Drug Design Group,
Institute of Pharmaceutical Chemistry,
Drug Design Group, Institute of Pharmaceutical Chemistry
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Price for Opening the Transient Specificity Pocket in Human Aldose Reductase upon Ligand Binding: Structural, Thermodynamic, Kinetic, and Computational Analysis.
ACS chemical biology 05, 2017 | Pubmed ID: 28287700
pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design.
Chembiochem : a European journal of chemical biology Mar, 2002 | Pubmed ID: 11921406
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors.
Angewandte Chemie (International ed. in English) Aug, 2002 | Pubmed ID: 12203463
DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein.
Journal of medicinal chemistry Sep, 2002 | Pubmed ID: 12213058
Trypsin mutants for structure-based drug design: expression, refolding and crystallisation.
Biological chemistry Jul-Aug, 2002 | Pubmed ID: 12437122
Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity.
Journal of molecular biology Jan, 2003 | Pubmed ID: 12527302
Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis.
Journal of medicinal chemistry Mar, 2003 | Pubmed ID: 12646024
Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre.
Journal of molecular biology May, 2003 | Pubmed ID: 12706720
ZZ made EZ: influence of inhibitor configuration on enzyme selectivity.
Journal of molecular biology Jul, 2003 | Pubmed ID: 12850145
Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design.
Chembiochem : a European journal of chemical biology Oct, 2003 | Pubmed ID: 14523925
Crystallographic study of inhibitors of tRNA-guanine transglycosylase suggests a new structure-based pharmacophore for virtual screening.
Journal of molecular biology Apr, 2004 | Pubmed ID: 15050823
Non-thiol farnesyltransferase inhibitors: N-(4-tolylacetylamino-3-benzoylphenyl)-3-arylfurylacrylic acid amides.
Bioorganic & medicinal chemistry Sep, 2004 | Pubmed ID: 15358286
Non-thiol farnesyltransferase inhibitors: utilization of the far aryl binding site by 5-cinnamoylaminobenzophenones.
Archiv der Pharmazie Sep, 2004 | Pubmed ID: 15362122
Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model.
Journal of medicinal chemistry Oct, 2004 | Pubmed ID: 15481976
An old target revisited: two new privileged skeletons and an unexpected binding mode for HIV-protease inhibitors.
Angewandte Chemie (International ed. in English) May, 2005 | Pubmed ID: 15822136
Mechanism and substrate specificity of tRNA-guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism.
Chembiochem : a European journal of chemical biology Nov, 2005 | Pubmed ID: 16206323
Hydroxyethylene sulfones as a new scaffold to address aspartic proteases: design, synthesis, and structural characterization.
Journal of medicinal chemistry Oct, 2005 | Pubmed ID: 16220977
A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates.
Angewandte Chemie (International ed. in English) Jan, 2006 | Pubmed ID: 16374786
An efficient method for the synthesis of peptide aldehyde libraries employed in the discovery of reversible SARS coronavirus main protease (SARS-CoV Mpro) inhibitors.
Chembiochem : a European journal of chemical biology Jul, 2006 | Pubmed ID: 16688706
Unexpected novel binding mode of pyrrolidine-based aspartyl protease inhibitors: design, synthesis and crystal structure in complex with HIV protease.
ChemMedChem Jan, 2006 | Pubmed ID: 16892342
Integrated approach using protein and ligand information to analyze selectivity- and affinity-determining features of carbonic anhydrase isozymes.
ChemMedChem Aug, 2006 | Pubmed ID: 16902938
Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes.
Proteins Nov, 2006 | Pubmed ID: 16927370
Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase.
Biochemical and biophysical research communications Dec, 2006 | Pubmed ID: 17083917
Atypical protonation states in the active site of HIV-1 protease: a computational study.
Journal of chemical information and modeling Jul-Aug, 2007 | Pubmed ID: 17503762
Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding.
Journal of molecular biology Jul, 2007 | Pubmed ID: 17524419
Use of biotin derivatives to probe conformational changes in proteins.
The Journal of biological chemistry Jul, 2007 | Pubmed ID: 17545162
Saccharin inhibits carbonic anhydrases: possible explanation for its unpleasant metallic aftertaste.
Angewandte Chemie (International ed. in English) , 2007 | Pubmed ID: 17705204
Novel deoxyxylulosephosphate-reductoisomerase inhibitors: fosmidomycin derivatives with spacious acyl residues.
Archiv der Pharmazie Sep, 2007 | Pubmed ID: 17806130
Thermodynamic inhibition profile of a cyclopentyl and a cyclohexyl derivative towards thrombin: the same but for different reasons.
Angewandte Chemie (International ed. in English) , 2007 | Pubmed ID: 17902081
Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies.
Journal of molecular biology Nov, 2007 | Pubmed ID: 17949745
KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding.
Angewandte Chemie (International ed. in English) , 2007 | Pubmed ID: 17955562
Use of 3D QSAR models for database screening: a feasibility study.
Journal of chemical information and modeling Feb, 2008 | Pubmed ID: 18211050
Structure-guided design of C2-symmetric HIV-1 protease inhibitors based on a pyrrolidine scaffold.
Journal of medicinal chemistry Apr, 2008 | Pubmed ID: 18348517
SFCscore: scoring functions for affinity prediction of protein-ligand complexes.
Proteins Nov, 2008 | Pubmed ID: 18442132
Studies addressing the importance of charge in the binding of fosmidomycin-like molecules to deoxyxylulosephosphate reductoisomerase.
ChemMedChem Aug, 2008 | Pubmed ID: 18470849
Development of benzophenone-based farnesyltransferase inhibitors as novel antimalarials.
ChemMedChem Aug, 2008 | Pubmed ID: 18470859
Structural and kinetic analysis of pyrrolidine-based inhibitors of the drug-resistant Ile84Val mutant of HIV-1 protease.
Journal of molecular biology Nov, 2008 | Pubmed ID: 18692068
Turns revisited: a uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions.
Proteins Feb, 2009 | Pubmed ID: 18704930
Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors.
ChemMedChem Sep, 2008 | Pubmed ID: 18720485
Computer-aided design and synthesis of nonpeptidic plasmepsin II and IV inhibitors.
ChemMedChem Sep, 2008 | Pubmed ID: 18752222
Achiral oligoamines as versatile tool for the development of aspartic protease inhibitors.
Bioorganic & medicinal chemistry Sep, 2008 | Pubmed ID: 18760609
Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT.
Chembiochem : a European journal of chemical biology Mar, 2009 | Pubmed ID: 19199329
Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules.
Bioinformatics (Oxford, England) Aug, 2009 | Pubmed ID: 19286830
Structure-based optimization of aldose reductase inhibitors originating from virtual screening.
ChemMedChem May, 2009 | Pubmed ID: 19301313
An integrative approach combining noncovalent mass spectrometry, enzyme kinetics and X-ray crystallography to decipher Tgt protein-protein and protein-RNA interaction.
Journal of molecular biology Nov, 2009 | Pubmed ID: 19627989
Secbase: database module to retrieve secondary structure elements with ligand binding motifs.
Journal of chemical information and modeling Oct, 2009 | Pubmed ID: 19807134
How to replace the residual solvation shell of polar active site residues to achieve nanomolar inhibition of tRNA-guanine transglycosylase.
ChemMedChem Dec, 2009 | Pubmed ID: 19894214
Pyrrolidine derivatives as plasmepsin inhibitors: binding mode analysis assisted by molecular dynamics simulations of a highly flexible protein.
ChemMedChem Mar, 2010 | Pubmed ID: 20112327
Fragment-based lead discovery: screening and optimizing fragments for thermolysin inhibition.
ChemMedChem Jun, 2010 | Pubmed ID: 20394106
Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth.
Acta crystallographica. Section D, Biological crystallography May, 2010 | Pubmed ID: 20445235
Bidentate Zinc chelators for alpha-carbonic anhydrases that produce a trigonal bipyramidal coordination geometry.
ChemMedChem Sep, 2010 | Pubmed ID: 20629007
GARLig: a fully automated tool for subset selection of large fragment spaces via a self-adaptive genetic algorithm.
Journal of chemical information and modeling Sep, 2010 | Pubmed ID: 20795677
fconv: Format conversion, manipulation and feature computation of molecular data.
Bioinformatics (Oxford, England) Apr, 2011 | Pubmed ID: 21335612
SEGA: semiglobal graph alignment for structure-based protein comparison.
IEEE/ACM transactions on computational biology and bioinformatics Sep-Oct, 2011 | Pubmed ID: 21339532
Superposition and alignment of labeled point clouds.
IEEE/ACM transactions on computational biology and bioinformatics Nov-Dec, 2011 | Pubmed ID: 21358005
Stereo- and regioselective azide/alkyne cycloadditions in carbonic anhydrase II via tethering, monitored by crystallography and mass spectrometry.
Chemistry (Weinheim an der Bergstrasse, Germany) May, 2011 | Pubmed ID: 21506176
MiniMuDS: a new optimizer using knowledge-based potentials improves scoring of docking solutions.
Journal of chemical information and modeling Jun, 2011 | Pubmed ID: 21528908
[M2 inhibitors and neuraminidase inhibitors].
Pharmazie in unserer Zeit Mar, 2011 | Pubmed ID: 21630541
Two solutions for the same problem: multiple binding modes of pyrrolidine-based HIV-1 protease inhibitors.
Journal of molecular biology Jul, 2011 | Pubmed ID: 21762812
DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes.
Journal of chemical information and modeling Oct, 2011 | Pubmed ID: 21863864
Development of improved PPARβ/δ inhibitors.
ChemMedChem Jan, 2012 | Pubmed ID: 22025402
Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space.
Proteins Feb, 2012 | Pubmed ID: 22095739
Concise and efficient syntheses of preQ1 base, Q base, and (ent)-Q base.
Organic & biomolecular chemistry Nov, 2012 | Pubmed ID: 23032613
Targeting the blind spot of polycationic nanocarrier-based siRNA delivery.
ACS nano Nov, 2012 | Pubmed ID: 23036046
Novel type II fatty acid biosynthesis (FAS II) inhibitors as multistage antimalarial agents.
ChemMedChem Mar, 2013 | Pubmed ID: 23341167
Launching spiking ligands into a protein-protein interface: a promising strategy to destabilize and break interface formation in a tRNA modifying enzyme.
ACS chemical biology , 2013 | Pubmed ID: 23534552
Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor.
PloS one , 2013 | Pubmed ID: 23704982
Cavities tell more than sequences: exploring functional relationships of proteases via binding pockets.
Journal of chemical information and modeling Aug, 2013 | Pubmed ID: 23834203
Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics.
Biochimica et biophysica acta Sep, 2014 | Pubmed ID: 24792574
Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme.
Journal of medicinal chemistry Jul, 2014 | Pubmed ID: 24955548
Beyond affinity: enthalpy-entropy factorization unravels complexity of a flat structure-activity relationship for inhibition of a tRNA-modifying enzyme.
Journal of medicinal chemistry Jul, 2014 | Pubmed ID: 24960372
Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme.
Proteins Oct, 2014 | Pubmed ID: 24975703
Large-scale mining for similar protein binding pockets: with RAPMAD retrieval on the fly becomes real.
Journal of chemical information and modeling Jan, 2015 | Pubmed ID: 25474400
Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors.
Angewandte Chemie (International ed. in English) Feb, 2015 | Pubmed ID: 25630461
What Glues a Homodimer Together: Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein-Protein Interface of the tRNA-Modifying Enzyme Tgt.
ACS chemical biology Aug, 2015 | Pubmed ID: 25951081
Structure-Based Optimization of Inhibitors of the Aspartic Protease Endothiapepsin.
International journal of molecular sciences Aug, 2015 | Pubmed ID: 26287174
Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data.
Journal of computer-aided molecular design Sep, 2015 | Pubmed ID: 26376645
An Immucillin-Based Transition-State-Analogous Inhibitor of tRNA-Guanine Transglycosylase (TGT).
Chemistry (Weinheim an der Bergstrasse, Germany) 05, 2016 | Pubmed ID: 26991861
Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study.
ACS chemical biology 06, 2016 | Pubmed ID: 27028906
Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.
Acta crystallographica. Section F, Structural biology communications 05, 2016 | Pubmed ID: 27139825
Fingerprint Kernels for Protein Structure Comparison.
Molecular informatics Jul, 2012 | Pubmed ID: 27477463
Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding?
Bioorganic & medicinal chemistry 10, 2016 | Pubmed ID: 27501913
A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch out for the Red Herring.
Angewandte Chemie (International ed. in English) 02, 2017 | Pubmed ID: 28097765
Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin.
Angewandte Chemie (International ed. in English) 04, 2017 | Pubmed ID: 28371253
Soaking suggests "alternative facts": Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition.
PloS one , 2017 | Pubmed ID: 28419165
From Structure to Function: A New Approach to Detect Functional Similarity among Proteins Independent from Sequence and Fold Homology.
Angewandte Chemie (International ed. in English) Sep, 2001 | Pubmed ID: 29712060
Homodimer Architecture of QTRT2, the Noncatalytic Subunit of the Eukaryotic tRNA-Guanine Transglycosylase.
Biochemistry 07, 2018 | Pubmed ID: 29862811
Paradoxically, Most Flexible Ligand Binds Most Entropy-Favored: Intriguing Impact of Ligand Flexibility and Solvation on Drug-Kinase Binding.
Journal of medicinal chemistry Jul, 2018 | Pubmed ID: 29909615
Swapping Interface Contacts in the Homodimeric tRNA-Guanine Transglycosylase: An Option for Functional Regulation.
Angewandte Chemie (International ed. in English) 08, 2018 | Pubmed ID: 29927035
Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase.
Chemistry (Weinheim an der Bergstrasse, Germany) Jul, 2018 | Pubmed ID: 29939431
On the Implication of Water on Fragment-to-Ligand Growth in Kinase Binding Thermodynamics.
ChemMedChem 09, 2018 | Pubmed ID: 30058283
Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.
Nature communications 09, 2018 | Pubmed ID: 30177695
Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
Journal of medicinal chemistry 11, 2019 | Pubmed ID: 31633354
Surprising Non-Additivity of Methyl Groups in Drug-Kinase Interaction.
ACS chemical biology 12, 2019 | Pubmed ID: 31638770
Protein-Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals.
Journal of chemical information and modeling 03, 2020 | Pubmed ID: 31922753
Conformational Changes in Alkyl Chains Determine the Thermodynamic and Kinetic Binding Profiles of Carbonic Anhydrase Inhibitors.
ACS chemical biology 03, 2020 | Pubmed ID: 32027480
Role of Water Molecules in Protein-Ligand Dissociation and Selectivity Discrimination: Analysis of the Mechanisms and Kinetics of Biomolecular Solvation Using Molecular Dynamics.
Journal of chemical information and modeling 03, 2020 | Pubmed ID: 32078307
The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II.
Biomolecules 03, 2020 | Pubmed ID: 32230853
A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II.
Biomolecules 03, 2020 | Pubmed ID: 32235320
F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.
Structure (London, England : 1993) 06, 2020 | Pubmed ID: 32413289
Fragment-Based Discovery of Non-bisphosphonate Binders of Trypanosoma brucei Farnesyl Pyrophosphate Synthase.
Chembiochem : a European journal of chemical biology Nov, 2020 | Pubmed ID: 32537808
Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK Shifts Mislead Popular Bioisosterism Concepts.
Angewandte Chemie (International ed. in English) 01, 2021 | Pubmed ID: 33021032
Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses.
ChemMedChem Jan, 2021 | Pubmed ID: 33029876
The Importance of Charge in Perturbing the Aromatic Glue Stabilizing the Protein-Protein Interface of Homodimeric tRNA-Guanine Transglycosylase.
ACS chemical biology 11, 2020 | Pubmed ID: 33166460
Advancing GIST-Based Solvent Functionals through Multiobjective Optimization of Solvent Enthalpy and Entropy Scoring Terms.
Journal of chemical information and modeling Dec, 2020 | Pubmed ID: 33264016
How a Fragment Draws Attention to Selectivity Discriminating Features between the Related Proteases Trypsin and Thrombin.
Journal of medicinal chemistry Feb, 2021 | Pubmed ID: 33471524
Jan Wollenhaupt1,
Tatjana Barthel1,2,
Gustavo M. A. Lima3,
Alexander Metz4,
Dirk Wallacher5,
Elmir Jagudin3,
Franziska U. Huschmann1,4,
Thomas Hauß1,
Christian G. Feiler1,
Martin Gerlach1,
Michael Hellmig1,
Ronald Förster1,
Michael Steffien1,
Andreas Heine4,
Gerhard Klebe4,
Uwe Mueller1,
Manfred S. Weiss1
1Macromolecular Crystallography, Helmholtz-Zentrum Berlin,
2Structural Biochemistry Group, Institute for Chemistry and Biochemistry, Freie Universität Berlin,
3BioMAX, MAX IV Laboratory,
4Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg,
5Department Sample Environment, Helmholtz-Zentrum Berlin
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