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Peer-reviewed journal articles

2020

[157]

W. Du, D. Machalz, Q. Yan, E. J. Sorensen, G. Wolber, and M. Bureik. Importance of asparagine-381 and arginine-487 for substrate recognition in CYP4Z1, Biochem Pharmacol, 174:113850, 2020.
Links: [doi:10.1016/j.bcp.2020.113850] [show BibTeX]

[156]

M. Grabowski, M. S. Murgueitio, M. Bermudez, G. Wolber, and G. Weindl. The novel small-molecule antagonist MMG-11 preferentially inhibits TLR2/1 signaling, Biochem Pharmacol, 171:113687, 2020.
Links: [doi:10.1016/j.bcp.2019.113687] [show BibTeX]

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2019

[155]

L. Agnetta, M. Bermudez, F. Riefolo, C. Matera, E. Claro, R. Messerer, T. Littmann, G. Wolber, U. Holzgrabe, and M. Decker. Fluorination of Photoswitchable Muscarinic Agonists Tunes Receptor Pharmacology and Photochromic Properties, J Med Chem, 62(6):3009-3020, 2019.
Links: [doi:10.1021/acs.jmedchem.8b01822] [show BibTeX]

[154]

H. Aygun Cevher, D. Schaller, M. A. Gandini, O. Kaplan, E. Gambeta, F. X. Zhang, M. Celebier, M. N. Tahir, G. W. Zamponi, G. Wolber, and M. G. Gunduz. Discovery of Michael acceptor containing 1,4-dihydropyridines as first covalent inhibitors of L-/T-type calcium channels, Bioorg Chem, 91:103187, 2019.
Links: [doi:10.1016/j.bioorg.2019.103187] [show BibTeX]

[153]

M. Bermudez, T. N. Nguyen, C. Omieczynski, and G. Wolber. Strategies for the discovery of biased GPCR ligands, Drug Discov Today, 24(4):1031-1037, 2019.
Links: [doi:10.1016/j.drudis.2019.02.010] [show BibTeX]

[152]

P. Durairaj, L. Fan, D. Machalz, G. Wolber, and M. Bureik. Functional characterization and mechanistic modeling of the human cytochrome P450 enzyme CYP4A22, Febs Lett, 593(16):2214-2225, 2019.
Links: [doi:10.1002/1873-3468.13489] [show BibTeX]

[151]

A. Nass, D. Schaller, and G. Wolber. Assessment of Flexible Shape Complementarity: New Opportunities to Explain and Induce Selectivity in Ligands of Protein Tyrosine Phosphatase 1B, Mol Inform, 38(5):1800141, 2019.
Links: [doi:10.1002/minf.201800141] [show BibTeX]

[150]

M. J. Ojeda-Montes, A. Casanova-Marti, A. Gimeno, S. Tomas-Hernandez, A. Cereto-Massague, G. Wolber, R. Beltran-Debon, C. Valls, M. Mulero, M. Pinent, G. Pujadas, and S. Garcia-Vallve. Mining large databases to find new leads with low similarity to known actives: application to find new DPP-IV inhibitors, Future Med Chem, 11(12):1387-1401, 2019.
Links: [doi:10.4155/fmc-2018-0597] [show BibTeX]

[149]

R. Ottanà, P. Paoli, G. Lori, I. Adornato, S. Previti, A. Naß, G. Wolber, and R. Maccari. Design and evaluation of non-carboxylate 5-arylidene-2-thioxo-4-imidazolidinones as novel non-competitive inhibitors of protein tyrosine phosphatase 1B, Bioorg Chem, 92:103211, 2019.
Links: [doi:10.1016/j.bioorg.2019.103211] [show BibTeX]

[148]

D. Schaller, S. Hagenow, H. Stark, and G. Wolber. Ligand-guided homology modeling drives identification of novel histamine H3 receptor ligands, Plos One, 14(6):e0218820, 2019.
Links: [doi:10.1371/journal.pone.0218820] [show BibTeX]

[147]

D. Schaller, S. Pach, and G. Wolber. PyRod: Tracing Water Molecules in Molecular Dynamics Simulations, J Chem Inf Model, 59(6):2818-2829, 2019.
Links: [doi:10.1021/acs.jcim.9b00281] [show BibTeX]

[146]

S. Schramm, L. Agnetta, M. Bermudez, H. Gerwe, M. Irmen, J. Holze, T. Littmann, G. Wolber, C. Trankle, and M. Decker. Novel BQCA- and TBPB-Derived M1 Receptor Hybrid Ligands: Orthosteric Carbachol Differentially Regulates Partial Agonism, ChemMedChem, 14(14):1349-1358, 2019.
Links: [doi:10.1002/cmdc.201900283] [show BibTeX]

[145]

D. Sribar, M. Grabowski, M. S. Murgueitio, M. Bermudez, G. Weindl, and G. Wolber. Identification and characterization of a novel chemotype for human TLR8 inhibitors, Eur J Med Chem, 179:744-752, 2019.
Links: [doi:10.1016/j.ejmech.2019.06.084] [show BibTeX]

[144]

A. Stoll, S. Loke, J. F. Joseph, D. Machalz, X. de la Torre, F. Botrè, G. Wolber, M. Bureik, and M. K. Parr. Fine-mapping of the substrate specificity of human steroid 21-hydroxylase (CYP21A2), The Journal of Steroid Biochemistry and Molecular Biology, :105446, 2019.
Links: [doi:https://.org/10.1016/j.jsbmb.2019.105446] [show BibTeX]

[143]

N. K. Wenke, J. Kreye, E. Andrzejak, A. van Casteren, J. Leubner, M. S. Murgueitio, S. M. Reincke, C. Secker, L. Schmidl, C. Geis, F. Ackermann, M. Nikolaus, C. C. Garner, H. Wardemann, G. Wolber, and H. Pruess. NMDA receptor dysfunction via unmutated human antibodies against the NR1 subunit, Ann Neurol, 85(5):771-776, 2019.
Links: [doi:10.1002/ana.25460] [show BibTeX]

[142]

O. Zierau, A. Kolodziejczyk, G. Vollmer, D. Machalz, G. Wolber, D. Thieme, and A. M. Keiler. Comparison of the three SARMs RAD-140, GLPG0492 and GSK-2881078 in two different in vitro bioassays, and in an in silico androgen receptor binding assay, The Journal of Steroid Biochemistry and Molecular Biology, 189:81-86, 2019.
Links: [doi:10.1016/j.jsbmb.2019.02.014] [show BibTeX]

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2018

[141]

M. Grabowski, M. S. Murgueitio, M. Bermudez, J. Rademann, G. Wolber, and G. Weindl. Identification of a pyrogallol derivative as a potent and selective human TLR2 antagonist by structure-based virtual screening, Biochem Pharmacol, 154:148-160, 2018.
Links: [doi:10.1016/j.bcp.2018.04.018] [show BibTeX]

[140]

A. M. Keiler, O. Zierau, S. Wolf, P. Diel, W. Schänzer, G. Vollmer, D. Machalz, G. Wolber, and M. K. Parr. Androgen- and estrogen-receptor mediated activities of 4-hydroxytestosterone, 4-hydroxyandrostenedione and their human metabolites in yeast based assays, Toxicol Lett, 292:39-45, 2018.
Links: [doi:10.1016/j.toxlet.2018.04.026] [show BibTeX]

[139]

J. Liu, L. Chen, J. F. Joseph, A. Naß, A. Stoll, X. de la Torre, F. Botrè, G. Wolber, M. K. Parr, and M. Bureik. Combined chemical and biotechnological production of 20βOH-NorDHCMT, a long-term metabolite of Oral-Turinabol (DHCMT), J Inorg Biochem, 183:165-171, 2018.
Links: [doi:10.1016/j.jinorgbio.2018.02.020] [show BibTeX]

[138]

R. Maccari, A. Del Corso, P. Paoli, I. Adornato, G. Lori, F. Balestri, M. Cappiello, A. Naß, G. Wolber, and R. Ottana. An investigation on 4-thiazolidinone derivatives as dual inhibitors of aldose reductase and protein tyrosine phosphatase 1B, in the search for potential agents for the treatment of type 2 diabetes mellitus and its complications, Bioorg Med Chem Lett, :, 2018.
Links: [doi:10.1016/j.bmcl.2018.10.024] [show BibTeX]

[137]

R. Maccari, R. Ettari, I. Adornato, A. Naß, G. Wolber, A. Bitto, F. Mannino, F. Aliquo, G. Bruno, F. Nicolo, S. Previti, S. Grasso, M. Zappala, and R. Ottana. Identification of 2-thioxoimidazolidin-4-one derivatives as novel noncovalent proteasome and immunoproteasome inhibitors, Bioorg Med Chem Lett, 28(3):278-283, 2018.
Links: [doi:10.1016/j.bmcl.2017.12.053] [show BibTeX]

[136]

D. Schaller, M. G. Gündüz, F. X. Zhang, G. W. Zamponi, and G. Wolber. Binding mechanism investigations guiding the synthesis of novel condensed 1,4-dihydropyridine derivatives with L-/T-type calcium channel blocking activity, Eur J Med Chem, 155:1-12, 2018.
Links: [doi:10.1016/j.ejmech.2018.05.032] [show BibTeX]

[135]

R. Schulz, A. Atef, D. Becker, F. Gottschalk, C. Tauber, S. Wagner, C. Arkona, A. A. Abdel-Hafez, H. H. Farag, J. Rademann, and G. Wolber. Phenylthiomethyl ketone-based fragments show selective and irreversible inhibition of enteroviral 3C proteases, J Med Chem, 61(3):1218-1230, 2018.
Links: [doi:10.1021/acs.jmedchem.7b01440] [show BibTeX]

[134]

A. Tkachenko, M. Bermudez, S. Irmer-Stooff, D. Genkinger, F. Henkler-Stephani, G. Wolber, and A. Luch. Nuclear transport of the human aryl hydrocarbon receptor and subsequent gene induction relies on its residue histidine 291, Arch Toxicol, 92(3):1151-1160, 2018.
Links: [doi:10.1007/s00204-017-2129-0] [show BibTeX]

[133]

F. Yang, D. Machalz, S. Wang, Z. Li, G. Wolber, and M. Bureik. A common polymorphic variant of UGT1A5 displays increased activity due to optimized cofactor binding, Febs Lett, 592(11):1837-1846, 2018.
Links: [doi:10.1002/1873-3468.13072] [show BibTeX]

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2017

[132]

H. A. Abuelizz, R. Al-Salahi, J. Al-Asri, J. Mortier, M. Marzouk, E. Ezzeldin, A. A. Ali, M. G. Khalil, G. Wolber, H. A. Ghabbour, A. A. Almehizia, and G. A. Abdel Jaleel. Synthesis, crystallographic characterization, molecular docking and biological activity of isoquinoline derivatives, Chem Cent J, 11(1):103, 2017.
Links: [doi:10.1186/s13065-017-0321-1] [show BibTeX]

[131]

M. Bermudez, A. Bock, F. Krebs, U. Holzgrabe, K. Mohr, M. J. Lohse, and G. Wolber. Ligand-specific restriction of extracellular conformational dynamics constrains signaling of the M2 muscarinic receptor, ACS Chem Biol, 12(7):1743-1748, 2017.
Links: [doi:10.1021/acschembio.7b00275] [show BibTeX]

[130]

J. Mortier, J. R. C. Prévost, D. Sydow, S. Teuchert, C. Omieczynski, M. Bermudez, R. Frédérick, and G. Wolber. Arginase Structure and Inhibition: Catalytic Site Plasticity Reveals New Modulation Possibilities, Scientific Reports, 7(1):13616, 2017.
Links: [doi:10.1038/s41598-017-13366-4] [show BibTeX]

[129]

M. S. Murgueitio, S. Ebner, P. Hörtnagl, C. Rakers, R. Bruckner, P. Henneke, G. Wolber, and S. Santos-Sierra. Enhanced immunostimulatory activity of in silico discovered agonists of Toll-like receptor 2 (TLR2), Biochimica et Biophysica Acta (BBA) - General Subjects, 1861(11):2680-2689, 2017.
Links: [doi:10.1016/j.bbagen.2017.07.011] [show BibTeX]

[128]

M. S. Murgueitio, C. Rakers, A. Frank, and G. Wolber. Balancing Inflammation: Computational Design of Small-Molecule Toll-like Receptor Modulators, Trends Pharmacol Sci, 38(2):155-168, 2017.
Links: [doi:10.1016/j.tips.2016.10.007] [show BibTeX]

[127]

R. Ottana, P. Paoli, A. Naß, G. Lori, V. Cardile, I. Adornato, A. Rotondo, A. C. Eleonora Graziano, G. Wolber, and R. Maccari. Discovery of 4-[(5-arylidene-4-oxothiazolidin-3-yl)methyl]benzoic acid derivatives active as novel potent allosteric inhibitors of protein tyrosine phosphatase 1B: In silico studies and in vitro evaluation as insulinomimetic and anti-inflammatory agents, Eur J Med Chem, 127:840-858, 2017.
Links: [doi:10.1016/j.ejmech.2016.10.063] [show BibTeX]

[126]

F. Sanz, F. Pognan, T. Steger-Hartmann, C. Díaz, M. Cases, M. Pastor, P. Marc, J. Wichard, K. Briggs, D. K. Watson, T. Kleinöder, C. Yang, A. Amberg, M. Beaumont, A. J. Brookes, S. Brunak, M. T. D. Cronin, G. F. Ecker, S. Escher, N. Greene, A. Guzmán, A. Hersey, P. Jacques, L. Lammens, J. Mestres, W. Muster, H. Northeved, M. Pinches, J. Saiz, N. Sajot, A. Valencia, J. van der Lei, N. P. E. Vermeulen, E. Vock, G. Wolber, and I. Zamora. Legacy data sharing to improve drug safety assessment: the eTOX project, Nat Rev Drug Discov, 16:811, 2017.
Links: [doi:10.1038/nrd.2017.177] [show BibTeX]

[125]

D. Schaller, S. Hagenow, G. Alpert, A. Naß, R. Schulz, M. Bermudez, H. Stark, and G. Wolber. Systematic Data Mining Reveals Synergistic H3R/MCHR1 Ligands, ACS Medicinal Chemistry Letters, 8(6):648-653, 2017.
Links: [doi:10.1021/acsmedchemlett.7b00118] [show BibTeX]

[124]

Q. Yan, D. Machalz, A. Zöllner, E. J. Sorensen, G. Wolber, and M. Bureik. Efficient substrate screening and inhibitor testing of human CYP4Z1 using permeabilized recombinant fission yeast, Biochem Pharmacol, 146:174-187, 2017.
Links: [doi:10.1016/j.bcp.2017.09.011] [show BibTeX]

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2016

[123]

J. Al-Asri, G. Gyémánt, E. Fazekas, G. Lehoczki, M. F. Melzig, G. Wolber, and J. Mortier. α-Amylase Modulation: Discovery of Inhibitors Using a Multi-Pharmacophore Approach for Virtual Screening, ChemMedChem, 11(21):2372-2377, 2016.
Links: [doi:10.1002/cmdc.201600427] [show BibTeX]

[122]

D. Becker, Z. Kaczmarska, C. Arkona, R. Schulz, C. Tauber, G. Wolber, R. Hilgenfeld, M. Coll, and J. Rademann. Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments, Nat Commun, 7:12761, 2016.
Links: [doi:10.1038/ncomms12761] [show BibTeX]

[121]

M. Bermudez, J. Mortier, C. Rakers, D. Sydow, and G. Wolber. More than a look into a crystal ball: protein structure elucidation guided by molecular dynamics simulations, Drug Discov Today, 21(11):1799-1805, 2016.
Links: [doi:10.1016/j.drudis.2016.07.001] [show BibTeX]

[120]

A. Bock, M. Bermudez, F. Krebs, C. Matera, B. Chirinda, D. Sydow, C. Dallanoce, U. Holzgrabe, M. De Amici, M. J. Lohse, G. Wolber, and K. Mohr. Ligand Binding Ensembles Determine Graded Agonist Efficacies at a G Protein-coupled Receptor, J Biol Chem, 291(31):16375-16389, 2016.
Links: [doi:10.1074/jbc.M116.735431] [show BibTeX]

[119]

S. Bock, M. S. Murgueitio, G. Wolber, and G. Weindl. Acute myeloid leukaemia-derived Langerhans-like cells enhance Th1 polarization upon TLR2 engagement, Pharmacol Res, 105:44-53, 2016.
Links: [doi:10.1016/j.phrs.2016.01.016] [show BibTeX]

[118]

E. Guerrieri, M. Bermudez, G. Wolber, I. P. Berzetei-Gurske, H. Schmidhammer, and M. Spetea. Structural determinants of diphenethylamines for interaction with the κ opioid receptor: Synthesis, pharmacology and molecular modeling studies, Bioorg Med Chem Lett, 26(19):4769-4774, 2016.
Links: [doi:10.1016/j.bmcl.2016.08.031] [show BibTeX]

[117]

J. R. Homoki, A. Nemes, E. Fazekas, G. Gyémánt, P. Balogh, F. Gál, J. Al-Asri, J. Mortier, G. Wolber, L. Babinszky, and J. Remenyik. Anthocyanin composition, antioxidant efficiency, and α-amylase inhibitor activity of different Hungarian sour cherry varieties (Prunus cerasus L.), Food Chem, 194:222-229, 2016.
Links: [doi:10.1016/j.foodchem.2015.07.130] [show BibTeX]

[116]

S. Köhling, G. Künze, K. Lemmnitzer, M. Bermudez, G. Wolber, J. Schiller, D. Huster, and J. Rademann. Chemoenzymatic Synthesis of Nonasulfated Tetrahyaluronan with a Paramagnetic Tag for Studying Its Complex with Interleukin-10, Chemistry - A European Journal, 22(16): 5563-5574, 2016.
Links: [doi:10.1002/chem.201504459] [show BibTeX]

[115]

B. Nizami, D. Sydow, G. Wolber, and B. Honarparvar. Molecular insight on the binding of NNRTI to K103N mutated HIV-1 RT: molecular dynamics simulations and dynamic pharmacophore analysis, Mol Biosyst, 12:3385-3395, 2016.
Links: [doi:10.1039/C6MB00428H] [show BibTeX]

[114]

V. Obermoser, M. E. Urban, M. S. Murgueitio, G. Wolber, U. Kintscher, and R. Gust. New telmisartan-derived PPARγ agonists: Impact of the 3D-binding mode on the pharmacological profile, Eur J Med Chem, 124:138-152, 2016.
Links: [doi:10.1016/j.ejmech.2016.08.027] [show BibTeX]

[113]

C. Rakers, F. Schumacher, W. Meinl, H. Glatt, B. Kleuser, and G. Wolber. In silico prediction of human sulfotransferase 1E1 activity guided by pharmacophores from molecular dynamics simulations, J Biol Chem, 291(1):58-71, 2016.
Links: [doi:10.1074/jbc.M115.685610] [show BibTeX]

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2015 and earlier

[112]

J. Al-Asri, E. Fazekas, G. Lehoczki, A. Perdih, C. Görick, M. F. Melzig, G. Gyémánt, G. Wolber, and J. Mortier. From carbohydrates to drug-like fragments: Rational development of novel α-amylase inhibitors, Bioorg Med Chem, 23(20):6725-6732, 2015.
Links: [doi:10.1016/j.bmc.2015.09.007] [show BibTeX]

[111]

M. Bermudez, C. Rakers, and G. Wolber. Structural characteristics of the allosteric binding site represent a key to subtype selective modulators of muscarinic acetylcholine receptors, Mol Inf, 34(8):526-530, 2015.
Links: [doi:10.1002/minf.201500025] [show BibTeX]

[110]

M. Bermudez, and G. Wolber. Structure vs. function - the impact of computational methods on the discovery of specific GPCR-ligands, Bioorg Med Chem, 23(14):3907-3912, 2015.
Links: [doi:10.1016/j.bmc.2015.03.026] [show BibTeX]

[109]

R. B. El-Houri, D. E. Kotowska, K. B. Christensen, S. Bhattacharya, N. Oksbjerg, G. Wolber, K. Kristiansen, and L. P. Christensen. Polyacetylenes from carrots (Daucus carota) improve glucose uptake in vitro in adipocytes and myotubes, Food and Function, 6(7):2135-44, 2015.
Links: [doi:10.1039/C5FO00223K] [show BibTeX]

[108]

R. B. El-Houri, J. Mortier, M. S. Murgueitio, G. Wolber, and L. P. Christensen. Identification of PPARγ Agonists from Natural Sources Using Different In Silico Approaches, Planta Med, 81(06):488-494, 2015.
Links: [doi:10.1055/s-0034-1383119] [show BibTeX]

[107]

S. Grosskopf, C. Eckert, C. Arkona, S. Radetzki, K. Böhm, U. Heinemann, G. Wolber, J. v. Kries, W. Birchmeier, and J. Rademann. Selective inhibitors of the protein tyrosine phosphatase SHP2 block cellular motility and growth of cancer cells in-vitro and in-vivo, ChemMedChem, 10(5):815-826, 2015.
Links: [doi:10.1002/cmdc.201500015] [show BibTeX]

[106]

C. Meinguet, C. Bruyère, R. Frédérick, V. Mathieu, C. Vancraeynest, L. Pochet, J. Laloy, J. Mortier, G. Wolber, R. Kiss, B. Masereel, and J. Wouters. 3D-QSAR, Design, Synthesis and characterization of trisubstituted harmine derivatives with in vitro antiproliferative properties, Eur J Med Chem, 94:45-55, 2015.
Links: [doi:10.1016/j.ejmech.2015.02.044] [show BibTeX]

[105]

J. Mortier, E. K. Nyakatura, O. Reimann, S. Huhmann, J. O. Daldrop, C. Baldauf, G. Wolber, M. S. Miettinen, and B. Koksch. Coiled-Coils in Phage Display Screening: Insight into Exceptional Selectivity Provided by Molecular Dynamics, J Chem Inf Model, 55(3):495-500, 2015.
Links: [doi:10.1021/ci500689c] [show BibTeX]

[104]

J. Mortier, C. Rakers, M. Bermudez, M. S. Murgueitio, S. Riniker, and G. Wolber. The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes, Drug Discov Today, 20(6):686-702, 2015.
Links: [doi:10.1016/j.drudis.2015.01.003] [show BibTeX]

[103]

M. K. Parr, F. Botrè, A. Naß, J. Hengevoss, P. Diel, and G. Wolber. Ecdysteroids: A novel class of anabolic agents?, Biol Sport, 32(2):169-173, 2015.
Links: [doi:10.5604/20831862.1144420] [show BibTeX]

[102]

A. Perdih, M. Hrast, K. Pureber, H. Barreteau, S. Grdadolnik, D. Kocjan, S. Gobec, T. Solmajer, and G. Wolber. Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization, J Comput Aided Mol Des, :1-20, 2015.
Links: [doi:10.1007/s10822-015-9843-6] [show BibTeX]

[101]

C. Rakers, M. Bermudez, B. G. Keller, J. Mortier, and G. Wolber. Computational close up on protein–protein interactions: how to unravel the invisible using molecular dynamics simulations?, WIREs Comput Mol Sci, 5(5):345-359, 2015.
Links: [doi:10.1002/wcms.1222] [show BibTeX]

[100]

V. Asante, J. Mortier, G. Wolber, and B. Koksch. Impact of fluorination on proteolytic stability of peptides: a case study with α-chymotrypsin and pepsin, Amino Acids, 46(12):2733-2744, 2014.
Links: [doi:10.1007/s00726-014-1819-7] [show BibTeX]

[99]

S. A. Galal, S. H. M. Khairat, F. A. F. Ragab, A. S. Abdelsamie, M. M. Ali, S. M. Soliman, J. Mortier, G. Wolber, and H. I. El Diwani. Design, synthesis and molecular docking study of novel quinoxalin-2(1H)-ones as anti-tumor active agents with inhibition of tyrosine kinase receptor and studying their cyclooxygenase-2 activity, Eur J Med Chem, 86:122-132, 2014.
Links: [doi:10.1016/j.ejmech.2014.08.048] [show BibTeX]

[98]

D. Kotowska, R. B. El-Houri, K. Borkowski, R. K. Petersen, X. C. Fretté, G. Wolber, K. Grevsen, K. B. Christensen, L. P. Christensen, and K. Kristiansen. Isomeric C12-Alkamides from the Roots of Echinacea purpurea Improve Basal and Insulin-Dependent Glucose Uptake in 3T3-L1 Adipocytes, Planta Med, 80(18):1712-1720, 2014.
Links: [doi:10.1055/s-0034-1383252] [show BibTeX]

[97]

M. S. Murgueitio, P. Henneke, H. Glossmann, S. Santos-Sierra, and G. Wolber. Prospective Virtual Screening in a Sparse Data Scenario: Design of Small-Molecule TLR2 Antagonists, ChemMedChem, 9(4):813-822, 2014.
Links: [doi:10.1002/Cmdc.201300445] [show BibTeX]

[96]

E. K. Nyakatura, R. R. Araghi, J. Mortier, S. Wieczorek, C. Baldauf, G. Wolber, and B. Koksch. An Unusual Interstrand H-Bond Stabilizes the Heteroassembly of Helical alpha beta gamma-Chimeras with Natural Peptides, ACS Chem Biol, 9(3):613-616, 2014.
Links: [doi:10.1021/Cb4007979] [show BibTeX]

[95]

E. K. Nyakatura, J. Mortier, V. S. Radtke, S. Wieczorek, R. Rezaei Araghi, C. Baldauf, G. Wolber, and B. Koksch. β- and γ-Amino Acids at α-Helical Interfaces: Toward the Formation of Highly Stable Foldameric Coiled Coils, ACS Medicinal Chemistry Letters, 5(12):1300-1303, 2014.
Links: [doi:10.1021/ml500361c] [show BibTeX]

[94]

R. Ottana, R. Maccari, J. Mortier, A. Caselli, S. Amuso, G. Camici, A. Rotondo, G. Wolber, and P. Paoli. Synthesis, biological activity and structure-activity relationships of new benzoic acid-based protein tyrosine phosphatase inhibitors endowed with insulinomimetic effects in mouse C2C12 skeletal muscle cells, Eur J Med Chem, 71:112-127, 2014.
Links: [doi:10.1016/J.Ejmech.2013.11.001] [show BibTeX]

[93]

A. Perdih, M. Hrast, H. Barreteau, S. Gobec, G. Wolber, and T. Solmajer. Benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC-MurF), Bioorg Med Chem, 22(15):4124-4134, 2014.
Links: [doi:10.1016/j.bmc.2014.05.058] [show BibTeX]

[92]

A. Perdih, M. Hrast, H. Barreteau, S. Gobec, G. Wolber, and T. Solmajer. Inhibitor Design Strategy Based on an Enzyme Structural Flexibility: A Case of Bacterial MurD Ligase, J Chem Inf Model, 54(5):1451-1466, 2014.
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C. Rakers, S. Schwerdtfeger, J. Mortier, S. Duwe, T. Wolff, G. Wolber, and M. F. Melzig. Inhibitory potency of flavonoid derivatives on influenza virus neuraminidase, Bioorg Med Chem Lett, 24(17):4312-4317, 2014.
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J. Schmitz, D. van der Mey, M. Bermudez, J. Klöckner, R. Schrage, E. Kostenis, C. Tränkle, G. Wolber, K. Mohr, and U. Holzgrabe. Dualsteric Muscarinic Antagonists - Orthosteric Binding Pose Controls Allosteric Subtype Selectivity, J Med Chem, 57(15):6739-6750, 2014.
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M. A. Seiter, S. Salcher, M. Rupp, J. Hagenbuchner, U. Kiechl-Kohlendorfer, J. Mortier, G. Wolber, J. M. Rollinger, P. Obexer, and M. J. Ausserlechner. Discovery of Sanggenon G as a natural cell-permeable small-molecular weight inhibitor of X-linked inhibitor of apoptosis protein (XIAP), FEBS Open Bio, 4:659-671, 2014.
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A. Temirak, Y. M. Shaker, F. A. F. Ragab, M. M. Ali, S. M. Soliman, J. Mortier, G. Wolber, H. I. Ali, and H. I. El Diwani. Synthesis, Biological Evaluation, and Docking Studies of New 2-Furylbenzimidazoles as Anti- Angiogenic Agents: Part II, Arch Pharm, 347(4):291-304, 2014.
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C. D. Cadicamo, J. Mortier, G. Wolber, M. Hell, I. E. Heinrich, D. Michel, L. Semlin, U. Berger, H. C. Korting, H. D. Holtje, B. Koksch, and C. Borelli. Design, synthesis, inhibition studies, and molecular modeling of pepstatin analogues addressing different secreted aspartic proteinases of Candida albicans, Biochem Pharmacol, 85(7):881-887, 2013.
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K. N. de Oliveira, V. Andermark, S. von Grafenstein, L. A. Onambele, G. Dahl, R. Rubbiani, G. Wolber, C. Gabbiani, L. Messori, A. Prokop, and I. Ott. Butyltin(IV) Benzoates: Inhibition of Thioredoxin Reductase, Tumor Cell Growth Inhibition, and Interactions with Proteins, ChemMedChem, 8(2):256-264, 2013.
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M. Enthammer, E. S. Papadakis, M. S. Gachet, M. Deutsch, S. Schwaiger, K. Koziel, M. I. Ashraf, S. Khalid, G. Wolber, G. Packham, R. I. Cutress, H. Stuppner, and J. Troppmair. Isolation of a Novel Thioflavin S-Derived Compound That Inhibits BAG-1-Mediated Protein Interactions and Targets BRAF Inhibitor-Resistant Cell Lines, Mol Cancer Ther, 12(11):2400-2414, 2013.
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S. A. Galar, A. S. Abdelsamie, S. M. Soliman, J. Mortier, G. Wolber, M. M. Ali, H. Tokuda, N. Suzuki, A. Lida, R. A. Ramadan, and H. I. El Diwani. Design, synthesis and structure-activity relationship of novel quinoxaline derivatives as cancer chemopreventive agent by inhibition of tyrosine kinase receptor, Eur J Med Chem, 69:115-124, 2013.
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J. Leschner, G. Wennerberg, J. Feierler, M. Bermudez, B. Welte, I. Kalatskaya, G. Wolber, and A. Faussner. Interruption of the Ionic Lock in the Bradykinin B-2 Receptor Results in Constitutive Internalization and Turns Several Antagonists into Strong Agonists, J Pharmacol Exp Ther, 344(1):85-95, 2013.
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M. Levay, K. A. Krobert, K. Wittig, N. Voigt, M. Bermudez, G. Wolber, D. Dobrev, F. O. Levy, and T. Wieland. NSC23766, a Widely Used Inhibitor of Rac1 Activation, Additionally Acts as a Competitive Antagonist at Muscarinic Acetylcholine Receptors, J Pharmacol Exp Ther, 347(1):69-79, 2013.
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A. Perdih, G. Wolber, and T. Solmajer. Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase, J Comput Aided Mol Des, 27(8):723-738, 2013.
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M. Spetea, M. F. Asim, S. Noha, G. Wolber, and H. Schmidhammer. Current kappa Opioid Receptor Ligands and Discovery of a New Molecular Scaffold as a kappa Opioid Receptor Antagonist Using Pharmacophore-Based Virtual Screening, Curr Pharm Design, 19(42):7362-7372, 2013.
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M. Spetea, M. F. Asim, G. Wolber, and H. Schmidhammer. The mu Opioid Receptor and Ligands Acting at the mu Opioid Receptor, as Therapeutics and Potential Therapeutics, Curr Pharm Design, 19(42):7415-7434, 2013.
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S. Distinto, F. Esposito, J. Kirchmair, M. C. Cardia, M. Gaspari, E. Maccioni, S. Alcaro, P. Markt, G. Wolber, L. Zinzula, and E. Tramontano. Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach, Eur J Med Chem, 50:216-229, 2012.
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S. Distinto, M. Yanez, S. Alcaro, M. C. Cardia, M. Gaspari, M. L. Sanna, R. Meleddu, F. Ortuso, J. Kirchmair, P. Markt, A. Bolasco, G. Wolber, D. Secci, and E. Maccioni. Synthesis and biological assessment of novel 2-thiazolylhydrazones and computational analysis of their recognition by monoamine oxidase B, Eur J Med Chem, 48:284-295, 2012.
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A. Faussner, S. Schussler, J. Feierler, M. Bermudez, J. Pfeifer, K. Schnatbaum, T. Tradler, M. Jochum, G. Wolber, and C. Gibson. Binding characteristics of [3H]-JSM10292: a new cell membrane-permeant non-peptide bradykinin B2 receptor antagonist, Br J Pharmacol, 167(4):839-853, 2012.
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L. Guasch, E. Sala, A. Castell-Auvi, L. Cedo, K. R. Liedl, G. Wolber, M. Muehlbacher, M. Mulero, M. Pinent, A. Ardevol, C. Valls, G. Pujadas, and S. Garcia-Vallve. Identification of PPARgamma Partial Agonists of Natural Origin (I): Development of a Virtual Screening Procedure and In Vitro Validation, Plos One, 7(11):, 2012.
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J. Mortier, C. Rakers, R. Frederick, and G. Wolber. Computational Tools for In Silico Fragment-Based Drug Design, Curr Top Med Chem, 12(17):1935-1943, 2012.
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M. S. Murgueitio, M. Bermudez, J. Mortier, and G. Wolber. In silico virtual screening approaches for anti-viral drug discovery, Drug Discov Today Technol, 9(3):e219-25, 2012.
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S. M. Noha, B. Jazzar, S. Kuehnl, J. M. Rollinger, H. Stuppner, A. M. Schaible, O. Werz, G. Wolber, and D. Schuster. Pharmacophore-based discovery of a novel cytosolic phospholipase A(2)alpha inhibitor, Bioorg Med Chem Lett, 22(2):1202-1207, 2012.
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R. Ottana, R. Maccari, S. Amuso, G. Wolber, D. Schuster, S. Herdlinger, G. Manao, G. Camici, and P. Paoli. New 4-[(5-arylidene-2-arylimino-4-oxo-3-thiazolidinyl)methyl]benzoic acids active as protein tyrosine phosphatase inhibitors endowed with insulinomimetic effect on mouse C2C12 skeletal muscle cells, Eur J Med Chem, 50:332-343, 2012.
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S. Santos-Sierra, J. Kirchmair, A. Perna, D. Reiss, K. Kemter, W. Roeschinger, H. Glossmann, S. Gersting, A. C. Muntau, G. Wolber, and F. B. Lagler. Discovery of Novel Pharmacological Chaperones for Pku That Correct Phenylketonuria in Vivo, J Inherit Metab Dis, 35:S3-S3, 2012.
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S. Santos-Sierra, J. Kirchmair, A. M. Perna, D. Reiss, K. Kemter, W. Roschinger, H. Glossmann, S. W. Gersting, A. C. Muntau, G. Wolber, and F. B. Lagler. Novel pharmacological chaperones that correct phenylketonuria in mice, Hum Mol Genet, 21(8):1877-1887, 2012.
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A. Schafer, A. Wellner, M. Strauss, A. Schafer, G. Wolber, and R. Gust. Influence of Chlorine or Fluorine Substitution on the Estrogenic Properties of 1-Alkyl-2,3,5-tris(4-hydroxyphenyl)-1H-pyrroles, J Med Chem, 55(22):9607-9618, 2012.
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S. von Grafenstein, J. Mihaly-Bison, G. Wolber, V. N. Bochkov, K. R. Liedl, and D. Schuster. Identification of Novel Liver X Receptor Activators by Structure-Based Modeling, J Chem Inf Model, 52(5):1391-1400, 2012.
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U. Grienke, J. M. Bison, D. Schuster, D. Guo, S. Guan, C. Cheng, V. N. Bochkov, B. R. Binder, G. Wolber, H. Stuppner, and J. M. Rollinger. In silico approaches to identify FXR-inducing constituents from Ganoderma lucidum - the Chinese mushroom of immortality, Planta Med, 77(12):1243-1244, 2011.
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U. Grienke, J. Mihaly-Bison, D. Schuster, T. Afonyushkin, M. Binder, S. H. Guan, C. R. Cheng, G. Wolber, H. Stuppner, D. A. Guo, V. N. Bochkov, and J. M. Rollinger. Pharmacophore-based discovery of FXR-agonists. Part II: Identification of bioactive triterpenes from Ganoderma lucidum, Bioorg Med Chem, 19(22):6779-6791, 2011.
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J. Kirchmair, S. Distinto, K. R. Liedl, P. Markt, J. M. Rollinger, D. Schuster, G. M. Spitzer, and G. Wolber. Development of anti-viral agents using molecular modeling and virtual screening techniques, Infect Disord Drug Targets, 11(1):64-93, 2011.
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D. V. Kratschmar, A. Vuorinen, T. Da Cunha, G. Wolber, D. Classen-Houben, O. Doblhoffe, D. Schuster, and A. Odermatt. Characterization of activity and binding mode of glycyrrhetinic acid derivatives inhibiting 11 beta-hydroxysteroid dehydrogenase type 2, J Steroid Biochem, 125(1-2):129-142, 2011.
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S. M. Noha, A. G. Atanasov, D. Schuster, P. Markt, N. Fakhrudin, E. H. Heiss, O. Schrammel, J. M. Rollinger, H. Stuppner, V. M. Dirsch, and G. Wolber. Discovery of a novel IKK-beta inhibitor by ligand-based virtual screening techniques, Bioorg Med Chem Lett, 21(1):577-583, 2011.
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P. H. Pfisterer, C. X. Shen, Z. Nikolovska-Coleska, L. Schyschka, D. Schuster, A. Rudy, G. Wolber, A. M. Vollmar, J. M. Rollinger, and H. Stuppner. In silico discovery of acylated flavonol monorhamnosides from Eriobotrya japonica as natural, small-molecular weight inhibitors of XIAP BIR3, Bioorg Med Chem, 19(2):1002-1009, 2011.
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A. Schafer, A. Wellner, M. Strauss, G. Wolber, and R. Gust. Development of 2,3,5-Triaryl-1H-pyrroles as Estrogen Receptor alpha Selective Ligands, ChemMedChem, 6(11):2055-2062, 2011.
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D. Schuster, D. Kowalik, J. Kirchmair, C. Laggner, P. Markt, C. Aebischer-Gumy, F. Strohle, G. Moller, G. Wolber, T. Wilckens, T. Langer, A. Odermatt, and J. Adamski. Identification of chemically diverse, novel inhibitors of 17 beta-hydroxysteroid dehydrogenase type 3 and 5 by pharmacophore-based virtual screening, J Steroid Biochem, 125(1-2):148-161, 2011.
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D. Schuster, P. Markt, U. Grienke, J. Mihaly-Bison, M. Binder, S. M. Noha, J. M. Rollinger, H. Stuppner, V. N. Bochkov, and G. Wolber. Pharmacophore-based discovery of FXR agonists. Part I: Model development and experimental validation, Bioorg Med Chem, 19(23):7168-7180, 2011.
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B. Waltenberger, D. Schuster, S. Paramapojn, W. Gritsanapan, G. Wolber, J. M. Rollinger, and H. Stuppner. Predicting cyclooxygenase inhibition by three-dimensional pharmacophoric profiling. Part II: Identification of enzyme inhibitors from Prasaplai, a Thai traditional medicine, Phytomedicine, 18(2-3):119-133, 2011.
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B. Waltenberger, K. Wiechmann, J. Bauer, P. Markt, S. M. Noha, G. Wolber, J. M. Rollinger, O. Werz, D. Schuster, and H. Stuppner. Pharmacophore Modeling and Virtual Screening for Novel Acidic Inhibitors of Microsomal Prostaglandin E-2 Synthase-1 (mPGES-1), J Med Chem, 54(9):3163-3174, 2011.
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M. Enthammer, G. Wolber, H. Stuppner, M. Deutsch, and J. Troppmair. Targeting the BAG-1/Hsp70 axis to inhibit tumor growth, Febs J, 277:176-176, 2010.
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N. Fakhrudin, A. Ladurner, A. Atanasov, E. Heiss, L. Baumgartner, P. Markt, D. Schuster, E. Ellmerer, G. Wolber, J. Rollinger, H. Stuppner, and V. Dirsch. Discovery and mechanistic characterization of neolignans as PPAR-gamma agonists, Febs J, 277:68-69, 2010.
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N. Fakhrudin, A. Ladurner, A. G. Atanasov, E. H. Heiss, L. Baumgartner, P. Markt, D. Schuster, E. P. Ellmerer, G. Wolber, J. M. Rollinger, H. Stuppner, and V. M. Dirsch. Computer-Aided Discovery, Validation, and Mechanistic Characterization of Novel Neolignan Activators of Peroxisome Proliferator-Activated Receptor γ, Mol Pharmacol, 77(4):559-566, 2010.
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M. Goebel, G. Wolber, P. Markt, B. Staels, T. Unger, U. Kintscher, and R. Gust. Characterization of new PPAR gamma agonists: Benzimidazole derivatives-importance of positions 5 and 6, and computational studies on the binding mode, Bioorg Med Chem, 18(16):5885-5895, 2010.
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U. Grienke, M. Schmidtke, J. Kirchmair, K. Pfarr, P. Wutzler, R. Durrwald, G. Wolber, K. R. Liedl, H. Stuppner, and J. M. Rollinger. Antiviral Potential and Molecular Insight into Neuraminidase Inhibiting Diarylheptanoids from Alpinia katsumadai, J Med Chem, 53(2):778-786, 2010.
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L. G. Nashev, D. Schuster, C. Laggner, S. Sodha, T. Langer, G. Wolber, and A. Odermatt. The UV-filter benzophenone-1 inhibits 17 beta-hydroxysteroid dehydrogenase type 3: Virtual screening as a strategy to identify potential endocrine disrupting chemicals, Biochem Pharmacol, 79(8):1189-1199, 2010.
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P. Pfisterer, Z. Nikolovska-Coleska, L. Schyschka, D. Schuster, A. Rudy, G. Wolber, A. Vollmar, J. Rollinger, and H. Stuppner. Acylated flavonol monorhamnosides from Eriobotrya japonica as XIAP BIR3 inhibitors revealed by in silica and HPLC-SPE-NMR techniques, Planta Med, 76(12):1344-1345, 2010.
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P. H. Pfisterer, G. Wolber, T. Efferth, J. M. Rollinger, and H. Stuppner. Natural products in structure-assisted design of molecular cancer therapeutics, Curr Pharm Design, 16(15):1718-1741, 2010.
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J. Rollinger, D. Kratschmar, D. Schuster, P. Pfisterer, S. Brandstotter, H. Stuppner, G. Wolber, and A. Odermatt. In silico access for the discovery of 11 beta-HSD 1 inhibiting triterpenes from Eriobotrya japonica, Planta Med, 76(12):1181-1181, 2010.
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J. M. Rollinger, D. V. Kratschmar, D. Schuster, P. H. Pfisterer, C. Gumy, E. M. Aubry, S. Brandstotter, H. Stuppner, G. Wolber, and A. Odermatt. 11 beta-Hydroxysteroid dehydrogenase 1 inhibiting constituents from Eriobotrya japonica revealed by bioactivity-guided isolation and computational approaches, Bioorg Med Chem, 18(4):1507-1515, 2010.
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R. Rubbiani, I. Kitanovic, H. Alborzinia, S. Can, A. Kitanovic, L. A. Onambele, M. Stefanopoulou, Y. Geldmacher, W. S. Sheldrick, G. Wolber, A. Prokop, S. Wolfl, and I. Ottt. Benzimidazol-2-ylidene Gold(I) Complexes Are Thioredoxin Reductase Inhibitors with Multiple Antitumor Properties, J Med Chem, 53(24):8608-8618, 2010.
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D. Schuster, L. Kern, D. P. Hristozov, L. Terfloth, B. Bienfait, C. Laggner, J. Kirchmair, U. Grienke, G. Wolber, T. Langer, H. Stuppner, J. Gasteiger, and J. M. Rollinger. Applications of Integrated Data Mining Methods to Exploring Natural Product Space for Acetylcholinesterase Inhibitors, Combinatorial Chemistry & High Throughput Screening, 13(1):54-66, 2010.
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D. Schuster, M. Spetea, M. Music, S. Rief, M. Fink, J. Kirchmair, J. Schutz, G. Wolber, T. Langer, H. Stuppner, H. Schmidhammer, and J. M. Rollinger. Morphinans and isoquinolines: Acetylcholinesterase inhibition, pharmacophore modeling, and interaction with opioid receptors, Bioorg Med Chem, 18(14):5071-5080, 2010.
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D. Schuster, B. Waltenberger, J. Kirchmair, S. Distinto, P. Markt, H. Stuppner, J. M. Rollinger, and G. Wolber. Predicting Cyclooxygenase Inhibition by Three-Dimensional Pharmacophoric Profiling. Part I: Model Generation, Validation and Applicability in Ethnopharmacology, Mol Inf, 29(1-2):75-86, 2010.
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D. Schuster, and G. Wolber. Identification of bioactive natural products by pharmacophore-based virtual screening, Curr Pharm Design, 16(15):1666-1681, 2010.
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D. Schuster, and G. Wolber. Pharmacophore-guided elucidation of the active principle from natural compounds, Planta Med, 76(12):1179-1179, 2010.
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A. M. Scutaru, M. Wenzel, H. Scheffler, G. Wolber, and R. Gust. Optimization of the N-Lost Drugs Melphalan and Bendamustine: Synthesis and Cytotoxicity of a New Set of Dendrimer-Drug Conjugates as Tumor Therapeutic Agents, Bioconjug Chem, 21(10):1728-1743, 2010.
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T. Seidel, G. Ibis, F. Bendix, and G. Wolber. Strategies for 3D pharmacophore-based virtual screening, Drug Discovery Today: Technologies, 7(4):e221-e228, 2010.
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G. M. Spitzer, M. Heiss, M. Mangold, P. Mark, J. Kirchmair, G. Wolber, and K. R. Liedl. One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space, J Chem Inf Model, 50(7):1241-1247, 2010.
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B. Waltenberger, D. Schuster, S. Paramapojn, W. Gritsanapan, G. Wolber, J. Rollinger, and H. Stuppner. In silico strategy for the identification of cyclooxygenase inhibitors from the Thai medicinal mixture Prasaplai, Planta Med, 76(12):1173-1173, 2010.
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G. Wolber. 3D pharmacophore elucidation and virtual screening, Drug Discovery Today: Technologies, 7(4):e203-e204, 2010.
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D. Classen-Houben, D. Schuster, T. Da Cunha, A. Odermatt, G. Wolber, U. Jordis, and B. Kueenburg. Selective inhibition of 11 beta-hydroxysteroid dehydrogenase 1 by 18 alpha-glycyrrhetinic acid but not 18 beta-glycyrrhetinic acid, J Steroid Biochem, 113(3-5):248-252, 2009.
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J. Kirchmair, S. Distinto, P. Markt, D. Schuster, G. M. Spitzer, K. R. Liedl, and G. Wolber. How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information, J Chem Inf Model, 49(3):678-692, 2009.
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P. Markt, C. Feldmann, J. M. Rollinger, S. Raduner, D. Schuster, J. Kirchmair, S. Distinto, G. M. Spitzer, G. Wolber, C. Laggner, K. H. Altmann, T. Langer, and J. Gertsch. Discovery of Novel CB2 Receptor Ligands by a Pharmacophore-Based Virtual Screening Workflow, J Med Chem, 52(2):369-378, 2009.
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A. Perdih, A. Kovac, G. Wolber, D. Blanot, S. Gobec, and T. Solmajer. Discovery of novel benzene 1,3-dicarboxylic acid inhibitors of bacterial MurD and MurE ligases by structure-based virtual screening approach, Bioorg Med Chem Lett, 19(10):2668-2673, 2009.
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J. M. Rollinger, D. Schuster, B. Danzl, S. Schwalger, P. Markt, M. Schmidtke, J. Gertsch, S. Raduner, G. Wolber, T. Langer, and H. Stuppner. In silico Target Fishing for Rationalized Ligand Discovery Exemplified on Constituents of Ruta graveolens, Planta Med, 75(3):195-204, 2009.
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P. Tiikkainen, P. Markt, G. Wolber, J. Kirchmair, S. Distinto, A. Poso, and O. Kallioniemi. Critical Comparison of Virtual Screening Methods against the MUV Data Set, J Chem Inf Model, 49(10):2168-2178, 2009.
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J. Kirchmair, S. Distinto, D. Schuster, G. Spitzer, T. Langer, and G. Wolber. Enhancing drug discovery through in silico screening: Strategies to increase true positives retrieval rates, Curr Med Chem, 15(20):2040-2053, 2008.
Links: [doi:10.2174/092986708785132843] [show BibTeX]

[27]

J. Kirchmair, P. Markt, S. Distinto, D. Schuster, G. M. Spitzer, K. R. Liedl, T. Langer, and G. Wolber. The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery, J Med Chem, 51(22):7021-7040, 2008.
Links: [doi:10.1021/Jm8005977] [show BibTeX]

[26]

J. Kirchmair, P. Markt, S. Distinto, G. Wolber, and T. Langer. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?, J Comput Aided Mol Des, 22(3-4):213-228, 2008.
Links: [doi:10.1007/S10822-007-9163-6] [show BibTeX]

[25]

P. Markt, C. McGoohan, B. Walker, J. Kirchmair, C. L. Feldmann, G. De Martino, G. Spitzer, S. Distinto, D. Schuster, G. Wolber, C. Laggner, and T. Langer. Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening, J Chem Inf Model, 48(8):1693-1705, 2008.
Links: [doi:10.1021/Ci800101j] [show BibTeX]

[24]

P. Markt, R. K. Petersen, E. N. Flindt, K. Krjstiansen, J. Kirchmair, G. Spitzer, S. Distinto, D. Schuster, G. Wolber, C. Laggner, and T. Langer. Discovery of novel PPAR ligands by a virtual screening approach based on pharmacophore modeling, 3D shape, and electrostatic similarity screening, J Med Chem, 51(20):6303-6317, 2008.
Links: [doi:10.1021/Jm800128k] [show BibTeX]

[23]

D. Schuster, L. G. Nashev, J. Kirchmair, C. Laggner, G. Wolber, T. Langer, and A. Odermatt. Discovery of nonsteroidal 17 beta-hydroxysteroid dehydrogenase 1 inhibitors by pharmacophore-based screening of virtual compound libraries, J Med Chem, 51(14):4188-4199, 2008.
Links: [doi:10.1021/Jm800054h] [show BibTeX]

[22]

G. Wolber, T. Seidel, F. Bendix, and T. Langer. Molecule-pharmacophore superpositioning and pattern matching in computational drug design, Drug Discov Today, 13(1–2):23-29, 2008.
Links: [doi:10.1016/j.drudis.2007.09.007] [show BibTeX]

[21]

J. Kirchmair, S. Ristic, K. Eder, P. Markt, G. Wolber, C. Laggner, and T. Langer. Fast and efficient in silico 3D screening: Toward maximum computational efficiency of pharmacophore-based and shape-based approaches, J Chem Inf Model, 47(6):2182-2196, 2007.
Links: [doi:10.1021/Ci700024q] [show BibTeX]

[20]

J. Kirchmair, G. Wolber, C. Laggner, and T. Langer. Comparative performance assessment of the conformational model generators omega and catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations, J Chem Inf Model, 46(4):1848-1861, 2006.
Links: [doi:10.1021/Ci060084g] [show BibTeX]

[19]

T. M. Steindl, D. Schuster, G. Wolber, C. Laggner, and T. Langer. High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening, J Comput Aided Mol Des, 20(12):703-715, 2006.
Links: [doi:10.1007/S10822-006-9066-Y] [show BibTeX]

[18]

G. Wolber, A. A. Dornhofer, and T. Langer. Efficient overlay of small organic molecules using 3D pharmacophores, J Comput Aided Mol Des, 20(12):773-788, 2006.
Links: [doi:10.1007/S10822-006-9078-7] [show BibTeX]

[17]

J. Kirchmair, C. Laggner, G. Wolber, and T. Langer. Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms, J Chem Inf Model, 45(2):422-430, 2005.
Links: [doi:10.1021/Ci0497531] [show BibTeX]

[16]

G. Wolber, and T. Langer. LigandScout: 3-d pharmacophores derived from protein-bound Ligands and their use as virtual screening filters, J Chem Inf Model, 45(1):160-169, 2005.
Links: [doi:10.1021/Ci049885e] [show BibTeX]

[15]

T. Langer, and G. Wolber. Pharmacophore definition and 3D searches, Drug Discovery Today: Technologies, 1(3):203-207, 2004.
Links: [doi:10.1016/j.ddtec.2004.11.015] [show BibTeX]

[14]

T. Langer, and G. Wolber. Virtual combinatorial chemistry and in silico screening: Efficient tools for lead structure discovery?, Pure Appl Chem, 76(5):991-996, 2004.
Links: [doi:10.1351/Pac200476050991] [show BibTeX]

Book chapters

[13]

D. Schuster and G. Wolber. Addressing drug safety by bioactivity profiling: panels of 3D pharmacophore models, In: Adverse side effect prediction in preclinical drug discovery, J. Scheiber and J. Jenkins, editors, Wiley VCH, Weinheim, Germany, in print, 2019. [show BibTeX]

[12]

T. Seidel, G. Wolber and M. S. Murgueitio. Pharmacophore Perception and Applications, In: Applied Chemoinformatics: Achievements and Future Opportunities, J. Gasteiger and T. Engel, editors, , pp. 259-282, 2018. [show BibTeX]

[11]

D. Schuster, J. Kirchmair, S. Distinto, P. Markt, C. Laggner, G. Wolber and T. Langer. Why drugs and advanced drug development projects fail, In: Why Drugs Fail, T. Langer and S. D. Bryant, editors, Wiley VCH, Weinheim, Germany, in print, 2017. [show BibTeX]

[10]

G. Wolber and W. Sippl. Pharmacophore Identification and Pseudo-Receptor Modelling, In: The Practice of Medicinal Chemistry (4th edition), C. G. Wermuth and D. Rognan, editors, Elsevier Ltd, Philadelphia, PA, USA, pp. 489-507, 2015.
Links: [Publisher] [show BibTeX]

[9]

G. Wolber and J. Rollinger. Virtual screening and target fishing for natural products using 3D pharmacophores, In: Computational Chemogenomics, E. Jacoby, editor, Pan Stanford Publishing Pte Ltd, Singapore, Malaysia, ISBN: 978-981-4411-39-4, pp. 117-139, 2013.
Links: [Publisher] [show BibTeX]

[8]

J. M. Rollinger and G. Wolber. Computational approaches for the discovery of natural lead structures, In: Bioactive Compounds from Natural Sources, 2nd edition, C. Tringali, editor, CRC Press, London, United Kingdom, ISBN: 1439822298, pp. 97-132, 2011.
Links: [Publisher] [show BibTeX]

[7]

C. Laggner, G. Wolber, J. Kirchmair, S. D. and L. T.. Pharmacophore-based virtual screening in drug discovery, In: Chemoinformatics: An approach to virtual screening, A. Varnek and A. Tropsha, editors, Royal Society of Chemistry, Cambridge, United Kingdom, ISBN: 978-0-85404-144-2, pp. 76-119, 2008.
Links: [Publisher] [show BibTeX]

[6]

A. A. Dornhofer, M. Biely, G. Wolber and T. Langer. A novel 2D depiction method using breadth-first ordering and an adapted 2D force field, In: QSAR and Molecular Modelling in Rational Design of Bioactive Molecules, E. Aki Sener and I. Yalcin, editors, Computer Aided Drug Design & Development Society, Ankara, Turkey, ISBN: 975-00782-0-9, pp. 421ff., 2006. [show BibTeX]

[5]

T. Langer and G. Wolber. Extracting pharmacophores from bio-active molecules, In: Virtual ADMET assessment in target Selection and maturation, B. Testa and L. Turski, editors, IOS Press, Amsterdam, Netherlands, ISBN: 978-1-58603-703-1, pp. 133-150, 2006. [show BibTeX]

[4]

G. Wolber, M. Biely and T. Langer. De novo drug design using randomized virtual chemistry and property filtering: a heuristic approach, In: QSAR and Molecular Modelling in Rational Design of Bioactive Molecules, E. Aki Sener and I. Yalcin, editors, Computer Aided Drug Design & Development Society, Ankara, Turkey, ISBN: 975-00782-0-9, pp. , 2006. [show BibTeX]

[3]

G. Wolber and R. Kosara. Pharmacophores from macromolecular complexes with LigandScout, In: Pharmacophores and pharmacophore searches, T. Langer and R. Hofmann, editors, Wiley-VCH, Weinheim, Germany, ISBN: 3-527-31250-1, pp. 131-148, 2006.
Links: [Publisher] [show BibTeX]

[2]

G. Wolber. Structure-based Pharmacophores From Protein-Bound Ligands (German: Strukturbasierte Pharmacophore aus proteingebundenen Liganden), In: Lecture notes in informatics (LNI) D-5, D. Wagner, editor, Bonner Koellen Verlag, Bonn-Buschdorf, Germany, ISBN: 3-88579-409-8, pp. 209-218, 2004. [show BibTeX]

[1]

T. Langer and G. Wolber. CombiGen: A Novel Software Package for the Rapid Generation of Virtual Combinatorial Libraries, In: Rational Approaches to Drug Design, W. Höltje, editor, Prous Science, Barcelona, Spain, ISBN: 84-8124-176-8, pp. 390-399, 2001. [show BibTeX]

[back to top]roaches. Thereby, in particular assessments of protein-ligand docking are facing remarkable interest in the scientific community. However, comparing virtual screening approaches is a non-trivial task. Several publications, especially in the field of molecular docking, suffer from shortcomings that are likely to affect the significance of the results considerably. These quality issues often arise from poor study design, biasing, by using improper or inexpressive enrichment descriptors, and from errors in interpretation of the data output. In this review we analyze recent literature evaluating 3D virtual screening methods, with focus on molecular docking. We highlight problematic issues and provide guidelines on how to improve the quality of computational studies. Since 3D virtual screening protocols are in general assessed by their ability to discriminate between active and inactive compounds, we summarize the impact of the composition and preparation of test sets on the outcome of evaluations. Moreover, we investigate the significance of both classic enrichment parameters and advanced descriptors for the performance of 3D virtual screening methods. Furthermore, we review the significance and suitability of RMSD as a measure for the accuracy of protein-ligand docking algorithms and of conformational space sub sampling algorithms.}, type = {Journal Article}, keywords = {virtual screening evaluation of computational methods pharmacophore modeling protein-ligand docking enrichment descriptors decoy selection virtual library design tautomerism rmsd protein-ligand docking high-throughput docking incremental construction algorithm automated molecular docking library design drug design pharmacophore models chemical similarity genetic algorithm scoring functions} }

[25]

P. Markt, C. McGoohan, B. Walker, J. Kirchmair, C. L. Feldmann, G. De Martino, G. Spitzer, S. Distinto, D. Schuster, G. Wolber, C. Laggner, and T. Langer. Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening, J Chem Inf Model, 48(8):1693-1705, 2008.
Links: [doi:10.1021/Ci800101j] [show BibTeX]

[24]

P. Markt, R. K. Petersen, E. N. Flindt, K. Krjstiansen, J. Kirchmair, G. Spitzer, S. Distinto, D. Schuster, G. Wolber, C. Laggner, and T. Langer. Discovery of novel PPAR ligands by a virtual screening approach based on pharmacophore modeling, 3D shape, and electrostatic similarity screening, J Med Chem, 51(20):6303-6317, 2008.
Links: [doi:10.1021/Jm800128k] [show BibTeX]

[23]

D. Schuster, L. G. Nashev, J. Kirchmair, C. Laggner, G. Wolber, T. Langer, and A. Odermatt. Discovery of nonsteroidal 17 beta-hydroxysteroid dehydrogenase 1 inhibitors by pharmacophore-based screening of virtual compound libraries, J Med Chem, 51(14):4188-4199, 2008.
Links: [doi:10.1021/Jm800054h] [show BibTeX]

[22]

G. Wolber, T. Seidel, F. Bendix, and T. Langer. Molecule-pharmacophore superpositioning and pattern matching in computational drug design, Drug Discov Today, 13(1–2):23-29, 2008.
Links: [doi:10.1016/j.drudis.2007.09.007] [show BibTeX]

[21]

J. Kirchmair, S. Ristic, K. Eder, P. Markt, G. Wolber, C. Laggner, and T. Langer. Fast and efficient in silico 3D screening: Toward maximum computational efficiency of pharmacophore-based and shape-based approaches, J Chem Inf Model, 47(6):2182-2196, 2007.
Links: [doi:10.1021/Ci700024q] [show BibTeX]

[20]

J. Kirchmair, G. Wolber, C. Laggner, and T. Langer. Comparative performance assessment of the conformational model generators omega and catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations, J Chem Inf Model, 46(4):1848-1861, 2006.
Links: [doi:10.1021/Ci060084g] [show BibTeX]

[19]

T. M. Steindl, D. Schuster, G. Wolber, C. Laggner, and T. Langer. High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening, J Comput Aided Mol Des, 20(12):703-715, 2006.
Links: [doi:10.1007/S10822-006-9066-Y] [show BibTeX]

[18]

G. Wolber, A. A. Dornhofer, and T. Langer. Efficient overlay of small organic molecules using 3D pharmacophores, J Comput Aided Mol Des, 20(12):773-788, 2006.
Links: [doi:10.1007/S10822-006-9078-7] [show BibTeX]

[17]

J. Kirchmair, C. Laggner, G. Wolber, and T. Langer. Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms, J Chem Inf Model, 45(2):422-430, 2005.
Links: [doi:10.1021/Ci0497531] [show BibTeX]

[16]

G. Wolber, and T. Langer. LigandScout: 3-d pharmacophores derived from protein-bound Ligands and their use as virtual screening filters, J Chem Inf Model, 45(1):160-169, 2005.
Links: [doi:10.1021/Ci049885e] [show BibTeX]

[15]

T. Langer, and G. Wolber. Pharmacophore definition and 3D searches, Drug Discovery Today: Technologies, 1(3):203-207, 2004.
Links: [doi:10.1016/j.ddtec.2004.11.015] [show BibTeX]