Search Results - "JAKALIAN, Araz"

Revealing Atropisomer Axial Chirality in Drug Discovery by LaPlante, Steven R., Edwards, Paul J., Fader, Lee D., Jakalian, Araz, Hucke, Oliver

“…An often overlooked source of chirality is atropisomerism, which results from slow rotation along a bond axis due to steric hindrance and/or electronic…”
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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation by Jakalian, Araz, Jack, David B., Bayly, Christopher I.

“…We present the first global parameterization and validation of a novel charge model, called AM1‐BCC, which quickly and efficiently generates high‐quality…”
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Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space by Naïm, Marwen, Bhat, Sathesh, Rankin, Kathryn N, Dennis, Sheldon, Chowdhury, Shafinaz F, Siddiqi, Imran, Drabik, Piotr, Sulea, Traian, Bayly, Christopher I, Jakalian, Araz, Purisima, Enrico O

“…We present a binding free energy function that consists of force field terms supplemented by solvation terms. We used this function to calibrate the solvation…”
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Preclinical Profile of BI 224436, a Novel HIV-1 Non-Catalytic-Site Integrase Inhibitor by FENWICK, Craig, AMAD, Ma'an, FADER, Lee D, FAUCHER, Anne-Marie, GARNEAU, Michel, JAKALIAN, Araz, KAWAI, Stephen, LAMORTE, Louie, LAPLANTE, Steven, LAIBIN LUO, MASON, Steve, POUPART, Marc-André, BAILEY, Murray D, RIOUX, Nathalie, SCHROEDER, Patricia, SIMONEAU, Bruno, TREMBLAY, Sonia, TSANTRIZOS, Youla, WITVROUW, Myriam, YOAKIM, Christiane, BETHELL, Richard, BÖS, Michael, BONNEAU, Pierre, CORDINGLEY, Michael, COULOMBE, René, DUAN, Jianmin, EDWARDS, Paul

“…BI 224436 is an HIV-1 integrase inhibitor with effective antiviral activity that acts through a mechanism that is distinct from that of integrase strand…”
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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method by Jakalian, Araz, Bush, Bruce L., Jack, David B., Bayly, Christopher I.

“…The AM1‐BCC method quickly and efficiently generates high‐quality atomic charges for use in condensed‐phase simulations. The underlying features of the…”
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Enantiomeric Atropisomers Inhibit HCV Polymerase and/or HIV Matrix: Characterizing Hindered Bond Rotations and Target Selectivity by LaPlante, Steven R., Forgione, Pat, Boucher, Colette, Coulombe, René, Gillard, James, Hucke, Oliver, Jakalian, Araz, Joly, Marc-André, Kukolj, George, Lemke, Christopher, McCollum, Robert, Titolo, Steve, Beaulieu, Pierre L., Stammers, Timothy

“…An anthranilic acid series of allosteric thumb pocket 2 HCV NS5B polymerase inhibitors exhibited hindered rotation along a covalent bond axis, and the…”
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Improved replicon cellular activity of non-nucleoside allosteric inhibitors of HCV NS5B polymerase: From benzimidazole to indole scaffolds by Beaulieu, Pierre L., Gillard, James, Bykowski, Darren, Brochu, Christian, Dansereau, Nathalie, Duceppe, Jean-Simon, Haché, Bruno, Jakalian, Araz, Lagacé, Lisette, LaPlante, Steven, McKercher, Ginette, Moreau, Elaine, Perreault, Stéphane, Stammers, Timothy, Thauvette, Louise, Warrington, Jeff, Kukolj, George

“…Benzimidazole-based allosteric inhibitors of the hepatitis C virus (HCV) NS5B polymerase were diversified to a variety of topologically related scaffolds…”
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Minimizing the Contribution of Enterohepatic Recirculation to Clearance in Rat for the NCINI Class of Inhibitors of HIV by Fader, Lee D, Carson, Rebekah, Morin, Sébastien, Bilodeau, François, Chabot, Catherine, Halmos, Ted, Bailey, Murray D, Kawai, Stephen H, Coulombe, René, Laplante, Steven, Mekhssian, Kevork, Jakalian, Araz, Garneau, Michel, Duan, Jianmin, Mason, Stephen W, Simoneau, Bruno, Fenwick, Craig, Tsantrizos, Youla, Yoakim, Christiane

“…A scaffold replacement approach was used to identifying the pyridine series of noncatalytic site integrase inhibitors. These molecules bind with higher…”
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An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis by Wang, Wei, Lim, Wendell A, Jakalian, Araz, Wang, Jian, Wang, Junmei, Luo, Ray, Bayly, Christopher I, Kollman, Peter A

“…The Src-homology-3 (SH3) domain of the Caenorhabditis elegans protein Sem−5 binds proline-rich sequences. It is reported that the SH3 domains broadly accept…”
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Ligand Bioactive Conformation Plays a Critical Role in the Design of Drugs That Target the Hepatitis C Virus NS3 Protease by LaPlante, Steven R., Nar, Herbert, Lemke, Christopher T., Jakalian, Araz, Aubry, Norman, Kawai, Stephen H.

“…A ligand-focused strategy employed NMR, X-ray, modeling, and medicinal chemistry to expose the critical role that bioactive conformation played in the design…”
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Design of a brain-penetrant CDK4/6 inhibitor for glioblastoma by Bronner, Sarah M., Merrick, Karl A., Murray, Jeremy, Salphati, Laurent, Moffat, John G., Pang, Jodie, Sneeringer, Christopher J., Dompe, Nicholas, Cyr, Patrick, Purkey, Hans, Boenig, Gladys de Leon, Li, Jun, Kolesnikov, Aleksandr, Larouche-Gauthier, Robin, Lai, Kwong Wah, Shen, Xiaoli, Aubert-Nicol, Samuel, Chen, Yi-Chen, Cheong, Jonathan, Crawford, James J., Hafner, Marc, Haghshenas, Pouyan, Jakalian, Araz, Leclerc, Jean-Philippe, Lim, Ngiap-Kie, O'Brien, Tom, Plise, Emile G., Shalan, Hadil, Sturino, Claudio, Wai, John, Xiao, Yang, Yin, Jianping, Zhao, Liang, Gould, Stephen, Olivero, Alan, Heffron, Timothy P.

“…[Display omitted] CDK4 and CDK6 are kinases with similar sequences that regulate cell cycle progression and are validated targets in the treatment of cancer…”
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Discovery of BI 224436, a Noncatalytic Site Integrase Inhibitor (NCINI) of HIV‑1 by Fader, Lee D, Malenfant, Eric, Parisien, Mathieu, Carson, Rebekah, Bilodeau, François, Landry, Serge, Pesant, Marc, Brochu, Christian, Morin, Sébastien, Chabot, Catherine, Halmos, Ted, Bousquet, Yves, Bailey, Murray D, Kawai, Stephen H, Coulombe, René, LaPlante, Steven, Jakalian, Araz, Bhardwaj, Punit K, Wernic, Dominik, Schroeder, Patricia, Amad, Ma’an, Edwards, Paul, Garneau, Michel, Duan, Jianmin, Cordingley, Michael, Bethell, Richard, Mason, Stephen W, Bös, Michael, Bonneau, Pierre, Poupart, Marc-André, Faucher, Anne-Marie, Simoneau, Bruno, Fenwick, Craig, Yoakim, Christiane, Tsantrizos, Youla

“…An assay recapitulating the 3′ processing activity of HIV-1 integrase (IN) was used to screen the Boehringer Ingelheim compound collection. Hit-to-lead and…”
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Optimization of a Novel DEL Hit That Binds in the Cbl‑b SH2 Domain and Blocks Substrate Binding by Liang, Jun, Lambrecht, Michael J., Arenzana, Teresita L., Aubert-Nicol, Samuel, Bao, Linda, Broccatelli, Fabio, Cai, Jianping, Eidenschenk, Celine, Everett, Christine, Garner, Thomas, Gruber, Felix, Haghshenas, Pouyan, Huestis, Malcolm P., Hsu, Peter L., Kou, Ponien, Jakalian, Araz, Larouche-Gauthier, Robin, Leclerc, Jean-Philippe, Leung, Dennis H., Martin, Aaron, Murray, Jeremy, Prangley, Madeleine, Rutz, Sascha, Kakiuchi-Kiyota, Satoko, Satz, Alexander Lee, Skelton, Nicholas J., Steffek, Micah, Stoffler, Daniel, Sudhamsu, Jawahar, Tan, Sophia, Wang, Jian, Wang, Shouliang, Wang, Qiuyue, Wendorff, Timothy J., Wichert, Moreno, Yadav, Arun, Yu, Christine, Wang, Xiaojing

“…We were attracted to the therapeutic potential of inhibiting Casitas B-lineage lymphoma proto-oncogene-b (Cbl-b), a RING E3 ligase that plays a critical role…”
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Conformation-Based Restrictions and Scaffold Replacements in the Design of Hepatitis C Virus Polymerase Inhibitors: Discovery of Deleobuvir (BI 207127) by LaPlante, Steven R., Bös, Michael, Brochu, Christian, Chabot, Catherine, Coulombe, René, Gillard, James R., Jakalian, Araz, Poirier, Martin, Rancourt, Jean, Stammers, Timothy, Thavonekham, Bounkham, Beaulieu, Pierre L., Kukolj, George, Tsantrizos, Youla S.

“…Conformational restrictions of flexible torsion angles were used to guide the identification of new chemotypes of HCV NS5B inhibitors. Sites for rigidification…”
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Investigation on the role of the tetrazole in the binding of thiotetrazolylacetanilides with HIV-1 wild type and K103N/Y181C double mutant reverse transcriptases by Gagnon, Alexandre, Landry, Serge, Coulombe, René, Jakalian, Araz, Guse, Ingrid, Thavonekham, Bounkham, Bonneau, Pierre R., Yoakim, Christiane, Simoneau, Bruno

“…Different acyclic, cyclic and heterocyclic tetrazole replacements were investigated in order to evaluate the conformational and electronic contribution of the…”
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Importance of Ligand Bioactive Conformation in the Discovery of Potent Indole-Diamide Inhibitors of the Hepatitis C Virus NS5B by LaPlante, Steven R, Gillard, James R, Jakalian, Araz, Aubry, Norman, Coulombe, René, Brochu, Christian, Tsantrizos, Youla S, Poirier, Martin, Kukolj, George, Beaulieu, Pierre L

“…Significant advances have led to receptor induced-fit and conformational selection models for describing bimolecular recognition, but a more comprehensive view…”
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Integrated Strategies for Identifying Leads That Target the NS3 Helicase of the Hepatitis C Virus by LaPlante, Steven R., Padyana, Anil K., Abeywardane, Asitha, Bonneau, Pierre, Cartier, Mireille, Coulombe, René, Jakalian, Araz, Wildeson-Jones, Jessi, Li, Xiang, Liang, Shuang, McKercher, Ginette, White, Peter, Zhang, Qiang, Taylor, Steven J.

“…Future treatments for individuals infected by the hepatitis C virus (HCV) will likely involve combinations of compounds that inhibit multiple viral targets…”
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Anthranilic acid-based Thumb Pocket 2 HCV NS5B polymerase inhibitors with sub-micromolar potency in the cell-based replicon assay by Stammers, Timothy A., Coulombe, René, Duplessis, Martin, Fazal, Gulrez, Gagnon, Alexandre, Garneau, Michel, Goulet, Sylvie, Jakalian, Araz, LaPlante, Steven, Rancourt, Jean, Thavonekham, Bounkham, Wernic, Dominik, Kukolj, George, Beaulieu, Pierre L.

“…Optimization efforts on the anthranilic acid-based Thumb Pocket 2 HCV NS5B polymerase inhibitors 1 and 2 resulted in the identification of multiple structural…”
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Structure-based design of novel HCV NS5B thumb pocket 2 allosteric inhibitors with submicromolar gt1 replicon potency: Discovery of a quinazolinone chemotype by Beaulieu, Pierre L., Coulombe, René, Duan, Jianmin, Fazal, Gulrez, Godbout, Cédrickx, Hucke, Oliver, Jakalian, Araz, Joly, Marc-André, Lepage, Olivier, Llinàs-Brunet, Montse, Naud, Julie, Poirier, Martin, Rioux, Nathalie, Thavonekham, Bounkham, Kukolj, George, Stammers, Timothy A.

“…We describe the structure-based design of a novel lead chemotype that binds to thumb pocket 2 of HCV NS5B polymerase and inhibits cell-based gt1 subgenomic…”
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Discovery of a novel series of non-nucleoside thumb pocket 2 HCV NS5B polymerase inhibitors by Stammers, Timothy A., Coulombe, René, Rancourt, Jean, Thavonekham, Bounkham, Fazal, Gulrez, Goulet, Sylvie, Jakalian, Araz, Wernic, Dominic, Tsantrizos, Youla, Poupart, Marc-André, Bös, Michael, McKercher, Ginette, Thauvette, Louise, Kukolj, George, Beaulieu, Pierre L.

“…A novel series of non-nucleoside thumb pocket 2 HCV NS5B polymerase inhibitors were derived from a fragment-based approach using information from X-ray…”
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