Items where Division is "05 Faculty of Science > Departement Pharmazeutische Wissenschaften > Ehemalige Einheiten Pharmazie > Molecular Modeling (Vedani)"

Article

Reinhardt, Jakob K. and Klemd, Amy M. and Danton, Ombeline and De Mieri, Maria and Smiesko, Martin and Huber, Roman and Bürgisser, Thomas and Gründemann, Carsten and Hamburger, Matthias. (2019) Sesquiterpene lactones from Artemisia argyi - absolute configuration and immunosuppressive activity. Journal of Natural Products, 82 (6). pp. 1424-1433.

Schönemann, Wojciech and Cramer, Jonathan and Mühlethaler, Tobias and Fiege, Brigitte and Silbermann, Marleen and Rabbani, Said and Dätwyler, Philipp and Zihlmann, Pascal and Jakob, Roman P. and Sager, Christoph P. and Smiesko, Martin and Schwardt, Oliver and Maier, Timm and Ernst, Beat. (2019) Improvement of Aglycone π-Stacking Yields Nano- to Subnanomolar FimH Antagonists. ChemMedChem, 14 (7). pp. 749-757.

Wahl, Joel and Smiesko, Martin. (2019) Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules. Journal of chemical information and modeling, 59 (2). pp. 754-765.

Don, Charleen G. and Smieško, Martin. (2018) Microsecond MD simulations of human CYP2D6 wild-type and five allelic variants reveal mechanistic insights on the function. PloS one, 13 (8). e0202534.

Don, Charleen G. and Smieško, Martin. (2018) Out-compute drug side effects: Focus on cytochrome P450 2D6 modeling. Wiley interdisciplinary reviews; computational molecular science, 8 (5). e1366.

Dusserre, Camille and Mollergues, Julie and Lo Piparo, Elena and Smieško, Martin and Marin-Kuan, Maricel and Schilter, Benoit and Fussell, Karma. (2018) Using bisphenol A and its analogs to address the feasibility and usefulness of the CALUX-PPARγ assay to identify chemicals with obesogenic potential. Toxicology in vitro : an international journal published in association with BIBRA, 53. pp. 208-221.

Fischer, André and Don, Charleen G. and Smieško, Martin. (2018) Molecular Dynamics Simulations Reveal Structural Differences among Allelic Variants of Membrane-Anchored Cytochrome P450 2D6. Journal of chemical information and modeling, 58 (9). pp. 1962-1975.

Mohebbi, Maryam and Bararjanian, Morteza and Ebrahimi, Samad N. and Smiesko, Martin and Salehi, Peyman. (2018) Noscapine Derivatives as New Chiral Catalysts in Asymmetric Synthesis: Highly Enantioselective Addition of Diethylzinc to Aldehydes. SYNTHESIS-STUTTGART, 50 (9). pp. 1841-1848.

Smieško, Martin and Don, Charleen G. and Meuwly, Roger and Kucsera, Stefan and Brüschweiler, Beat J.. (2018) Large-scale in silico screening of compounds contained in printing inks for food packaging materials. Toxicology Letters, 295. S96.

Wahl, Joel and Smieško, Martin. (2018) Endocrine Disruption at the Androgen Receptor: Employing Molecular Dynamics and Docking for Improved Virtual Screening and Toxicity Prediction. International journal of molecular sciences, 19 (6). p. 1784.

Wahl, Joel and Smieško, Martin. (2018) Thermodynamic Insight into Effects of Water Displacement and Rearrangement upon Ligand Modification using Molecular Dynamics Simulations. ChemMedChem, 13 (13). pp. 1325-1335.

De Mieri, M. and Smiesko, M. and Ismajili, I. and Kaiser, M. and Hamburger, M.. (2017) Acid-induced rearrangement of epoxygermacranolides: synthesis of furanoheliangolides and cadinanes from nobilin. Molecules, 22 (12). E2252.

Guccione, Clizia and Oufir, Mouhssin and Piazzini, Vieri and Eigenmann, Daniela Elisabeth and Jähne, Evelyn Andrea and Zabela, Volha and Faleschini, Maria Teresa and Bergonzi, Maria Camilla and Smiesko, Martin and Hamburger, Matthias and Bilia, Anna Rita. (2017) Andrographolide-loaded nanoparticles for brain delivery: formulation, charcterization and in vitro permeability using hCMEC/D3 cell line. European Journal of Pharmaceutics and Biopharmaceutics, 119. pp. 253-263.

Gürsoy, Oya and Smieško, Martin. (2017) Searching for bioactive conformations of drug-like ligands with current force fields: how good are we? Journal of Cheminformatics, 9 (29). pp. 1-13.

Moradi-Afrapoli, Fahimeh and Ebrahimi, Samad Nejad and Smiesko, Martin and Hamburger, Matthias. (2017) HPLC-Based Activity Profiling for GABAA Receptor Modulators in Extracts: Validation of an Approach Utilizing a Larval Zebrafish Locomotor Assay. Journal of Natural Products, 80 (5). pp. 1548-1557.

Moradi-Afrapoli, Fahimeh and Oufir, Mouhssin and Walter, Fruzsina R. and Deli, Maria A. and Smieško, Martin and Zabela, Volha and Butterweck, Veronika and Hamburger, Matthias. (2016) Validation of UHPLC-MS/MS methods for the determination of kaempferol and its metabolite 4-hydroxyphenyl acetic acid, and application to in vitro BBB and intestinal drug permeability studies. Journal of Pharmaceutical and Biomedical Analysis, 128. pp. 264-274.

Hu, Zhenquan and Wahl, Joël and Hamburger, Matthias and Vedani, Angelo. (2016) Molecular mechanisms of endocrine and metabolic disruption: An in silico study on antitrypanosomal natural products and some derivatives. Toxicology Letters, 252. pp. 29-41.

Eigenmann, Daniela E. and Dürig, Carmen and Jähne, Evelyn A. and Smieško, Martin and Culot, Maxime and Gosselet, Fabien and Cecchelli, Romeo and Cederberg Helms, Hans Christian and Brodin, Birger and Wimmer, Laurin and Mihovilovic, Marko D. and Hamburger, Matthias and Oufir, Mouhssin. (2016) In vitro blood-brain barrier permeability predictions of piperine analogues with GABAA receptor modulating properties. European Journal of Pharmaceutics and Biopharmaceutics, 103. pp. 118-126.

Jähne, E. A. and Eigenmann, D. E. and Moradi-Afrapoli, F. and Verjee, S. and Butterweck, V. and Hebeisen, S. and Hettich, T. and Schlotterbeck, G. and Smiesko, M. and Hamburger, M. and Oufir, M.. (2016) Caco-2 permeability studies and hERG liability assessment of tryptanthrin and indolinone. Planta Medica, 82 (13). pp. 1192-1201.

Jähne, E. A. and Eigenmann, D. E. and Sampath, C. and Butterweck, V. and Culot, M. and Cecchelli, R. and Walter, F. R. and Deli, M. A. and Smiesko, M. and Hamburger, M. and Oufir, M.. (2016) Pharmacokinetics and in vitro blood-brain barrier screening of the plant-derived alkaloid tryptanthrin. Planta Medica, 82 (11-12). pp. 1021-1029.

Moridi Farimani, M. and Taleghani, A. and Aliabadi, A. and Aliahmadi, A. and Esmaeili, M. A. and Sarvestani, N. N. and Khavasi, H. R. and Smiesko, M. and Hamburger, M. and Ebrahimi, S. N.. (2016) New labdane diterpenoids from Salvia leriifolia: Absolute configuration, antimicrobial and cytotoxic activities. Planta Medica, 82 (14). pp. 1279-1285.

Bezençon, Jacqueline and Wittwer, Matthias B. and Cutting, Brian and Smieško, Martin and Wagner, Bjoern and Kansy, Manfred and Ernst, Beat. (2014) pKa determination by 1H NMR spectroscopy - an old methodology revisited. Journal of Pharmaceutical and Biomedical Analysis, 93. pp. 147-155.

Don, Charleen G. and Riniker, Sereina. (2014) Scents and sense: in silico perspectives on olfactory receptors. Journal of Computational Chemistry, 35 (32). pp. 2279-2287.

Eid, Sameh and Saleh, Noureldin and Zalewski, Adam and Vedani, Angelo. (2014) Exploring the free-energy landscape of carbohydrate-protein complexes : development and validation of scoring functions considering the binding-site topology. Journal of computer-aided molecular design, Vol. 28, H. 12. pp. 1191-1204.

Jähne, E. A. and Eigenmann, D. E. and Culot, M. and Cecchelli, R. and Walter, F. R. and Deli, M. A. and Tremmel, R. and Fricker, G. and Smiesko, M. and Hamburger, M. and Oufir, M.. (2014) Development and validation of an LC-MS/MS method for assessment of an anti-inflammatory indolinone derivative by in vitro blood-brain barrier models. Journal of Pharmaceutical and Biomedical Analysis, 98. pp. 235-246.

Vedani, Angelo and Dobler, Max and Hu, Zhenquan and Smiesko, Martin. (2014) OpenVirtualToxLab - a platform for generating and exchanging in silico toxicity data. Toxicology letters, Vol. 232, H. 2. pp. 519-532.

Biedermann, Sandra and Zurfluh, Michael and Grob, Koni and Vedani, Angelo and Brüschweiler, Beat J.. (2013) Migration of cyclo-diBA from coatings into canned food : method of analysis, concentration determined in a survey and in silico hazard profiling. Food and chemical toxicology, Vol. 58. pp. 107-115.

Ebrahimi, Samad N. and Zimmermann, Stefanie and Zaugg, Janine and Smiesko, Martin and Brun, Reto and Hamburger, Matthias. (2013) Abietane Diterpenoids from Salvia sahendica - Antiprotozoal Activity and Determination of Their Absolute Configurations. Planta medica, Vol. 79, H. 2. pp. 150-156.

Eid, Sameh and Zalewski, Adam and Smiesko, Martin and Ernst, Beat and Vedani, Angelo. (2013) A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences. International Journal of Molecular Sciences, 14 (1). pp. 684-700.

Moradi-Afrapoli, Fahimeh and Ebrahimi, Samad Nejad and Smiesko, Martin and Raith, Melanie and Zimmermann, Stefanie and Nadjafi, Farsad and Brun, Reto and Hamburger, Matthias. (2013) Bisabololoxide derivatives from Artemisia persica, and determination of their absolute configurations by ECD. Phytochemistry, Vol. 85. pp. 143-152.

Smiesko, Martin. (2013) DOLINA - Docking Based on a Local Induced-Fit Algorithm : Application toward Small-Molecule Binding to Nuclear Receptors. Journal of chemical information and modeling, Vol. 53, H. 6. pp. 1415-1423.

Schwizer, Daniel and Patton, John T. and Cutting, Brian and Smiesko, Martin and Wagner, Beatrice and Kato, Ako and Weckerle, Céline and Binder, Florian P. C. and Rabbani, Said and Schwardt, Oliver and Magnani, John L. and Ernst, Beat. (2012) Pre-organization of the core structure of E-selectin antagonists. Chemistry - A European Journal, 18 (5). pp. 1342-1351.

Titz, Alexander and Marra, Alberto and Cutting, Brian and Smiesko, Martin and Papandreou, George and Dondoni, Alessandro and Ernst, Beat. (2012) Conformational constraints : nature does it best with Sialyl Lewisx. European Journal of Organic Chemistry, 2012 (28). pp. 5534-5539.

Vedani, Angelo and Dobler, Max and Smiesko, Martin. (2012) VirtualToxLab - a platform for estimating the toxic potential of drugs, chemicals and natural products. Toxicology and applied pharmacology, Vol. 261, H. 2. pp. 142-153.

Rossato, G. and Ernst, Beat and Vedani, Angelo and Smiesko, Martin. (2011) AcquaAlta: a directional approach to the solvation of ligand-protein complexes. Journal of Chemical Information and Modeling, 51 (8). pp. 1867-1881.

Zaugg, Janine and Ebrahimi, Samad Nejad and Smiesko, Martin and Baburin, Igor and Hering, Steffen and Hamburger, Matthias. (2011) Identification of GABAA receptor modulators in Kadsura longipedunculata and assignment of absolute configurations by quantum-chemical ECD calculations. Phytochemistry, Vol. 72, H. 18. pp. 2385-2395.

Rossato, Gianluca and Ernst, Beat and Smiesko, Martin and Spreafico, Morena and Vedani, Angelo. (2010) Probing small-molecule binding to cytochrome P450 2D6 and 2C9: an in silico protocol for generating toxicity alerts. ChemMedChem, 5 (12). pp. 2088-2101.

Spreafico, Morena and Smiesko, Martin and Peristera, Ourania and Rossato, Gianluca and Vedani, Angelo. (2010) Probing small-molecule binding to the liver-X receptor : a mixed-model QSAR study. Molecular informatics, Vol. 29, H. 1-2 , S. 27–36.

Thesis

Hu, Zhenquan. Docking, scoring and binding-affinity prediction in computer-aided drug discovery : I development of a scoring function for quantifying binding affinities. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

Eid, Sameh Mansour Abbas. Molecular simulations of carbohydrate-protein complexes. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

Zalewski, Adam. In pursuit of a novel UTI treatment strategy - an "in silico" study of the FimH adhesin. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

Rossato, Gianluca. Molecular simulations on proteins of biomedical interest : A. Ligand-protein hydration B. Cytochrome P450 2D6 and 2C9 C. Myelin associated glycoprotein (MAG). 2011, Doctoral Thesis, University of Basel, Faculty of Science.

Peristera, Ourania. QSAR at the estrogen and mineralocorticoid receptors. 2010, Doctoral Thesis, University of Basel, Faculty of Science.

Other

Vedani Angelo, Dobler Max and Smiesko, Martin. (2013) Software VirtualToxLab : user reference and manual - version 4.8. [Basel].