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Design

AIMMS has structural and molecular biologists and theoretical, organic and medicinal chemists that have the tools and understanding to design and make (bio)active molecules, including catalysts, small drug-like molecules and fragments, large biomimetic peptides and nanobodies.

We have compound libraries, molecular modeling tools (combining both mechanistic, structure-based modeling and data-driven AI/ML approaches) and synthesis labs to design and make molecules fit for purpose.

Methods

  • Structural biology and medicinal chemistry

  • Molecular microbiology and (bio) organic chemistry

  • Theoretical chemistry

Structural biology and medicinal chemistry

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

Medicinal chemistry

AIMMS is strong in all aspects of medicinal chemistry and is specialized in G-protein coupled receptors (GPCRs). GPCRs are one the most successful drug targets to date and remain an important focus point in modern drug discovery. 

Expertise in AIMMS goes from understanding their structure-function relationship, AI-assisted predictions of ligand-receptor interactions, design, making and testing of novel ligands [link to Griffin services?] and the [understanding] of the action of GPCRs in biological networks,

We also are strong in fragment-based drug discovery. Fragment-based approaches are ideal for academic and small biotech drug discovery efforts, as these technologies are design-intensive rather than resource-intensive.

We have established a fragment library containing 1500 low molecular weight compounds. Currently, this library is effectively used as a starting point to develop ligands against a variety of targets: GPCRs, kinases, ligand-gated ion channels, protein-protein interactions, etc.

Next to pharmacological screening, alternative fragment screening technologies are being explored such as in silico docking, SPR screening, NMR and X-ray analysis. 

Contacts:

Martine Smit, Rob Leurs, Iwan de Esch

Techniques or applications?

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Mass spec-based methods

We have advanced analytical methods for metabolomics, proteomics and glycomics for the analysis of human fluids, intracellular metabolites, tissues and cell culture media. We hyphen separation techniques as HPLC, CE and GC with high-end (tandem) mass spectrometry (high-resolution, ion mobility and UVPD/IRMPD). We also have MS-based imaging facilities.

Contacts:

Pim Leonards, Govert Somsen, Sofia Moco

NMR and crystallography

We have 300 – 600 MHz NMR machines for compound identification and analysis of complex fluids for metabolite quantification. 

For protein structure determination, the workflow includes liquid handling for sample crystallization, optimizing crystals, crystal handling including cryo-protection and storage. Diffraction analysis and data collection is done on an in-house, state of the art Bruker D8 Quest X-ray source attached to an cutting edge PhotonII detector including downstream software suits for structure determination. 

Contact:

Elwin Janssen (nmr.beta@vu.nl).

Techniques

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Molecular microbiology and (bio) organic chemistry

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



Techniques

Peptides and proteins

AIMMS has strong expertise in the synthesis of peptide-derived molecules and the engineering of proteins using organic chemistry. Central aspects are the synthesis of non-natural amino acids as well as modified peptides, and the use of biocompatible reactions for the selective functionalization of unprotected peptides and proteins. We use these techniques e.g. for the development of novel bioactive peptidomimetics and for chemical protein engineering.

Contact:

Tom Grossmann



Nanoparticles and bacteriophages

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Contacts:

Joen Luirink, Yuval Mulla

Sample projects

Meet the Scientist: Thomas Hansen

| Meet the Scientist | No Comments
Thomas Hansen Assistant Professor in the Synthetic Organic Chemistry & Catalysis Group "People with different personal, cultural, and scientific backgrounds bring unique insights...the beauty of…
Sofia discussing metabolism with PhD candidate Victoria Pozo Photo credit: David Poole III

Meet the Scientist: Sofia Moco

| Meet the Scientist | No Comments
Sofia Moco PI at the Chemistry and Pharmaceutical Sciences department of the VU. Birthplace:  Portugal "I was always curious about how things work, and somehow…

Do NMR Experiments with AIMMS

| Equipment hire, Research | No Comments
Interested in using our NMR equipment? Nuclear Magnetic Resonance (NMR) spectroscopy is widely used to determine the structure of organic molecules and is closely tied to…

Using metabolomics to study the dynamics of metabolism

| Fermentation, Food, Research | No Comments
Dysregulation of metabolism is closely linked to the development of various diseases and lifetime changes, including metabolic disorders, cancer, and ageing. Understanding the nuances of…

AIMMS researchers win €5M NWO Perspective Grant for the plant-based fermentation proposal

| Fermentation, Food, Research | No Comments
This week The Netherlands Organisation for Scientific Research (NWO) granted the FERMI Perspective proposal led by Herwig Bachmann from the Systems Biology Lab. The project…

Stringing Science Together: Bead-azzling Macrocyclization for Biochemistry Bling!

| Research | No Comments
Imagine making a necklace. You start with various colors and shapes of beads, and you decide which specific beads you want to connect to form…

Theorectical chemistry

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.

Antimicrobials and vaccines

Development of new vaccins: Bacterial nanoparticle platforms (outer membrane vesicles and protein bodies) for antigen and drug delivery.

Type VII secretion system of M tuberculosis. The structure (determined a.o. by AIMMS researchers) allows design of novel antibiotics against tuberculosis.