Design

Intro text? In effect-directed analysis, we combine chromatography for fractionation of complex samples, and split these fractions for simultaneous functional assessment (cell-based assay) and compound identification (using mass spec). 

In this way we can identify bioactive compounds in complex samples such as environmental samples, snake venoms, foods or body fluids.

Protein structures and function

With our own X-ray crystallography expertise [link measure] and recent breakthroughs in AI-based structural identification, we excel in modeling of molecular dynamics, structure-function relationships, protein-protein interactions, ligand docking and in silico screening of small molecules.

Contacts:
Structure function relationships: Joen Luirink, Rob Leurs, others
Protein-Protein interaction: Tom Grossmann, Ivana Drienovska
Ligand docking: Halima Mouhib, Daan Geerke, Barbara Zarzycka

AIMMS can design, make, or screen for increasingly complex biologically active molecules or molecular complexes, from small molecules, peptides, proteins, nanoparticles, vaccins to bacteriophages.

Small molecules

Our organic chemists focus on the development of highly efficient, asymmetric synthetic methodologies and their application to the synthesis of diverse, biologically relevant compounds, with an emphasis on atom, step, and resource efficiency.

• Rational design and development of flexible novel cascade reactions.
• Transition metal (cascade) catalysis for the synthesis of highly functionalized heterocycles.
• Application of developed synthetic methods in the total synthesis of natural products and complex pharmaceuticals.

Contacts: 

Eelco Ruijter

At AIMMS we develop powerful chemical theories and methods to predict and rational design target molecules, nanostructures, and materials as well as new, more efficient chemical processes toward these compounds, based on quantum mechanics and computer simulations.
We cover all areas of molecular chemistry, ranging from elementary physical chemistry, via organic and inorganic chemistry, to biological and medicinal chemistry.

An essential part of these efforts is theory-driven experimentation, the application of our theories and models in cooperation with experimental groups to initiate and guide new developments in experimental chemistry.

The theoretical chemistry expertise is focused on:

Structure and Chemical Bonding in Kohn-Sham Density Functional Theory (DFT) with topic such as hypervalence and aromaticity
Theoretical Biochemistry and multi-level QM/MM methods
Elementary Chemical Reactions
Fragment-oriented Design of Catalysts

We actively work to move from understanding to rationally designing chemical reactions and catalysts in various areas of theoretical organic, inorganic and biological chemistry.

Contacts:
Lucas Visscher, Matthias Bickelhaupt, Celia Fonseca Guerra

Food

Identification of enzymes responsible for removal of antinutritional factors through fermentation. [link Fermi]

Taste and olfactory receptor studies. Halima Mouhib, David Poole

Pharma

G-protein coupled receptors (GPCRs); the design and synthesis of new ligands for several GPCRs, like the histamine receptors H1, H3 and H4 as well as chemokine receptors CXCR3, CXCR4 and CXCR7. We have obtained detailed understanding of the action of selected ligands by combining modern molecular pharmacological concepts (e.g. allosteric modulation, dimerization, inverse agonism, ligand-biased signaling and signalling networks), receptor mutagenesis and computational modeling.