Search Results - "Duca, Jose S."

Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening by Chen, Lieyang, Cruz, Anthony, Ramsey, Steven, Dickson, Callum J, Duca, Jose S, Hornak, Viktor, Koes, David R, Kurtzman, Tom

“…Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to…”
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Rethinking drug design in the artificial intelligence era by Schneider, Petra, Walters, W. Patrick, Plowright, Alleyn T., Sieroka, Norman, Listgarten, Jennifer, Goodnow, Robert A., Fisher, Jasmin, Jansen, Johanna M., Duca, José S., Rush, Thomas S., Zentgraf, Matthias, Hill, John Edward, Krutoholow, Elizabeth, Kohler, Matthias, Blaney, Jeff, Funatsu, Kimito, Luebkemann, Chris, Schneider, Gisbert

“…Artificial intelligence (AI) tools are increasingly being applied in drug discovery. While some protagonists point to vast opportunities potentially offered by…”
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Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling by Dickson, Callum J, Hornak, Viktor, Pearlstein, Robert A, Duca, Jose S

“…Passive membrane permeation of small molecules is essential to achieve the required absorption, distribution, metabolism, and excretion (ADME) profiles of drug…”
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Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K‑Ras4B Dimer Stability by Andreadelis, Ioannis, Kiriakidi, Sofia, Lamprakis, Christos, Theodoropoulou, Anastasia, Doerr, Stefan, Chatzigoulas, Alexios, Manchester, John, Velez-Vega, Camilo, Duca, José S, Cournia, Zoe

“…Ras proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can…”
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Revealing Molecular Determinants of hERG Blocker and Activator Binding by Dickson, Callum J, Velez-Vega, Camilo, Duca, Jose S

“…The Kv11.1 potassium channel, encoded by the human ether-a-go-go-related gene (hERG), plays an essential role in the cardiac action potential. hERG blockade by…”
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Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease by Pavlova, Anna, Lynch, Diane L, Daidone, Isabella, Zanetti-Polzi, Laura, Smith, Micholas Dean, Chipot, Chris, Kneller, Daniel W, Kovalevsky, Andrey, Coates, Leighton, Golosov, Andrei A, Dickson, Callum J, Velez-Vega, Camilo, Duca, José S, Vermaas, Josh V, Pang, Yui Tik, Acharya, Atanu, Parks, Jerry M, Smith, Jeremy C, Gumbart, James C

“…The main protease (M pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many…”
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Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications by Koukos, Panagiotis I., Dehghani-Ghahnaviyeh, Sepehr, Velez-Vega, Camilo, Manchester, John, Tieleman, D. Peter, Duca, José S., Souza, Paulo C. T., Cournia, Zoe

“…Protein lipidations are vital co/post-translational modifications that tether lipid tails to specific protein amino acids, allowing them to anchor to…”
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Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations by Velez-Vega, Camilo, McKay, Daniel J. J, Kurtzman, Tom, Aravamuthan, Vibhas, Pearlstein, Robert A, Duca, José S

“…A statistical-mechanical framework for estimation of solvation entropies and enthalpies is proposed, which is based on the analysis of water as a mixture of…”
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Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation by Pearlstein, Robert A, MacCannell, K Andrew, Erdemli, Gül, Yeola, Sarita, Helmlinger, Gabriel, Hu, Qi-Ying, Farid, Ramy, Egan, William, Whitebread, Steven, Springer, Clayton, Beck, Jeremy, Wang, Hao-Ran, Maciejewski, Mateusz, Urban, Laszlo, Duca, José S

“…Blockade of the hERG potassium channel prolongs the ventricular action potential (AP) and QT interval, and triggers early after depolarizations (EADs) and…”
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LMX1B Mutations Cause Hereditary FSGS without Extrarenal Involvement by BOYER, Olivia, WOERNER, Stéphanie, SZUSTAKOWSKI, Joseph D, HEIBEL, Françoise, MATIGNON, Marie, BAUDOUIN, Véronique, CHANTREL, François, CHAMPIGNEULLE, Jacqueline, MARTIN, Laurent, NITSCHKE, Patrick, GUBLER, Marie-Claire, JOHNSON, Keith J, FAN YANG, CHIBOUT, Salah-Dine, ANTIGNAC, Corinne, OAKELEY, Edward J, LINGHU, Bolan, GRIBOUVAL, Olivier, TETE, Marie-Josèphe, DUCA, José S, KLICKSTEIN, Lloyd, DAMASK, Amy J

“…LMX1B encodes a homeodomain-containing transcription factor that is essential during development. Mutations in LMX1B cause nail-patella syndrome, characterized…”
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Structure-based design and optimization of 2-aminothiazole-4-carboxamide as a new class of CHK1 inhibitors by Huang, Xiaohua, Cheng, Cliff C., Fischmann, Thierry O., Duca, José S., Richards, Matthew, Tadikonda, Praveen K., Reddy, Panduranga Adulla, Zhao, Lianyun, Arshad Siddiqui, M., Parry, David, Davis, Nicole, Seghezzi, Wolfgang, Wiswell, Derek, Shipps, Gerald W.

“…Drug design efforts in the emerging 2-aminothiazole-4-carboxamide class of CHK1 inhibitors have uncovered specific combinations of key substructures within the…”
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Structure-guided discovery of cyclin-dependent kinase inhibitors by Fischmann, Thierry O., Hruza, Alan, Duca, José S., Ramanathan, Lata, Mayhood, Todd, Windsor, William T., Le, Hung V., Guzi, Timothy J., Dwyer, Michael P., Paruch, Kamil, Doll, Ronald J., Lees, Emma, Parry, David, Seghezzi, Wolfgang, Madison, Vincent

“…CDK2 inhibitors containing the related bicyclic heterocycles pyrazolopyrimidines and imidazopyrazines were discovered through high‐throughput screening…”
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Discovery of a Novel Series of CHK1 Kinase Inhibitors with a Distinctive Hinge Binding Mode by Huang, Xiaohua, Cheng, Cliff C, Fischmann, Thierry O, Duca, José S, Yang, Xianshu, Richards, Matthew, Shipps, Gerald W

“…A novel series of CHK1 inhibitors with a distinctive hinge binding mode, exemplified by 2-aryl-N-(2-(piperazin-1-yl)phenyl)thiazole-4-carboxamide, was…”
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Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach—Part 1 by Dwyer, Michael P., Paruch, Kamil, Labroli, Marc, Alvarez, Carmen, Keertikar, Kerry M., Poker, Cory, Rossman, Randall, Fischmann, Thierry O., Duca, Jose S., Madison, Vincent, Parry, David, Davis, Nicole, Seghezzi, Wolfgang, Wiswell, Derek, Guzi, Timothy J.

“…The synthesis and SAR development of a pyrazolo[1,5-a]pyrimidine-based structural series is described which led to the identification of potent, selective CHK1…”
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Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach—Part 2 by Labroli, Marc, Paruch, Kamil, Dwyer, Michael P., Alvarez, Carmen, Keertikar, Kartik, Poker, Cory, Rossman, Randall, Duca, Jose S., Fischmann, Thierry O., Madison, Vincent, Parry, David, Davis, Nicole, Seghezzi, Wolfgang, Wiswell, Derek, Guzi, Timothy J.

“…Previous efforts by our group have established pyrazolo[1,5-a]pyrimidine as a viable core for the development of potent and selective CDK inhibitors. As part…”
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Thermodynamics of Nucleotide and Inhibitor Binding to Wild-Type and Ispinesib-Resistant Forms of Human Kinesin Spindle Protein by Sheth, Payal R, Basso, Andrea, Duca, José S, Lesburg, Charles A, Ogas, Polina, Gray, Kimberly, Nale, Lissette, Mannarino, Anthony F, Prongay, Andrew J, Le, Hung V

“…Current antimitotic cancer chemotherapy based on vinca alkaloids and taxanes target tubulin, a protein required not only for mitotic spindle formation but also…”
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Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots by Dickson, Callum J, Hornak, Viktor, Duca, Jose S

“…Relative binding free-energy (RBFE) calculations are experiencing resurgence in the computer-aided drug design of novel small molecules due to performance…”
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Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments by Lamprakis, Christos, Andreadelis, Ioannis, Manchester, John, Velez-Vega, Camilo, Duca, José S, Cournia, Zoe

“…Protein–protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would…”
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Inhibitors of hepatitis C virus polymerase: Synthesis and characterization of novel 2-oxy-6-fluoro- N-(( S)-1-hydroxy-3-phenylpropan-2-yl)-benzamides by Cheng, Cliff C., Shipps, Gerald W., Yang, Zhiwei, Kawahata, Noriyuki, Lesburg, Charles A., Duca, José S., Bandouveres, Jamie, Bracken, Jack D., Jiang, Chuan-kui, Agrawal, Sony, Ferrari, Eric, Huang, H.-C.

“…The crystal structure of NS5B (green) complexed with 44 (yellow). The intramolecular hydrogen bond is shown in orange. The intermolecular hydrogen bond from…”
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Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design by Danilack, Aaron D., Dickson, Callum J., Soylu, Cihan, Fortunato, Mike, Rodde, Stephane, Munkler, Hagen, Hornak, Viktor, Duca, Jose S.

“…Covalent inhibition offers many advantages over non-covalent inhibition, but covalent warhead reactivity must be carefully balanced to maintain potency while…”
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