kolblab.org

Kolb Lab Heisenberg DFG

Networks

The Kolb Lab is located at the Department of Pharmaceutical Chemistry at Philipps-Universität Marburg.

We are a member lab of GLUE,
SYNMIKRO,
the transregional collaborative research centre 81 (SFB/Transregio81),
and DRUID.
We are also part of ERNEST, the "European Research Network on Signal Transduction".
Together with the Selent and Bouvier labs, we are investigating biased ligands of the 5-HT2A receptor in the context of the ERANET NEURON project PSYBIAS. Funding is provided by the Federal Ministry of Education and Research under grant number 01EW1909.



The lab was deeply involved in COST Action CM1207 "GLISTEN: GPCR-Ligand Interactions, Structures, and Transmembrane Signalling: a European Research Network"
and part of SynChemBio.
The lab started through the generous funding provided within the DFG's Emmy Noether Programme. Emmy Noether DFG
[en][de]

Research interests

Docking
Word cloud generated with WordClouds.com from publication abstracts.

Small molecules are frequently used both in Nature and therapeutically to modulate the activity of the protein they bind to. Yet, many aspects of small-molecule:protein interactions are surprisingly poorly understood. For instance, ligand polypharmacology, i.e. binding to multiple proteins, often comes as a surprise, although it is frequently precisely the reason for a drug's efficacy or its side effects. On the protein side, a point mutation in the binding site, although only a small change, can abolish drug binding, leading to resistance. Thus, it is highly relevant to develop a comprehensive understanding of small-molecule:protein interaction profiles in molecular detail and correlate these profiles with signaling and metabolic pathways.

Our main tool is small molecule docking, but we also use chemoinformatic approaches and molecular dynamics. The research spans method development, basic research and applications. Currently the investigations deal with kinases and G protein-coupled receptors (GPCRs).


Publications

Most recent:
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. Comm. 2021, 57, 10516-10519.
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]
full list

Lab members

Viviane Corrêa Santos [Former Guest Scientist]
Matthäus Drabek [Graduate Student]
Anja Flöser [Graduate Student]
Janik Hedderich [Graduate Student]
Jonas Kammertöns [Graduate Student]
Peter Kolb [Principal Investigator]
Victor Lim [Graduate Student]
Lea Löffler [Former Student Researcher]
Stefania Monteleone [Former Postdoc]
Maria Giovanna Papadopoulos [Graduate Student]
Margherita Persechino [Graduate Student]
Naiá Porã Santos [Former Intern]
Magdalena Scharf [Former Graduate Student]
Johanna Senst [Graduate Student]
Corey Taylor [Former Graduate Student]
Not in picture:
Frank Balzer [IT Administrator]
Steffi Dörr [Technician Molecular Biology]
Linn Evenseth [Postdoc]
Philipp Geisel [PJ Student]
Hans-Dieter Gerber [Technician Medicinal Chemistry]
Fiona Morhard [Student Researcher]
Anja Moser [Assistant]
Jan-Niklas Pütz [Student Researcher]
Raquel Reilly [Fulbright Fellow]
Klaus Reuter [apl Professor]
Aida Shahraki [Postdoc]
Beatrice Stöhr [Student Researcher/MOS]

Teaching

We are involved in lectures and lab courses in Pharmaceutical Chemistry. Moreover, we accept students in the Chemistry and Pharmacy curricula for internships. Students with a keen interest in computation, chemistry, and biochemistry and their application to pharmaceutical questions are accepted for B.Sc., M.Sc., and Ph.D. theses (see also below, "Joining the lab").


Scubidoo & Pingui


PrenDB


Daim – a program to generate fragments


Joining the Lab




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