English Intern
    AK Sotriffer



    “Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities.”
    J. Kehrein and C. Sotriffer
    ACS Biomater. Sci. Eng. (2023) Article ASAP
    DOI: 10.1021/acsbiomaterials.3c00636

    “MD-Based Assessment of Covalent Inhibitors in Noncovalent Association Complexes: Learning from Cathepsin K as a Test Case”
    E. Endres, N. Yuan Chen and C. Sotriffer
    J. Chem. Inf. Model. 63 (10) (2023) 3186-3197
    DOI: 10.1021/acs.jcim.3c00061

    “Unraveling an Alternative Mechanism in Polymer Self-Assemblies: An Order–Order Transition with Unusual Molecular Interactions between Hydrophilic and Hydrophobic Polymer Blocks”
    L. Hahn, T. Zorn, J. Kehrein, T. Kielholz, A.-L. Ziegler, S. Forster, B. Sochor, E. S. Lisitsyna, N. A. Durandin, T. Laaksonen, V. Aseyev, C. Sotriffer, K. Saalwächter, M. Windbergs, A.-C. Pöppler and R. Luxenhofer
    ACS Nano 17 (7) (2023) 6932-6942
    DOI: 10.1021/acsnano.3c00722

    “Bridging the Binding Sites: Dualsteric Ligands for the Cannabinoid 2 Receptor (CB2R)”
    A. Tutov, S. A. M. Steinmüller, Y. A. Ramírez, C. E. Jack, D. A. Rodríguez-Soacha, C. Sotriffer, J. N. Hislop and M. Decker
    Adv. Therap. 6 (4) (2023) 2200260
    DOI: 10.1002/adtp.202200260

    “Crystal structure of a covalently linked Aurora-A-MYCN complex”
    M. Diebold, L. Schonemann, M. Eilers, C. Sotriffer and H. Schindelin
    Acta Cryst. D. 79 (1) (2023) 1-9
    DOI: 10.1107/S2059798322011433


    “Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97”
    S. Bothe, P. Hänzelmann, S. Böhler, J. Kehrein, M. Zehe, C. Wiedemann, U. A. Hellmich, R. Brenk, H. Schindelin and C. Sotriffer
    Commun. Chem. 5 (1) (2022) 169
    DOI: 10.1038/s42004-022-00782-5

    "Glycolytic flux control by drugging phosphoglycolate phosphatase"
    E. Jeanclos, J. Schlötzer, K. Hadamek, N. Yuan-Chen, M. Alwahsh, R. Hollmann, S. Fratz, D. Yesilyurt-Gerhards, T. Frankenbach, D. Engelmann, A. Keller, A. Kaestner, W. Schmitz, M. Neuenschwander, R. Hergenröder, C. Sotriffer, J. P. von Kries, H. Schindelin and A. Gohla
    Nat. Commun. 13 (1) (2022) 6845
    DOI: 10.1038/s41467-022-34228-2

    “Development of an Indole-Amide-Based Photoswitchable Cannabinoid Receptor Subtype 1 (CB1R) “Cis-On” Agonist”
    D. A. Rodríguez-Soacha, S. A. M. Steinmüller, A. Işbilir, J. Fender, M. H. Deventer, Y. A. Ramírez, A. Tutov, C. Sotriffer, C. P. Stove, K. Lorenz, M. J. Lohse, J. N. Hislop and M. Decker
    ACS Chem. Neurosci. 13 (16) (2022) 2410-2435
    DOI: 10.1021/acschemneuro.2c00160

    “Predicting Bile and Lipid Interaction for Drug Substances”
    J. Schlauersbach, J. Kehrein, S. Hanio, B. Galli, C. Harlacher, C. Heidenreich, B. Lenz, C. Sotriffer and L. Meinel
    Mol. Pharm. 19 (8) (2022) 2868-2876
    DOI: 10.1021/acs.molpharmaceut.2c00227

    "New peptidomimetic rhodesain inhibitors with improved selectivity towards human cathepsins"
    S. Jung, N. Fuchs, C. Grathwol, U. A. Hellmich, A. Wagner, E. Diehl, T. Willmes, C. Sotriffer and T. Schirmeister
    Eur. J. Med. Chem. 238 (2022) 114460
    DOI: 10.1016/j.ejmech.2022.114460

    "Photoswitchable Pseudoirreversible Butyrylcholinesterase Inhibitors Allow Optical Control of Inhibition in Vitro and Enable Restoration of Cognition in an Alzheimer’s Disease Mouse Model upon Irradiation"
    M. Scheiner, A. Sink, M. Hoffmann, C. Vrigneau, E. Endres, A. Carles, C. Sotriffer, T. Maurice and M. Decker
    J. Am. Chem. Soc. 144 (7) (2022) 3279-3284
    DOI: 10.1021/jacs.1c13492


    “Molecular Insights into Site-Specific Interferon-α2a Bioconjugates Originated from PEG, LPG, and PEtOx”
    N. Hauptstein, P. Pouyan, J. Kehrein, M. Dirauf, M. D. Driessen, M. Raschig, K. Licha, M. Gottschaldt, U. S. Schubert, R. Haag, L. Meinel, C. Sotriffer and T. Lühmann
    Biomacromolecules. 22 (11) (2021) 4521-4534
    DOI: 10.1021/acs.biomac.1c00775

    “Sesquiterpenes and sesquiterpenoids harbor modulatory allosteric potential and affect inhibitory GABAA receptor function in vitro”
    D. Janzen, B. Slavik, M. Zehe, C. Sotriffer, H. M. Loos, A. Buettner and C. Villmann
    J. Neurochem. 159 (1) (2021) 101-115
    DOI: 10.1111/jnc.15469

    "Design, Synthesis, and Evaluation of WD-Repeat-Containing Protein 5 (WDR5) Degraders"
    A. Dölle, B. Adhikari, A. Krämer, J. Weckesser, N. Berner, L.-M. Berger, M. Diebold, M. M. Szewczyk, D. Barsyte-Lovejoy, C. H. Arrowsmith, J. Gebel, F. Löhr, V. Dötsch, M. Eilers, S. Heinzlmeir, B. Kuster, C. Sotriffer, E. Wolf and S. Knapp
    J. Med. Chem. 64 (15) (2021) 10682-10710
    DOI: 10.1021/acs.jmedchem.1c00146

    "“Photo-Rimonabant”: Synthesis and Biological Evaluation of Novel Photoswitchable Molecules Derived from Rimonabant Lead to a Highly Selective and Nanomolar “Cis-On” CB1R Antagonist"
    D. Rodríguez-Soacha, A., J. Fender, Y. A. Ramírez, J. A. Collado, E. Muñoz, R. Maitra, C. Sotriffer, K. Lorenz and M. Decker
    ACS Chem. Neurosci. 12 (9) (2021) 1632-1647

    "Melatonin- and Ferulic Acid-Based HDAC6 Selective Inhibitors Exhibit Pronounced Immunomodulatory Effects In Vitro and Neuroprotective Effects in a Pharmacological Alzheimer’s Disease Mouse Model"
    F. He, C. J. Chou, M. Scheiner, E. Poeta, N. Yuan Chen, S. Gunesch, M. Hoffmann, C. Sotriffer, B. Monti, T. Maurice and M. Decker
    J. Med. Chem. 64 (7) (2021) 3794–3812
    DOI: 10.1021/acs.jmedchem.0c01940

    "Warhead Reactivity Limits the Speed of Inhibition of the Cysteine Protease Rhodesain"
    P. Johe, S. Jung, E. Endres, C. Kersten, C. Zimmer, W. Ye, C. Sönnichsen, U. A. Hellmich, C. Sotriffer, T. Schirmeister and H. Neuweiler
    ACS Chem. Biol. 16 (4) (2021) 661–670
    DOI: 10.1021/acschembio.0c00911

    "A Long Residence Time Enoyl-Reductase Inhibitor Explores an Extended Binding Region with Isoenzyme-Dependent Tautomer Adaptation and Differential Substrate-Binding Loop Closure"
    S. Eltschkner, J. Kehrein, T. A. Le, S. Davoodi, B. Merget, S. Basak, J. D. Weinrich, J. Schiebel, P. J. Tonge, B. Engels, C. Sotriffer and C. Kisker
    ACS Infect. Dis. 7 (4) (2021) 746–758
    DOI: 10.1021/acsinfecdis.0c00437

    "C-2-Linked Dimeric Strychnine Analogues as Bivalent Ligands Targeting Glycine Receptors"
    D. P. Zlotos, C. M. Abdelmalek, L. S. Botros, M. M. Banoub, Y. M. Mandour, U. Breitinger, A. El Nady, H.-G. Breitinger, C. Sotriffer, C. Villmann, A. A. Jensen, U. Holzgrabe
    J. Nat. Prod. 84 (2) (2021) 382-394
    DOI: 10.1021/acs.jnatprod.0c01030

    "Structure-Activity Relationships of Benzamides and Isoindolines Designed as SARS-CoV Protease Inhibitors Effective against SARS-CoV-2"
    A. Welker, C. Kersten, C. Müller, R. Madhugiri, C. Zimmer, P. Müller, R. A. Zimmermann, S. Hammerschmidt, H. Maus, J. Ziebuhr, C. Sotriffer, T. Schirmeister
    Chem. Med. Chem. 16 (2) (2021) 340-354
    DOI: 10.1002/cmdc.202000548


    "Controlling Supramolecular Structures of Drugs by Light"
    J. Wiest, J. Kehrein, M. Saedtler, K. Schilling, E. Cataldi, C. A. Sotriffer, U. Holzgrabe, T. Rasmussen, B. Böttcher, M. Cronin-Golomb, M. Lehmann, N. Jung, M. Windbergs, L. Meinel
    Mol. Pharmaceutics 17 (12) (2020) 4704-4708
    DOI: 10.1021/acs.molpharmaceut.0c00720

    "PROTAC-mediated degradation reveals a non-catalytic function of AURORA-A kinase"
    B. Adhikari, J. Bozilovic, M. Diebold, J. D. Schwarz, J. Hofstetter, M. Schröder, M. Wanior, A. Narain, M. Vogt, N. D. Stankovic, A. Baluapuri, L. Schönemann, L. Eing, P. Bhandare, B. Kuster, A. Schlosser, S. Heinzlmeir, C. Sotriffer, S. Knapp, E. Wolf 
    Nat. Chem. Biol. 16 (2020) 1179-1188
    DOI: 10.1038/s41589-020-00652-y

    "Melatonin receptor ligands: A pharmaco‐chemical perspective"
    J. A. Boutin, P. A. Witt‐Enderby, C. Sotriffer, D. P. Zlotos
    J. Pineal. Res69 (2020) e12672
    DOI: 10.1111/jpi.12672

    "How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study Using N-Myristoyltransferases as a Model System"
    C. Kersten, E. Fleischer, J. Kehrein, C. Borek, E. Jaenicke, C. Sotriffer, R. Brenk
    J. Med. Chem. 63 (5) (2020) 2095-2113
    DOI: 10.1021/acs.jmedchem.9b00586

    "Tacrine-xanomeline and tacrine-iperoxo hybrid ligands: Synthesis and biological evaluation at acetylcholinesterase and M1 muscarinic acetylcholine receptors"
    M. Maspero, D. Volpato, D. Cirillo, N. Yuan Chen, R. Messerer, C. Sotriffer, M. De Amici, U. Holzgrabe, C. Dallanoce
    Bioorg. Chem. 96 (2020) 103633
    DOI: 10.1016/j.bioorg.2020.103633


    "Highly Selective Butyrylcholinesterase Inhibitors with Tunable Duration of Action by Chemical Modification of Transferable Carbamate Units Exhibit Pronounced Neuroprotective Effect in an  Alzheimer’s Disease Mouse Model"
    M. Hoffmann, C. Stiller, E. Endres, M. Scheiner, S. Gunesch, C. Sotriffer, T. Maurice, M. Decker
    J. Med. Chem. 62 (20) (2019) 9116-9140
    DOI: 10.1021/acs.jmedchem.9b01012

    "11-Aminostrychnine and N-(Strychnine-11-yl)propionamide: Synthesis, Configuration, and Pharmacological Evaluation at Glycine Receptors"
    D. P. Zlotos, A. M. Y. Mohsen, Y. M. Mandour, M. A. Marzouk, U. Breitinger, C. Villmann, H.-G. Breitinger, C. Sotriffer, A. A. Jensen, U. Holzgrabe
    J. Nat. Prod. 82 (2019) 2332-2336
    DOI: 10.1021/acs.jnatprod.9b00180

    "Autoinhibition Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination"
    A. K. L. Liess, A. Kucerova, K. Schweimer, L. Yu, T. I. Roumeliotis, M. Diebold, O. Dybkov, C. Sotriffer, H. Urlaub, J. S. Choudhary, J. Mansfeld, S. Lorenz
    Structure 27 (2019) 1195-1210
    DOI 10.1016/j.str.2019.05.008

    "Elucidating the Molecular Basis for Inhibitory Neurotransmission Regulation by Artemisinins"
    V. B. Kasaragod, T. J. Hausrat, N. Schaefer, M. Kuhn, N. R. Christensen, I. Tessmer, H. M. Maric, K. L. Madsen, C. Sotriffer, C. Villmann, M. Kneussel, H. Schindelin
    Neuron 101 (2019) 673-689
    DOI 10.1016/j.neuron.2019.01.001


    "Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis"
    Y. A. Ramirez, T. B. Adler, E. Altmann, T. Klemm, C. Tiesmeyer, F. Sauer, S. G. Kathman, A. V. Statsyuk, C. Sotriffer, C. Kisker
    ChemMedChem 13 (2018) 2014-2023
    DOI 10.1002/cmdc.201800364

    "Docking of covalent ligands: challenges and approaches"
    C. Sotriffer
    Molecular Informatics 37 (2018) 1800062
    DOI 10.1002/minf.201800062

    "Activity-based classification circumvents affinity prediction problems for pyrrolidine carboxamide inhibitors of InhA"
    Y. Narkhede, B. Merget, S. Wagner, C. Sotriffer
    J. Mol. Graph. Model. 80 (2018) 76-84
    DOI 10.1016/j.jmgm.2017.12.012


    "Mapping the pharmaceutical design space by amorphous ionic liquid strategies"
    J. Wiest, M. Saedtler, A. Balk, B. Merget, T. Widmer, H. Bruhn, M. Raccuglia, E. Walid, F. Picard, H. Stopper, W. Dekant, T. Lühmann, C. Sotriffer, B. Galli, U. Holzgrabe, L. Meinel
    J. Controll. Release 268 (2017) 314-322
    DOI 10.1016/j.jconrel.2017.10.040

    "Extending the Scope of GTFR Glucosylation Reactions with Tosylated Substrates for Rare Sugars Synthesis"
    J. Görl, C. Possiel, C. Sotriffer, J.Seibel
    ChemBioChem 18 (2017) 2012-2015
    DOI 10.1002/cbic.201700320

    "Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme"
    M. Misra, M. Kuhn, M. Löbel, H. An, A.V. Statsyuk, C. Sotriffer, H. Schindelin
    Structure 25 (2017) 1120-1129
    DOI 10.1016/j.str.2017.05.001

    "Novel bipharmacophoric inhibitors of the cholinesterases with affinity to the muscarinic receptors M1 and M2"
    R. Messerer, C. Dallanoce, C. Matera, S. Wehle, L. Flammini, B. Chirinda, A. Bock, M. Irmen, C. Tränkle, E. Barocelli, M. Decker, C. Sotriffer, M. De Amici, U. Holzgrabe
    Med. Chem. Commun.
    8 (2017) 1346-1359
    DOI 10.1039/c7md00149e


    "Oxime Ethers of (E)‑11-Isonitrosostrychnine as Highly Potent Glycine Receptor Antagonists"
    A.M.Y. Mohsen, Y.M. Mandour, E. Sarukhanyan, U. Breitinger, C. Villmann, M.M. Banoub, H.G. Breitinger, T. Dandekar, U. Holzgrabe, C. Sotriffer, A.A. Jensen, D.P. Zlotos
    J. Nat. Prod. 79 (2016) 2997-3005
    DOI 10.1021/acs.jnatprod.6b00479

    "Experimental and theoretical investigations into the stability of cyclic aminals"
    E. Sawatzky, A. Drakopoulos, M. Rölz, C. Sotriffer, B. Engels, M. Decker
    Beilstein J. Org. Chem. 12 (2016) 2280-2292
    DOI 10.3762/bjoc.12.221

    "Development, synthesis and structure–activity-relationships of inhibitors of the macrophage infectivity potentiator (Mip) proteins of Legionella pneumophila and Burkholderia pseudomallei"
    F. Seufert, M. Kuhn, M. Hein, M. Weiwad, M. Vivoli, I.H. Norville, M. Sarkar-Tyson, L.E. Marshall, K. Schweimer, H. Bruhn, P. Rösch, N.J. Harmer, C.A. Sotriffer, U. Holzgrabe
    Bioorg. Med. Chem. 24 (2016) 5134-5147
    DOI 10.1016/j.bmc.2016.08.025

    "Empirircal scoring functions for affinity prediction of protein-ligand complexes"
    L. Pason, C.A. Sotriffer
    Molecular Informatics 35 (2016) 541-548
    DOI 10.1002/minf.201600048

    "Correlating drug–target kinetics and in vivo pharmacodynamics: long residence time inhibitors of the FabI enoyl-ACP reductase "
    F. Daryaee, A. Chang, J. Schiebel, Y. Lu, Z. Zhang, K. Kapilashrami, S.G. Walker, C. Kisker, C.A. Sotriffer, S.L. Fisher, P.J. Tonge
    Chemical Science 7 (2016) 5945-5954
    DOI 10.1039/c6sc01000h

    "Conformational flexibility of DENV NS2B/NS3pro: from the inhibitor effect to the serotype influence"
    E. Piccirillo, B.Merget, C.A. Sotriffer, A.T. do Amaral
    J. Comp.-Aided Mol. Des. 30 (2016) 251-270
    DOI 10.​1007/​s10822-016-9901-8

    "Discovery of Highly Selective and Nanomolar Carbamate-Based Butyrylcholinesterase Inhibitors by Rational Investigation into Their Inhibition Mode"
    E. Sawatzky, S. Wehle, B. Kling, J. Wendrich, G. Bringmann, C.A. Sotriffer, J. Heilmann, M. Decker
    J. Med. Chem. 59 (2016) 2067-2082
    DOI 10.1021/acs.jmedchem.5b01674

    "Aminobenzimidazoles and structural isomers as templates for dual-acting butyrylcholinesterase inhibitors and hCB2R ligands to combat neurodegenerative disorders"
    D. Dolles, M. Nimczick, M. Scheiner, J. Ramler, P. Stadtmueller, E. Sawatzky, A. Drakopoulos, C. Sotriffer, H.-J. Wittmann, A. Strasser, M. Decker
    ChemMedChem 11 (2016) 1270-1283
    DOI 10.1002/cmdc.201500418


    "Protein-Ligand Docking: From Basic Principles to Advanced Applications"
    C.A. Sotriffer
    in: In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications (editor: C.N. Cavasotto), pp. 155-188; CRC Press, Boca Raton, FL, USA, 2015
    book website at crcpress.com

    "Slow-Onset Inhibition of Mycobacterium tuberculosis InhA: Revealing Molecular Determinants of Residence Time by MD Simulations"
    B. Merget, C.A. Sotriffer
    PLoS ONE e0127009 10(5) (2015) e0127009
    DOI 10.1371/journal.pone.0127009

    "An ordered water channel in Staphylococcus aureus FabI: Unraveling the mechanism of substrate recognition and reduction"
    J. Schiebel, A. Chang, B. Merget, G.R. Bommineni, W. Yu, L.A. Spagnuolo, M.V. Baxter, M. Tareilus, P.J. Tonge, C.F. Kisker, C.A. Sotriffer
    Biochemistry 54 (2015) 1943-1955
    DOI 10.1021/bi5014358

    "Anti-trypanosomal activities and structural chemical properties of selected compound classes"
    A. Ponte-Sucre, H. Bruhn, T. Schirmeister, A. Cecil, C.R. Albrecht, C. Buechold, M. Tischer, S. Schlesinger, T. Goebel, A. Fuss, D. Mathein, B. Merget, C.A. Sotriffer, A. Stich, G. Krohne, M. Engstler, G. Bringmann, and U. Holzgrabe
    Parasitology Research 114 (2015) 501-512
    DOI 10.1007/s00436-014-4210-4


    "Protocol for Rational Design of Covalently Interacting Inhibitors"
    T.C. Schmidt, A. Welker, M. Rieger, P.K. Sahu, C.A. Sotriffer, T. Schirmeister and B. Engels
    ChemPhysChem 15 (2014) 3226-3235
    DOI 10.1002/cphc.201402542

    "Amine substitution of quinazolinones leads to selective nanomolar AChE inhibitors with 'inverted' binding mode"
    F.H. Darras, S. Wehle, G. Huang, C.A. Sotriffer, and M. Decker
    Bioorganic and Medicinal Chemistry 22 (2014) 4867-4881
    DOI 10.1016/j.bmc.2014.06.045

    C. Sotriffer
    Pharmakon, 2 (2014) 284-290
    DOI 10.1691/pn.20140029

    "Rational Design of Broad-Spectrum Antibacterial Activity based on a Clinically Relevant Enoyl-ACP Reductase Inhibitor "
    J. Schiebel, A. Chang, S. Shah, Y. Lu, L. Liu, P. Pan, M. W. Hirschbeck, M. Tareilus, S. Eltschkner, W. Yu, J. E. Cummings, S. E. Knudson, G. R. Bommineni, S. G. Walker, R. A. Slayden, C.A. Sotriffer, P. J. Tonge and C. Kisker
    Journal of Biological Chemistry 289 (2014) 15987-16005
    DOI 10.1074/jbc.M113.532804

    "Acetylcholinesterase Inhibitors with Photoswitchable Inhibition of β-Amyloid Aggregation"
    X. Chen, S. Wehle, N. Kuzmanovic , B. Merget, U. Holzgrabe, B. König, C.A. Sotriffer, and M. Decker
    ACS Chemical Neuroscience, 5 (2014) 377-389
    DOI 10.1021/cn500016p

    "Synthesis, Biological Evaluation, and Computational Studies of Tri- and Tetracyclic Nitrogen-Bridgehead Compounds as Potent Dual-Acting AChE Inhibitors and hH3 Receptor Antagonists"
    F.H. Darras, S. Pockes, G. Huang, S. Wehle, A. Strasser, H.J. Wittmann, M. Nimczick, C.A. Sotriffer, and M. Decker
    ACS Chemical Neuroscience 5 (2014) 225-242
    DOI 10.1021/cn4002126


    "SFCscoreRF: A Random-Forest-Based Scoring Function for Improved Affinity Prediction of Protein-Ligand Complexes"
    D. Zilian, C.A. Sotriffer
    J. Chem. Inf. Model. 53(8) (2013) 1923-1933
    DOI 10.1021/ci400120b

    "Rational optimization of drug-target residence time: Insights from inhibitor binding to the S. aureus FabI enzyme-product complex"
    A. Chang, J. Schiebel, W. Yu, G.R. Bommineni, P. Pan, M.V. Baxter, A. Khanna, C.A. Sotriffer, C.F. Kisker, P.J. Tonge
    Biochemistry 52 (2013) 4217-4228
    DOI 10.1021/bi400413c

    "1,4-Substituted 4-(1H)-pyridylene-hydrazone-type inhibitors of AChE, BuChE, and amyloid-β aggregation crossing the blood-brain barrier"
    M. Prinz, S. Parlar, G. Bayraktar, V. Alptüzün, E. Erciyas, A. Fallarero, D. Karlsson, P. Vuorela, M. Burek, C. Förster, E. Turunc, G. Armagan, A. Yalcin, C. Schiller, K. Leuner, M. Krug, C.A. Sotriffer, U. Holzgrabe
    Europ. J. Pharm. Sci. 49 (2013) 603-613
    DOI 10.1016/j.ejps.2013.04.024

    "Structure-Based Search for New Inhibitors of Cholinesterases"
    M. Bajda, A. Więckowska, M. Hebda, N. Guzior, C.A. Sotriffer, B. Malawska
    Int. J. Mol. Sci. 14 (2013) 5608-5632
    DOI 10.3390/ijms14035608

    "Molecular Dynamics Reveal Binding Mode of Glutathionylspermidine by Trypanothione Synthetase"
    O. Koch, D. Cappel, M. Nocker, T. Jaeger, L. Flohe, C.A. Sotriffer, P.M. Selzer
    PLOSone 8(2) (2013) e56788
    DOI 10.1371/journal.pone.0056788

    "MycPermCheck: The Mycobacterium tuberculosis permeability prediction tool for small molecules"
    B. Merget, D. Zilian, T. Müller, C.A. Sotriffer
    Bioinformatics 29(1) (2013) 62-68
    DOI 10.1093/bioinformatics/bts641


    "Scoring functions for protein-ligand interactions"
    C. Sotriffer
    in: Protein-Ligand Interactions (editor: H. Gohlke), Methods and Principles in Medicinal Chemistry, Vol. 53 (series editors: R. Mannhold, H. Kubinyi, G. Folkers), pp. 237-263; Wiley-VCH, Weinheim, 2012
    book website at eu.wiley.com

    "Structure of the Yersinia pestis FabV Enoyl-ACP Reductase and its Interaction with two 2-Pyridone Inhibitors"
    M.W. Hirschbeck, J. Kuper, H. Lu, N. Liu, C. Neckles, S. Shah, S. Wagner, C.A. Sotriffer, P.J. Tonge, and C. Kisker
    Structure, 20 (2012) 89-100
    DOI 10.1016/j.str.2011.07.019


    "Molecular dynamics of Mycobacterium tuberculosis KasA: implications for inhibitor and substrate binding and consequences for drug design"
    B. Schaefer, C. Kisker, C. A. Sotriffer
    J. Comp.-Aided Mol. Des.., 25 (2011) 1053-1069
    DOI: 10.1007/s10822-011-9483-4

    "Probing the Dynamic Nature of Water Molecules and Their Influences on Ligand Binding in a Model Binding Site"
    D.Cappel, R. Wahlström, R. Brenk, C.A. Sotriffer
    J. Chem. Inf. Model., 51 (2011) 2581-2594
    DOI 10.1021/ci200052j

    "The challenge of affinity prediction: Scoring functions for structure-based virtual screening"
    C. Sotriffer, H. Matter
    in: Virtual Screening: Principles, Challenges, and Practical Guidelines (editor: C. Sotriffer), Methods and Principles in Medicinal Chemistry, Vol. 48 (series editors: R. Mannhold, H. Kubinyi, G. Folkers), pp. 177-221; Wiley-VCH, Weinheim, 2011
    book website at eu.wiley.com

    "Applications and success stories in virtual screening"
    H. Matter, C. Sotriffer
    in: Virtual Screening: Principles, Challenges, and Practical Guidelines (editor: C. Sotriffer), Methods and Principles in Medicinal Chemistry, Vol. 48 (series editors: R. Mannhold, H. Kubinyi, G. Folkers), pp. 319-358; Wiley-VCH, Weinheim, 2011
    book website at eu.wiley.com

    "Accounting for induced-fit effects in docking: What is possible and what is not?"
    C. A. Sotriffer
    Curr. Top. Med. Chem., 11 (2011) 179-191

    "Pipecolic Acid Derivatives As Small-Molecule Inhibitors of the Legionella MIP Protein"
    C. Juli, M. Sippel, Jens Jäger, A. Thiele, M. Weiwad, K. Schweimer, P. Rösch, M. Steinert, C. A. Sotriffer,U. Holzgrabe
    J. Med. Chem., 54 (2011) 277-283
    DOI 10.1021/jm101156y


    "Docking compared to 3D-pharmacophores: the scoring function challenge"
    M. Hein, D. Zilian, C.A. Sotriffer
    Drug Discovery Today: Technologies, 7 (2010) e229--e236
    DOI: 10.1016/j.ddtec.2010.12.003

    "Molecular Dynamics Simulations of the HIV-1 Integrase Dimerization Interface: Guidelines for the Design of a Novel Class of Integrase Inhibitors"
    M. Sippel, C. A. Sotriffer
    J. Chem. Inf. Model., 50 (2010) 604–614
    DOI 10.1021/ci900403s

    "Pyrrolidine derivatives as plasmepsin inhibitors: binding mode analysis assisted by molecular dynamics simulations of a highly flexible protein"
    T. Luksch, A. Blum, N. Klee, W. E. Diederich, C. A. Sotriffer, G. Klebe
    ChemMedChem, 5 (2010) 443-454
    DOI 10.1002/cmdc.200900452


    "Probing dynamic water molecules with rigid ligand complexes"
    D. Cappel, C. A. Sotriffer
    Chemistry Central Journal, 3(Suppl 1) (2009) O20
    DOI 10.1186/1752-153X-3-S1-O20


    "From Ligand to Complexes. Part 2. Remarks on Human Immunodeficiency Virus Type 1 Integrase inhibition by β-Diketo Acid Metal Complexes."
    A. Bacchi, M. Biemmi, M. Carcelli, F. Carta, C. Compari, E. Fisicaro, D. Rogolino, M. Sechi, M. Sippel, C. A. Sotriffer, T. W. Sanchez, N. Neamati
    J. Med. Chem.,51 (2008) 7253-7264
    DOI 10.1021/jm800893q

    "Target Flexibility: An Emerging Consideration in Drug Discovery and Design"
    P. Cozzini, G. E. Kellogg, F. Spyrakis, D. J. Abraham, G. Costantino, A. Emerson, F. Fanelli, H. Gohlke, L. A. Kuhn, G. M. Morris, M. Orozco, T. A. Pertinhez, M. Rizzi, C. A. Sotriffer
    J. Med. Chem. , 51 (2008) 6237-6255
    DOI 10.1021/jm800562d

    "Computer-aided Design and Synthesis of non-peptidic Plasmepsin II and IV inhibitors"
    T. Luksch, N. S. Chan, S. Brass, C. A. Sotriffer, G. Klebe, W. E. Diederich
    ChemMedChem. , 3 (2008) 1323-1336
    DOI 10.1002/cmdc.200700270

    "SFCscore: Scoring functions for affinity prediction of protein-ligand complexes"
    C. A. Sotriffer, P. Sanschagrin, H. Matter, G. Klebe
    Proteins: Structure, Function, and Bioinformatics, 73 (2008) 395-419
    DOI 10.1002/prot.22058



    "Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase"
    H. Steuber, P. Czodrowski, C. A. Sotriffer, G. Klebe
    J. Mol. Biol. , 373 (2007) 1305-1320
    DOI 10.1016/j.jmb.2007.08.063

    "Thermodynamisches Inhibitionsprofil eines Cyclopentyl- und eines Cyclohexylderivats gegenüber Thrombin: gleich, jedoch aus unterschiedlichem Grund"
    C. Gerlach, M. Smolinski, H. Steuber, C. A. Sotriffer, A. Heine, D. G. Hangauer, G. Klebe
    Angew. Chem., 119 (2007) 8664-8667
    DOI 10.1002/ange.200701169<br/>
    "Thermodynamic inhibition profile of a cyclopentyl and a cyclohexyl derivative towards thrombin: the same but for different reasons"
    C. Gerlach, M. Smolinski, H. Steuber, C. A. Sotriffer, A. Heine, D. G. Hangauer, G. Klebe
    Angewandte Chemie Int. Ed. , 46 (2007) 8511-8514
    DOI 10.1002/anie.200701169

    "Atypical protonation states in the active site of HIV-1 protease: a computational study"
    P. Czodrowski, C. A. Sotriffer, G. Klebe
    J. Chem. Inf. Model. , 47 (2007) 1590-1598
    DOI 10.1021/ci600522c

    "Wie verlässlich sind aktuelle Docking-Ansätze für strukturbasiertes Wirkstoffdesign? - Fallstudie zur Aldose-Reduktase"
    M. Zentgraf, H. Steuber, C. Koch, C. La Motta, S. Sartini, C. A. Sotriffer, G. Klebe
    Angew. Chem., 119 (2007) 3645-3649
    DOI 10.1002/ange.200603625
    "How reliable are current docking approaches for structure-based drug design? Lessons from Aldose Reductase"
    M. Zentgraf, H. Steuber, C. Koch, C. La Motta, S. Sartini, C. A. Sotriffer, G. Klebe
    Angew. Chem. Int. Ed., 46 (2007) 3575-3578
    DOI 10.1002/anie.200603625

    "Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pKa calculations and ITC experiments"
    P. Czodrowski, C. A. Sotriffer, G. Klebe
    J. Mol. Biol., 367 (2007) 1347-1356
    DOI 10.1016/j.jmb.2007.01.022

    "Understanding oligomerization in 3alpha-hydroxysteroid dehydrogenase / carbonyl reductase from Comamonas testosteroni: An in-silico approach and evidence for an active protein"
    F. Hoffmann, C. Sotriffer, A. Evers, G. Xiong, E. Maser
    J. Biotechnol., 129 (2007) 131-139
    DOI 10.1016/j.jbiotec.2006.11.024


    "Addressing protein flexibility and ligand selectivity by 'in-situ cross-docking'"
    M. Zentgraf, J. Fokkens, C. A. Sotriffer
    ChemMedChem, 1 (2006) 1355-1359
    DOI 10.1002/cmdc.200600073

    "Expect the Unexpected or Caveat for Drug Designers: Multiple Structure Determinations Using Aldose Reductase Crystals Treated under Varying Soaking and Co-crystallisation Conditions"
    H. Steuber, M. Zentgraf, C. Gerlach, C. A. Sotriffer, A. Heine, G. Klebe
    J. Mol. Biol., 363 (2006) 174-187
    DOI 10.1016/j.jmb.2006.08.011

    "3D QSAR selectivity analyses of carbonic anhydrase inhibitors: Insights for the design of isozyme selective inhibitors"
    A.Weber, M. Böhm, C. T. Supuran, A. Scozzafava, C. A. Sotriffer, G. Klebe
    J. Chem. Inf. Model., 46 (2006) 2737-2760
    DOI 10.1021/ci600298r

    "Physicochemical descriptors to discriminate between protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms"
    P. Block, J. Paern, E. Hüllermeier, P. Sanschagrin, C. A. Sotriffer, G. Klebe
    Proteins: Structure, Function, and Bioinformatics, 65 (2006) 607-622
    DOI 10.1002/prot

    "Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes"
    P. Czodrowski, I. Dramburg, C. A. Sotriffer, G. Klebe
    Proteins, 65 (2006) 424-437
    DOI 10.1002/prot.21110

    "The Potential of P1 Site Alterations in Peptidomimetic Protease Inhibitors as Suggested by Virtual Screening and Explored by the Use of C--C-Coupling Reagents"
    S. Weik, T. Luksch, A. Evers, J. Böttcher, C. A. Sotriffer, A. Hasilik, H. G. Löeffler, G. Klebe, J. Rademann
    ChemMedChem, 1 (2006) 445-457
    DOI 10.1002/cmdc.200500027

    "Lock-and-key motif as a concept for designing affinity adsorbents for protein purification"
    D. Platis, C. A. Sotriffer, Y. Clonis, N. E. Labrou
    J. Chromatogr. A, 1128 (2006) 138-151
    DOI 10.1016/j.chroma.2006.06.051

    "AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB"
    P. Block, C. A. Sotriffer, I. Dramburg, G. Klebe
    Nucleic Acids Res., 34 (2006) D522-D526 (Database issue) 

    "A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP"
    D. Vigil, J. H. Lin, C. A. Sotriffer, J. K. Pennypacker, J. A. McCammon, S. S. Taylor
    Protein Science, 15 (2006) 113-121
    DOI 10.1110/ps.051723606

    "Molecular Dynamics Simulations in Drug Design"
    C. A. Sotriffer
    in: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine,
    Springer, Heidelberg (Germany), pp. 1153-1160; Springer, Berlin, Heidelberg, 2006
    DOI 10.1007/3-540-29623-9_0820


    "Hydroxyethylene Sulfones as a New Scaffold To Address Aspartic Proteases: Design, Synthesis, and Structural Characterization"
    E. Specker, J. Böttcher, A. Heine, C. A. Sotriffer, H. Lilie, A. Schoop, G. Müller, N. Griebenow, G. Klebe
    J. Med. Chem., 48 (2005) 6607-6619
    DOI 10.1021/jm050224y

    "'In Situ Cross-Docking' To Simultaneously Address Multiple Targets"
    C. A. Sotriffer, I. Dramburg
    J. Med. Chem., 48 (2005) 3122-3125
    DOI 10.1021/jm050075j

    "Structural aspects of oligomerization in 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni: New approaches for efficient protein design"
    F. Hoffmann, C.A. Sotriffer, A. Evers, G. Xiong, E. Maser
    in: Enzymology and Molecular Biology of Carbonyl Metabolism (editors: H. Weiner, B. Plapp, R. Lindahl, E. Maser), 12, pp. 308-314; Purdue University Press, 2005


    "Neue Konzepte zur Arzneistoffsuche und Synthese"
    W. Diederich, P. Haebel, A. Heine, K. Reuter, C. Sotriffer, G. Klebe
    Labor und Praxis, 28 (2004) 24-26 

    "Probing Flexibility and 'Induced-Fit' Phenomena in Aldose Reductase by Comparative Crystal Structure Analysis and Molecular Dynamics Simulations"
    C. A. Sotriffer, O. Kraemer, G. Klebe
    Proteins, 56 (2004) 52-66
    DOI 10.1002/prot.20021

    "Discovery of a Novel Binding Trench in HIV Integrase"
    J. R. Schames, R. H. Henchman, J. S. Siegel, C. A. Sotriffer, H. H. Ni, J. A. McCammon
    J. Med. Chem., 47 (2004) 1879-1881
    DOI 10.1021/jm0341913

    "Strategies for the design of inhibitors of aldose reductase, an enzyme showing pronounced induced-fit adaptations"
    G. Klebe, O. Kraemer, C. Sotriffer
    Cell. Mol. Life Sci., 61 (2004) 783-793
    DOI 10.1007/s00018-003-3406-z

    "Multiple Binding Modes Observed in X-ray Structures of Carbonic Anhydrase Inhibitor Complexes and Other Systems: Consequences for Structure-Based Drug Design."
    J. Antel, A. Weber, C. A. Sotriffer, G. Klebe
    in: Carbonic Anhydrase - its inhibitors and activators, pp. 45-66; CRC press, Boca Raton (FL, USA), 2004


    "Structural Aspects of Oligomerization in 3alpha-hydroxysteroid Dehydrogenase from Comamonas testosteroni: Redesign of an "Extraloop"-Domain on the Basis of 3alpha/20beta-HSD."
    F. Hoffmann, G. Xiong, C.A. Sotriffer, K. Reuter, E. Maser
    in: Genes, Gene Families, and Isozymes, pp. 123-132; Medimond, Internat. Proceedings, Bologna, 2003 

    "The Docking Problem"
    C. Sotriffer, M. Stahl, G. Klebe
    in: Handbook of Chemoinformatics, Vol. 4, pp. 1732-1766; Wiley-VCH, Weinheim, 2003 

    "Structural and energetic determinants for enantiopreferences in kinetic resolution of lipases"
    M. Bocola, M. T. Stubbs, C. Sotriffer, B. Hauer, T. Friedrich,K. Dittrich, G. Klebe
    Protein Engineering, 16 (2003) 319-322
    DOI 10.1093/protein/gzg047

    "Docking and Scoring Functions/Virtual Screening"
    C. Sotriffer, M. Stahl, H.J. Boehm, G. Klebe
    in: Burger's Medicinal Chemistry and Drug Discovery , Vol. 1, Chapt. 7, pp. 281-333; Wiley, New York, 2003


    "Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase"
    D. C. Rowley, M. S. T. Hansen, D. Rhodes, C. A. Sotriffer, H. H. Ni, J. A. McCammon, F. D. Bushman, W. Fenical
    Bioorg. Med. Chem., 10 (2002) 3619-3625
    DOI 10.1016/S0968-0896(02)00241-9

    "Docking into knowledge-based potential fields: A comparative evaluation of DrugScore"
    C. A. Sotriffer, H. Gohlke, G. Klebe
    J. Med. Chem., 45 (2002) 1967-1970
    DOI 10.1021/jm025507u

    "Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design"
    (invited review)
    C. Sotriffer, G. Klebe
    Il Farmaco, 57 (2002) 243-251


    "Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study"
    H. H. Ni, C. A. Sotriffer, J. A. McCammon
    J. Med. Chem., 44 (2001) 3043-3047
    DOI 10.1021/jm010205y

    "Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine"
    H. H. Loeffler, C. A. Sotriffer, R. H. Winger, K. R. Liedl, B. M. Rode
    J. Comp. Chem., 22 (2001) 846-860


    "Active site binding modes of HIV-1 integrase inhibitors"
    C. A. Sotriffer, H. H. Ni, J. A. McCammon
    J. Med. Chem., 43 (2000) 4109-4117
    DOI 10.1021/jm000194t

    "HIV-1 Integrase inhibitor interactions at the active site: prediction of binding modes unaffected by crystal packing"
    C. A. Sotriffer, H. H. Ni, J. A. McCammon
    J. Am. Chem. Soc., 122 (2000) 6136-6137
    DOI 10.1021/ja001152x

    "Elbow flexibility and ligand-induced domain rearrangements in antibody Fab NC6.8:  large effects of a small hapten"
    C. A. Sotriffer, B. M. Rode, J. M. Varga, K. R. Liedl
    Biophysical Journal, 79 (2000) 614-628 

    "Automated docking of ligands to antibodies: methods and applications"
    (invited article)
    C. A. Sotriffer, W. Flader, R. H. Winger, B. M. Rode, K. R. Liedl, J. M. Varga
    Methods: A Companion to Methods in Enzymology 20 (2000) 280-291


    "Are prions a relic of an early stage of peptide evolution?"
    B. M. Rode, W. Flader, C. Sotriffer, A. Righi
    Peptides 20 (1999) 1513-1516
    DOI 10.1016/S0196-9781(99)00163-1

    "Ligand-binding by antibody IgE Lb4: assessment of binding site preferences using microcalorimetry, docking, and free energy simulations"
    C. A. Sotriffer, W. Flader, A. Cooper, B. M. Rode, D. S. Linthicum, K. R. Liedl, J. M. Varga
    Biophysical Journal 76 (1999) 2966-2977 

    "Application of multivariate data analysis methods to Comparative Molecular Field Analysis (CoMFA) data. Proton affinities and pKa prediction for nucleic acids components"
    R. Gargallo, C. A. Sotriffer, K. R. Liedl, B. M. Rode
    J. Comput. Aid. Molec. Design 13 (1999) 611-623
    DOI 10.1023/A:1008005522776


    "Ligand-induced domain movement in an antibody Fab: Molecular Dynamics studies confirm the unique domain movement observed experimentally for Fab NC6.8 upon complexation and reveal its segmental flexibility"
    C. A. Sotriffer, K. R. Liedl, D. S. Linthicum, B. M. Rode, J. M. Varga
    Journal of Molecular Biology 278 (1998) 301-306
    DOI 10.1006/jmbi.1998.1684


    "Comparative Molecular Field Analysis of HIV-1 Reverse Transcriptase inhibitors in the class of 1[(2-Hydroxyethoxy)-methyl]-6-(phenylthio)thymine"
    S. Hannongbua, L. Lawtrakul, C. A. Sotriffer, B. M. Rode
    Quant. Struct.-Act. Relat. 15 (1996) 389-394
    DOI 10.1002/qsar.19960150504

    "Comparative Molecular Field Analysis (CoMFA) of haptens docked to the multispecific antibody IgE(Lb4)"
    A. M. Gamper, R. H. Winger, K. R. Liedl, C. A. Sotriffer, J. M. Varga, R. T. Kroemer, B. M. Rode
    Journal of Medicinal Chemistry 39 (1996) 3882-3888
    DOI 10.1021/jm960229i

    "Comparative docking studies on ligand-binding to multispecific antibodies IgE-La2 and -Lb4"
    C. A. Sotriffer, R. H. Winger, K. R. Liedl, B. M. Rode, J. M. Varga
    J. Comput. Aid. Molec. Design 10 (1996) 305-320
    DOI 10.1007/BF00124500

    "Prediction of IgE(Lb4) complex structures by automated docking"
    R. H. Winger, K. R. Liedl, C. A. Sotriffer, A. M. Gamper, R. T. Kroemer, B. M. Rode, J. M. Varga
    Journal of Molecular Recognition 9 (1996) 239-246
    DOI 10.1002/(SICI)1099-1352(199605)9:3<239::AID-JMR265>3.0.CO;2-F

    Heteroligation of a mouse monoclonal IgE antibody (IgE-La2) with small molecules, analysed by computer-aided automated docking"
    C. A. Sotriffer, K. R. Liedl, R. H. Winger, A. M. Gamper, R. T. Kroemer, D. S. Linthicum, B. M. Rode, J. M. Varga
    Molecular Immunology 33 (1996) 129-144
    DOI 10.1016/0161-5890(95)00124-7