T.-T., Burger M.C., Dabbas B., Moitessier N., White J.H., Gleason J.L.  An o-aminoanilide analogue of 1α,25-dihydroxyvitamin D-3 functions as a strong vitamin D receptor antagonist. Journal of Medicinal Chemistry (2010), 53, 7461-7465

Corbeil C.R., Moitessier N.  Theory and application of medium to high throughput prediction method techniques for asymmetric catalyst design. Journal of Molecular Catalysis A: Chemical (2010), 324, 146-155

Corbeil C.R., Therrien E., Moitessier N. Modeling reality for optimal docking of small molecules to biological targets. Current Computer-Aided Drug Design (2009), 5, 241-263

Lawandi J., Toumieux S., Seyer V., Campbell P., Thielges S., Juillerat-Jeanneret L., Moitessier N. Constrained peptidomimetics reveal detailed geometric requirements of covalent prolyl oligopeptidase inhibitors. Journal of Medicinal Chemistry (2009), 52, 6672-6684

Moitessier N., Englebienne P., Lee D., Lawandi J., Corbeil C.R. Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go. British Journal of Pharmacology (2008), 153, SUPPL. 1, S7-S26