Main Content

Publications

2022

59 | How Carvedilol activates β2-adrenoceptors.
Tobias Benkel, Mirjam Zimmermann, Julian Zeiner, Sergi Bravo, Nicole Merten, Victor Jun Yu Lim, Edda Sofie Fabienne Matthees, Julia Drube, Elke Miess-Tanneberg, Daniela Malan, Martyna Szpakowska, Stefania Monteleone, Jak Grimes, Zsombor Koszegi, Yann Lanoiselée, Shannon O’Brien, Nikoleta Pavlaki, Nadine Dobberstein, Asuka Inoue, Viacheslav Nikolaev, Davide Calebiro, Andy Chevigné, Philipp Sasse, Stefan Schulz, Carsten Hoffmann, Peter Kolb, Maria Waldhoer, Katharina Simon, Jesus Gomeza, Evi Kostenis
Nat. Commun. 2022, 13, 7109. [pdf]

58 | Pose, Duplicate, Then Elaborate: Steps Towards Increased Affinity for Inhibitors Targeting the Specificity Surface of the Pim-1 Kinase.
Lukas Heyder†, Phil M. M. Hochban†, Corey Taylor†, Florent Chevillard, Christof Siefker, Christian Iking, Achim Aigner, Gerhard Klebe, Andreas Heine, Peter Kolb*, Wibke E. Diederich*
Eur. J. Med. Chem. 2022, 245, 114914. [pdf].

57 | The isoleucine at position 118 in transmembrane 2 is responsible for the selectivity of xamoterol, nebivolol and ICI89406 for the human β1-adrenoceptor.
Victor J. Y. Lim
†, Richard G. W. Proudman†, Stefania Monteleone, Peter Kolb*, Jillian G. Baker*
Mol. Pharm. 2022, accepted. [pdf]

56 | The extracellular N-terminus of natural receptor isoforms allosterically modulates GPR35-transducer coupling and mediates intracellular pathway bias.
Hannes Schihada*, Thomas M. Klompstra, Laura J. Humphrys, Igor Cervenka, Shamim Dadvar, Peter Kolb, Jorge L. Ruas, Gunnar Schulte*
J. Biol. Chem. 2022, 298, 102328. [pdf]

55 | Allosteric modulation of GPCRs: From structural insights to in silico drug discovery.
Margherita Persechino†, Janik B. Hedderich†, Peter Kolb*, Daniel Hilger*
Pharmacol. Ther. 2022, 237, 108242. [pdf][review]

54 | The pocketome of G-protein-coupled receptors reveals previously untargeted allosteric sites.
Janik B. Hedderich, Margherita Persechino, Katharina Becker, Franziska M. Heydenreich, Torben Gutermuth, Michel Bouvier, Moritz Bünemann, Peter Kolb
Nat. Commun. 2022, 13, 2567. [pdf]

53 | Community guidelines for GPCR ligand bias: IUPHAR review 32.
Peter Kolb†*, Terry Kenakin†*, Stephen P. H. Alexander, Marcel Bermudez, Laura M. Bohn, Christian S. Breinholt, Michel Bouvier, Stephen J. Hill, Evi Kostenis, Kirill A. Martemyanov, Richard R. Neubig, H. Ongun Onaran, Sudarshan Rajagopal, Bryan L. Roth, Jana Selent, Arun K. Shukla, Martha E. Sommer, David E. Gloriam*
Br. J. Pharmacol. 2022, 179, 3651-3674. [pdf]

2021 

52 | Disentangling bias between Gq, GRK2 and arrestin3 recruitment at the M3 muscarinic acetylcholine receptor.
Anja Flöser†, Katharina Becker†, Evi Kostenis, Gabriele König, Cornelius Krasel, Peter Kolb*, Moritz Bünemann*
eLife 2021, 0:e58442. [pdf]

51 | Fragment evolution for GPCRs: the role of secondary binding sites in optimization.
Florent Chevillard, Ádám Kelemen, Jillian G. Baker, Vivien A. Aranyodi, Frank Balzer, Peter Kolb*, György M. Keserű*
Chem. Commun. 2021, 57, 10516-10519. [pdf]

50 | Systematic investigation of PRMT6 substrate recognition reveals broad specificity with a preference for an RG motif or basic and bulky residues.
Joshua J. Hamey, Sinja Rakow, Caroline Bouchard, Johanna M. Senst, Peter Kolb, Uta-Maria Bauer, Marc R. Wilkins, Gene Hart-Smith
FEBS J. 2021, 288, 5668-5691. [pdf]

49 | Analyzing kinase similarity in small molecule and protein structural space to explore the limits of multi-target screening.
Denis Schmidt, Magdalena M. Scharf, Dominique Sydow, Eva Aßmann, Maria Martí-Solano, Marina Keul, Andrea Volkamer*, Peter Kolb*
Molecules 2021, 26, 629. [pdf]

2020

48 | Structure-based Discovery of Novel Ligands for the Orexin 2 Receptor.
Jakub Gunera, Jillian G. Baker, Niek van Hilten, Daniel M. Rosenbaum, Peter Kolb
J. Med. Chem. 2020, 63, 11045-11053. [pdf]

47 | Structure-based development of a subtype-selective orexin 1 receptor antagonist.
Jan Hellmann†, Matthäus Drabek†, Jie Yin†, Jakub Gunera, Theresa Pröll, Frank Kraus, Christopher J. Langmead, Harald Hübner, Dorothee Weikert, Peter Kolb*, Daniel M. Rosenbaum*, Peter Gmeiner*
Proc. Natl. Acad. Sci. U.S.A. 2020, 117, 18059-18067. [pdf]

46 | GPCRmd uncovers the dynamics of the 3D-GPCRome.
Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, Johanna K. S. Tiemann, David Aranda-García, Juan Manuel Ramírez-Anguita, Tomasz Maciej Stepniewski, Nathalie Worp, Alejandro Varela-Rial, Adrián Morales-Pastor, Brian Medel-Lacruz, Gáspár Pándy-Szekeres, Eduardo Mayol, Toni Giorgino, Jens Carlsson, Xavier Deupi, Slawomir Filipek, Marta Filizola, José Carlos Gómez-Tamayo, Angel Gonzalez, Hugo Gutiérrez-de-Terán, Mireia Jiménez-Rosés, Willem Jespers, Jon Kapla, George Khelashvili, Peter Kolb, Dorota Latek, Maria Martí-Solano, Pierre Matricon, Minos-Timotheos Matsoukas, Przemyslaw Miszta, Mireia Olivella, Laura Perez-Benito, Davide Provasi, Santiago Ríos, Iván R. Torrecillas, Jessica Sallander, Agnieszka Sztyler, Silvana Vasile, Harel Weinstein, Ulrich Zachariae, Peter W. Hildebrand, Gianni De Fabritiis, Ferran Sanz, David E. Gloriam, Arnau Cordomi, Ramon Guixà-González*, Jana Selent*
Nat. Methods 2020, 17, 777-787. [pdf]

45 | The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling.
Martha E. Sommer*, Jana Selent, Jens Carlsson, Chris De Graaf, David E. Gloriam, György M. Keserű, Mickey Kosloff, Stefan Mordalski, Aurelien Rizk, Mette M. Rosenkilde, Eddy Sotelo, Johanna K. S. Tiemann, Andrew Tobin, Nina Vardjan, Maria Waldhoer, Peter Kolb*
ACS Pharmacol. Transl. Sci. 2020, 3, 361-370. [pdf] [perspective] 

44 | A Focus on Unusual ECL2 Interactions Yields β2-adrenergic Receptor Antagonists with Unprecedented Scaffolds.
Magdalena M. Scharf†, Mirjam Zimmermann†, Florian Wilhelm, Raimond Stroe, Maria Waldhoer*, Peter Kolb*
ChemMedChem 2020, 15, 882-890. [pdf]

43 | A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands.
Kamil J. Kuder*, Ilona Michalik, Katarzyna Kieć-Kononowicz, Peter Kolb*
J. Comput. Aided Mol. Des. 2020, 34, 697-707. [pdf]

2019

42 | Comparative docking to distinct G protein-coupled receptor conformations exclusively yields ligands with agonist efficacy.
Magdalena M. Scharf, Moritz Bünemann, Jillian G. Baker*, Peter Kolb*
Mol. Pharmacol. 2019, 96, 851-861. [pdf]

41 | Interrogating dense ligand chemical space with a forward-synthetic library.
Florent Chevillard†, Silvia Stotani†, Anna Karawajczyk, Stanimira Hristeva, Els Pardon, Jan Steyaert, Dimitrios Tzalis*, Peter Kolb*
Proc. Natl. Acad. Sci. U.S.A. 2019, 116, 11496-11501. [pdf]

40 | Direct targeting of Gαq and Gα11 oncoproteins in cancer cells.
Suvi Annala, Xiaodong Feng, Naveen Shridhar, Funda Eryilmaz, Julian Patt, JuHee Yang, Eva M. Pfeil, Rodolfo Daniel Cervantes-Villagrana, Asuka Inoue, Felix Häberlein, Tanja Slodczyk, Raphael Reher, Stefan Kehraus, Stefania Monteleone, Ramona Schrage, Nina Heycke, Ulrike Rick, Sandra Engel, Alexander Pfeifer, Peter Kolb, Gabriele König, Moritz Bünemann, Thomas Tüting, José Vázquez-Prado, J. Silvio Gutkind, Evelyn Gaffal, Evi Kostenis
Sci. Signal. 2019, 12, eaau5948. [pdf] [peer recommendation]

39 | Virtual Compound Libraries in Computer-Assisted Drug Discovery.
Niek van Hilten, Florent Chevillard, Peter Kolb
J. Chem. Inf. Model. 2019, 59, 644-651. [pdf][perspective]

2018

38 | Nanobody-enabled reverse pharmacology on GPCRs.
Els Pardon, Cecilia Betti, Toon Laeremans, Florent Chevillard, Karel Guillemyn, Peter Kolb, Steven Ballet, Jan Steyaert
Angew. Chem. Int. Ed. 2018, 57, 5292-5295. [pdf] [Comment @ In the pipeline]

37 | Binding-site compatible fragment growing applied to the design of β2-adrenergic receptor ligands.
Florent Chevillard, Helena Rimmer, Cecilia Betti, Els Pardon, Steven Ballet, Niek van Hilten, Jan Steyaert, Wibke E. Diederich, Peter Kolb
J. Med. Chem. 2018, 61, 1118-1129. [pdf] [Comment @ Practical Fragments]

2017

36 | The allosteric site regulates the voltage sensitivity of muscarinic receptors.
Annika Hoppe, Maria Martí-Solano, Matthäus Drabek, Moritz Bünemann, Peter Kolb, Andreas Rinne
Cell Signal. 2017, 42, 114-126. [pdf]

35 | Identification and in silico structural analysis of Gallus gallus Protein Arginine Methyltransferase 4 (PRMT4).
Hannah Berberich, Felix Terwesten, Sinja Rakow, Peeyush Sahu, Caroline Bouchard, Sjaak Philipsen, Peter Kolb, Uta-Maria Bauer
FEBS Open Bio 2017, 7, 1909-1923. [pdf]

34 | An open source pharma roadmap.
Manica Balasegaram, Peter Kolb, John McKew, Jaykumar Menon, Piero Olliaro, Tomasz Sablinski, Zakir Thomas, Matthew H. Todd, Els Torreele, John Wilbanks
PLOS Med 2017, 14, e1002276. [pdf][essay]

33 | Similarity- and substructure-based development of β2-adrenergic receptor ligands based on unusual scaffolds.
Denis Schmidt, Jakub Gunera, Jillian G. Baker, Peter Kolb
ACS Med. Chem. Lett. 2017, 8, 481-485. [pdf]

32 | PrenDB: A Substrate Prediction Database to Enable Biocatalytic Use of Prenyltransferases.
Jakub Gunera, Florian Kindinger, Shu-Ming Li, Peter Kolb
J. Biol. Chem. 2017, 292, 4003-4021. [pdf]

2016

31 | GPCRdb: The G protein-coupled receptor database - An introduction.
Christian Munk, Vignir Isberg, Stefan Mordalski, Kaspar Harpsøe, Krzysztof Rataj, Alexander Hauser, Peter Kolb, Andrzej J. Bojarski, Gert Vriend, David E. Gloriam
Br. J. Pharmacol. 2016, 173, 2195-2207. [pdf][review]

30 | Structure-based virtual screening for dopamine D2 receptor ligands as potential antipsychotics.
Agnieszka A. Kaczor, Andrea G. Silva, María I. Loza, Peter Kolb, Marián Castro, Antti Poso
ChemMedChem 2016, 11, 718-729. [pdf]

29 | Three stories on Eph kinase inhibitors: from in silico discovery to in vivo validation.
Andrea Unzue, Karine Lafleur, Hongtao Zhao, Ting Zhou, Jing Dong, Peter Kolb, Johanna Liebl, Stefan Zahler, Amedeo Caflisch, Cristina Nevado
Eur. J. Med. Chem. 2016, 112, 347-366. [pdf][review]

28 | Drugging specific conformational states of GPCRs: challenges and opportunities for computational chemistry.
Maria Martí-Solano, Denis Schmidt, Peter Kolb, Jana Selent
Drug Discov. Today 2016, 21, 625-631. [pdf][review]

2015

27 | The quorum-sensing regulator ComA from Bacillus subtilis activates transcription using topologically distinct DNA motifs.
Diana Wolf, Valentina Rippa, Juan Carlos Mobarec, Patricia Sauer, Lorenz Adlung, Peter Kolb, Ilka Bischofs
Nucleic Acids Res. 2015, 44, 2160-2172. [pdf]

26 | The mode of agonist binding to a G protein-coupled receptor switches the effect that voltage changes have on signaling.
Andreas Rinne, Juan Carlos Mobarec, Martyn Mahaut-Smith, Peter Kolb, Moritz Bünemann
Sci. Signal. 2015, 8, ra110. [pdf] [podcast]

25 | SCUBIDOO: A Large yet Screenable and Easily Searchable Database of Computationally Created Chemical Compounds Optimized toward High Likelihood of Synthetic Tractability.
Florent Chevillard, Peter Kolb
J. Chem. Inf. Model. 2015, 55, 1824-1835. [pdf] [peer recommendation]

24 | Fragment-based similarity searching with infinite color space.
Jakub Gunera, Peter Kolb
J. Comput. Chem. 2015, 36, 1597-1608. [pdf]

23 | Tryptophan C5-, C6- and C7-Prenylating Enzymes Displaying a Preference for C-6 of the Indole Ring in the Presence of Unnatural Dimethylallyl Diphosphate Analogues.
Julia Winkelblech, Mike Liebhold, Jakub Gunera, Xiulan Xie, Peter Kolb, Shu-Ming Li
Adv. Synth. Catal. 2015, 357, 975-986. [pdf]

22 | Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant.
Jie Yin, Juan Carlos Mobarec, Peter Kolb, Daniel M. Rosenbaum
Nature 2015, 519, 247-250. [pdf] [press release] [news item @ derstandard.at] [peer recommendation]

21 | Identifying Modulators of CXC Receptors 3 and 4 with Tailored Selectivity using Multi-Target Docking.
Denis Schmidt, Viachaslau Bernat, Regine Brox, Nuska Tschammer*, Peter Kolb*
ACS Chem. Biol. 2015, 10, 715-724. [pdf]

2014

20 | Functional Annotation and Structural Characterization of a Novel Lactonase Hydrolyzing D-Xylono-1,4-lactone-5-phosphate and L-Arabino-1,4-lactone-5-phosphate.
Magdalena Korczynska, Dao Feng Xiang, Zhening Zhang, Chengfu Xu, Tamari Narindoshvili, Siddhesh Kamat, Howard J. Williams, Shawn S. Chang, Peter Kolb, Brandan S. Hillerich, J. Michael Sauder, Stephen K. Burley, Steven C. Almo, Subramanyam Swaminathan, Brian K. Shoichet, Frank M. Raushel
Biochemistry 2014, 53, 4727-4738. [pdf]

2013

19 | Structure of Active Coagulation Factor XIII Triggered by Calcium Binding: Basis for the Design of Next-Generation Anticoagulants.
Martin Stieler, Johannes Weber, Martin Hils, Peter Kolb, Andreas Heine, Christian Büchold, Ralf Pasternack, Gerhard Klebe
Angew. Chem. Int. Ed. 2013, 52, 11930-11934. [pdf]

18 | Computergestützte Entwicklung selektiver Liganden G Protein-gekoppelter Rezeptoren.
Denis Schmidt, Peter Kolb
Dtsch. Med. Wochenschr. 2013, 138, 2260-2264. [pdf] [review]

17 | Structural and functional characterization of a phosphatase domain within yeast general transcription factor TFIIIC.
Nicholas M. I. Taylor, Sebastian Glatt, Marco L. Hennrich, Gudrun von Scheven, Helga Grötsch, Carlos Fernández-Tornero, Vladimir Rybin, Anne-Claude Gavin, Peter Kolb, Christoph W. Müller
J. Biol. Chem. 2013, 288, 15110-15120. [pdf]

2012

16 | Limits of ligand selectivity from docking to models: In silico screening for A1 adenosine receptor antagonists.
Peter Kolb*, Khai Phan, Zhan-Guo Gao, Adam C. Marko, Andrej Sali, Kenneth A. Jacobson*
PLOS ONE 2012, 7, e49910. [pdf]

15 | Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones.
Dao Feng Xiang†, Peter Kolb†, Alexander A. Fedorov†, Chengfu Xu†, Elena V. Fedorov, Tamari Narindoshivili, Howard J. Williams, Brian K. Shoichet*, Steven C. Almo*, Frank M. Raushel*
Biochemistry 2012, 51, 1762-1773. [pdf]

2011

14 | The Golden Age of GPCR Structural Biology: Any Impact on Drug Design?
Peter Kolb*, Gerhard Klebe*
Angew. Chem. Int. Ed. 2011, 50, 11573-11575. [comment] [pdf]

2010

13 | The hunt for 8-Oxoguanine Deaminase.
Richard S. Hall, Alexander A. Fedorov, Ricardo Marti-Arbona, Elena V. Fedorov, Peter Kolb, J. Michael Sauder, Stephen K. Burley, Brian K. Shoichet, Steven C. Almo, Frank M. Raushel
J. Am. Chem. Soc. 2010, 132, 1762-1763. [pdf] [peer recommendation]

12 | Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to Human Renal Dipeptidase.
Jennifer A. Cummings, Tinh T. Nguyen, Alexander A. Fedorov, Peter Kolb, Chengfu Xu, Elena V. Fedorov, Brian K. Shoichet, David P. Barondeau, Steven C. Almo, Frank M. Raushel
Biochemistry 2010, 49, 611-622. [pdf]

2009

11 | Docking & chemoinformatic screens for new ligands and targets.
Peter Kolb, Rafaela S. Ferreira, John J. Irwin, Brian K. Shoichet
Curr. Op. Biotech. 2009, 20, 429-436. [review] [pdf]

10 | Docking screens: right for the right reasons?
Peter Kolb, John J. Irwin
Curr. Top. Med. Chem. 2009, 9, 755-770. [review] [pdf]

9 | Structure-based discovery of β2-adrenergic receptor ligands.
Peter Kolb†, Daniel M. Rosenbaum†, John J. Irwin, Juan José Fung, Brian K. Kobilka*, Brian K. Shoichet*
Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6843-6848. [pdf] [sup] [Comment @ Curious Wavefunction]           
The x-ray structure of compound 1 described in this paper has been solved by Wacker et al., and our predicted pose corresponds to the crystallographic one within 0.9 Å RMSD!

8 | Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans: a close relative of Phosphotriesterase in the Amidohydrolase Superfamily.
Dao Feng Xiang, Peter Kolb, Alexander A. Fedorov, Monika M. Meier, Elena V. Fedorov, Tinh T. Nguyen, Reinhard Sterner*, Steven C. Almo*, Brian K. Shoichet*, Frank M. Raushel*
Biochemistry 2009, 48, 2237-2247. [pdf] [sup]

2008

7 | A double-headed Cathepsin B inhibitor devoid of warhead.
Patricia Schenker, Pietro Alfarano, Peter Kolb, Amedeo Caflisch, Antonio Baici
Prot. Sci. 2008, 17, 2145-2155. [pdf] [sup]

6 | Structure-based tailoring of compound libraries for high-throughput screening: Discovery of novel EphB4 kinase inhibitors.
Peter Kolb, Catherine Berset Kipouros, Danzhi Huang, Amedeo Caflisch
Proteins: Struct. Funct. Bioinf. 2008, 73, 11-18. [pdf] [sup]

5 | Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model.
Peter Kolb†, Danzhi Huang†, Fabian Dey†, Amedeo Caflisch
J. Med. Chem. 2008, 51, 1179-1188. [pdf] [sup]

2006

4 | Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking.
Peter Kolb*, Amedeo Caflisch*
J. Med. Chem. 2006, 49, 7384-7392. [pdf]

3 | In silico discovery of β-secretase inhibitors.
Danzhi Huang, Urs Lüthi, Peter Kolb, Marco Cecchini, Alcide Barberis, Amedeo Caflisch
J. Am. Chem. Soc. 2006, 128, 5436-5443. [pdf] [sup]

2005

2 | Discovery of cell-permeable nonpeptide inhibitors of β-secretase.
Danzhi Huang, Urs Lüthi, Peter Kolb, Karin Edler, Marco Cecchini, Stephan Audétat, Alcide Barberis, Amedeo Caflisch
J. Med. Chem. 2005, 48, 5108-5111. [pdf] [sup]

2004

1 | Automated docking of highly flexible ligands by genetic algorithms: A critical assessment.
Marco Cecchini, Peter Kolb, Nicolas Majeux, Amedeo Caflisch
J. Comput. Chem. 2004, 25, 412-422. [pdf]

†these authors contributed equally. *co-corresponding authors.

Book chapters

B2 | Fragment-based High-throughput Docking and Library Tailoring.
Peter Kolb
In: Rachelle J. Bienstock (Ed.) Library Design, Search Methods and Applications of Fragment-Based Drug Design. ACS Books, 2011, 131-147. [pdf]

B1 | Fragment-based high-throughput docking.
Peter Kolb, Marco Cecchini, Danzhi Huang, Amedeo Caflisch
In: Juan Alvarez and Brian K. Shoichet (Eds.) Virtual Screening. CRC Press, 2005, 349-378. [pdf]

Other writings

W2 | The 15 things that surprised me most when I started out as an independent group leader.
Peter Kolb†, Verena Klappstein†, Ralf Tonner†
J. Postdoc. Aff. 2012, 2, 30-34. [pdf]

W1 | Explicit and implicit barriers to the international mobility of scientists.
Peter Kolb
J. Postdoc. Aff. 2011, 1, 46-48. [pdf]